Identification and characterization of noncoding RNAs-associated competing endogenous RNA networks in major depressive disorder

BACKGROUND Major depressive disorder(MDD)is a common and serious mental illness.Many novel genes in MDD have been characterized by high-throughput methods such as microarrays or sequencing.Recently,noncoding RNAs(ncRNAs)were suggested to be involved in the complicated environmental-genetic regulatory network of MDD occurrence;however,the interplay among RNA species,including protein-coding RNAs and ncRNAs,in MDD remains unclear.AIM To investigate the RNA expression datasets downloaded from a public database and construct a network based on differentially expressed long noncoding RNA(lncRNAs),microRNAs(miRNAs),and mRNAs between MDD and controls.METHODS Gene expression data were searched in NCBI Gene Expression Omnibus using the search term“major depressive disorder.”Six array datasets from humans were related to the search term:GSE19738,GSE32280,GSE38206,GSE52790,GSE76826,and GSE81152.These datasets were processed for initial assessment and subjected to quality control and differential expression analysis.Differentially expressed lncRNAs,miRNAs,and mRNAs were determined,Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed,and protein-protein interaction network was generated.The results were analyzed for their association with MDD.RESULTS After analysis,3 miRNAs,12 lncRNAs,and 33 mRNAs were identified in the competing endogenous RNA network.Two of these miRNAs were earlier shown to be involved in psychiatric disorders,and differentially expressed mRNAs were found to be highly enriched in pathways related to neurogenesis and neuroplasticity as per Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses.The expression of hub gene fatty acid 2-hydroxylase was enriched,and the encoded protein was found to be involved in myelin formation,indicating that neurological development and signal transduction are involved in MDD pathogenesis.CONCLUSION The present study presents candidate nc RNAs involved in the neurogenesis and neuroplasticity pathways related to MDD.

Exploring prognostic potential of long noncoding RNAs in colorectal cancer based on a competing endogenous RNA network

BACKGROUND Colorectal cancer(CRC)is one of the most prevalent tumors worldwide.Recently,long noncoding RNAs(lncRNAs)have been shown to influence tumorigenesis and tumor progression by acting as competing endogenous RNAs(ceRNAs).It is difficult to extract prognostic lncRNAs and useful bioinformation from most ceRNA networks constructed previously.AIM To construct a prognostic related ceRNA regulatory network and lncRNA related signature based on risk score in CRC.METHODS RNA transcriptome profile and clinical information of 506 CRC patients were downloaded from the Cancer Genome Atlas database.R packages and Perl program were used for data processing.Cox regression analysis was used for prognostic model construction.Quantitative real-time polymerase chain reaction was used to detect the expression of lncRNAs.RESULTS A prognostic-related ceRNA network was constructed,including 9 lncRNAs,44 mRNAs,and 30 miRNAs.In addition,a four-lncRNA model was constructed using multivariate Cox regression analysis,which could be an independent prognostic model in CRC.The risk score for each patient was calculated,and the 506 patients were divided into high and low-risk groups(253 for each group)based on the median risk score.The results of the survival analysis showed that patients with a high-risk score had a poor survival rate.Furthermore,the predictive value of the four-lncRNA model was evaluated in GSE38832.Patient survival probabilities could be better predicted when combing the risk score and clinical features.Gene Set Enrichment Analysis results verified that a number of cancer-related signaling pathways were enriched with a high-risk score in CRC.Finally,we validated a novel lncRNA(LINC00488)using quantitative real-time polymerase chain reaction in 22 paired CRC patient tumor tissues compared to adjacent non-tumor tissues.CONCLUSION The four-lncRNA model could give better predictive value for CRC patients.Our understanding of the lncRNA-related ceRNA regulatory mechanism could provide a potential diagnostic indicator for CRC patients.

基于高通量测序技术构建糖尿病肾病小鼠lncRNA相关ceRNA调控网络

目的:筛选糖尿病肾病(DKD)小鼠肾脏组织中差异表达的长链非编码RNA(lncRNA)、小RNA(miRNA),构建lncRNA相关竞争性内源RNA(ceRNA)调控网络。方法:选取6只BKS-db/m雄性小鼠为对照组,6只BKS-db/db雄性小鼠为模型组,模型组构建DKD小鼠模型。处死小鼠后取肾脏组织进行高通量测序,利用DESeq软件筛选两组差异表达的lncRNA、miRNA,使用Miranda软件进行差异表达的miRNA靶基因预测。构建lncRNA相关ceRNA调控网络并进行GO功能富集分析以及KEGG信号通路富集分析。结果:共筛选出DKD小鼠差异表达的lncRNA 1495个、差异表达的miRNA 72个。成功构建由MSTRG.7252.3、MSTRG.10465.2、MSTRG.16253.3等23个lncRNA、23个miRNA与2个mRNA组成,与lncRNA相关的ceRNA网络。GO功能富集分析显示,该网络主要涉及生物学过程、细胞组成和分子功能;KEGG信号通路富集显示,主要与PPAR信号通路、造血细胞谱系、细胞黏附分子、TNF信号通路等有关。结论:成功构建DKD小鼠lncRNA相关的ceRNA调控网络。

ceRNAs在软骨损伤中作用机制的研究进展

正常的关节软骨对肢体活动有重要作用,关节创伤、生物力学改变及年龄等危险因素均可导致关节软骨受到损伤,先前的研究虽然已在分子层面上对关节软骨损伤的原因做出报道,但关于软骨损伤发生及预后的分子间调控机制了解并不充分。竞争性内源RNA(competing endogenous RNAs,ceRNAs)是一种包括非编码RNA(non-coding RNA,ncRNA)等分子在内的庞大RNA分子间调控网络,其作为一种新兴的调控机制参与关节软骨的损伤与修复。研究发现,ceRNAs通过竞争结合微小RNA(microRNA,miRNA)可调控关节软骨细胞的增殖、凋亡及软骨细胞外基质降解等过程进而影响关节软骨的健康。笔者查阅近几年相关研究文献,就ceRNAs在关节软骨损伤中的作用机制及潜在性应用展开综述,以期为关节软骨损伤的防治提供新的思路和方向。

Long noncoding RNA RP4 functions as a competing endogenous RNA through miR-7-5p sponge activity in colorectal cancer

AIM To investigate the role of long noncoding RNA(lnc RNA) RP4 in colorectal cancer.METHODS Lentivirus-mediated lnc RNA RP4 overexpression and knockdown were performed in the colorectal cancer cell line SW480. Cell proliferation, tumor growth, and early apoptosis were evaluated by a cell counting kit-8 assay, an in vivo xenograft tumor model, and annexin V/propidium iodide staining, respectively. Analysis of the lnc RNA RP4 mechanism involved assessment of the association of its expression with mi R-7-5 p and the SH3 GLB1 gene. Western blot analysis was also performed to assess the effect of lnc RNA RP4 on the autophagy-mediated cell death pathway and phosphatidylinositol-3-kinase(PI3 K)/Akt signaling.RESULTS Cell proliferation, tumor growth, and early apoptosis in SW480 cells were negatively regulated by lnc RNA RP4. Functional experiments indicated that lnc RNA RP4 directly upregulated SH3 GLB1 expression by acting as a competing endogenous RNA(ce RNA) for mi R-7-5 p. This interaction led to activation of the autophagy-mediated cell death pathway and de-repression of PI3 K and Akt phosphorylation in colorectal cancer cells in vivo.CONCLUSION Our results demonstrated that lnc RNA RP4 is a ce RNA that plays an important role in the pathogenesis of colorectal cancer, and could be a potential therapeutic target for colorectal cancer treatment.

Competing endogenous RNA networks and gastric cancer

Recent studies have showed that RNAs regulate each other with micro RNA(mi RNA) response elements(MREs) and this mechanism is known as "competing endogenous RNA(ce RNA)" hypothesis. Long noncoding RNAs(lnc RNAs) are supposed to play important roles in cancer. Compelling evidence suggests that lnc RNAs can interact with mi RNAs and regulate the expression of mi RNAs as ce RNAs. Several lnc RNAs such as H19, HOTAIR and MEG3 have been found to be associated with mi RNAs in gastric cancer(GC), generating regulatory crosstalk across the transcriptome. These MRE sharing elements implicated in the ce RNA networks(ce RNETs) are able to regulate m RNA expression. The ce RNA regulatory networks including m RNAs, mi RNAs, lnc RNAs and circular RNAs may play critical roles in tumorigenesis, and the perturbations of ce RNETs may contribute to the pathogenesis of GC.

Identification and prediction of novel non-coding and coding RNA-associated competing endogenous RNA networks in colorectal cancer

AIM To identify and predict the competing endogenous RNA(ce RNA) networks in colorectal cancer(CRC) by bioinformatics analysis. METHODS In the present study, we obtained CRC tissue and normal tissue gene expression profiles from The Cancer Genome Atlas project. Differentially expressed(DE) genes(DEGs) were identified. Then, upregulated and downregulated mi RNA-centered ceRNA networks were constructed by analyzing the DEGs using multiple bioinformatics approaches. DEm RNAs in the ceRNA networks were identified in Kyoto Encyclopedia of Genes and Genomes(KEGG) pathways using KEGG Orthology Based Annotation System 3.0. The interactions between proteins were analyzed using the STRING database. Kaplan-Meier survival analysis was conducted for DEGs and real time quantitative polymerase chain reaction(RT-qPCR) was also performed to validate the prognosis-associated lncRNAs in CRC cell lines.RESULTS Eighty-one DElncRNAs, 20 DEmiRNAs, and 54 DEmRNAs were identified to construct the ceRNA networks of CRC. The KEGG pathway analysis indicated that nine out of top ten pathways were related with cancer and the most significant pathway was "colorectal cancer". Kaplan-Meier survival analysis showed that the overall survival was positively associated with five DEGs(IGF2-AS, POU6 F2-AS2, hsa-miR-32, hsa-miR-141, and SERPINE1) and it was negatively related to three DEGs(LINC00488, hsamiR-375, and PHLPP2). Based on the STRING protein database, it was found that SERPINE1 and PHLPP2 interact with AKT1. Besides, SERPINE1 can interact with VEGFA, VTN, TGFB1, PLAU, PLAUR, PLG, and PLAT. PHLPP2 can interact with AKT2 and AKT3. RT-qPCR revealed that the expression of IGF2-AS, POU6 F2-AS2, and LINC00488 in CRC cell lines was consistent with the in silico results.CONCLUSION Ce RNA networks play an important role in CRC. Multiple DEGs are related with clinical prognosis, suggesting that they may be potential targets in tumor diagnosis and treatment.

Role of long noncoding RNA-mediated competing endogenous RNA regulatory network in hepatocellular carcinoma

Long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) are noncodingRNAs (ncRNAs) that occupy over 90% of the human genome, and their mainfunction is to directly or indirectly regulate messenger RNA (mRNA) expressionand participate in the tumorigenesis and progression of malignances. Inparticular, some lncRNAs can interact with miRNAs as competing endogenousRNAs (ceRNAs) to modulate mRNA expression. Accordingly, these RNAmolecules are interrelated and coordinate to form a dynamic lncRNA-mediatedceRNA regulatory network. Mounting evidence has revealed that lncRNAs thatact as ceRNAs are closely related to tumorigenesis. To date, numerous studieshave established many different regulatory networks in hepatocellular carcinoma(HCC), and perturbations in these ceRNA interactions may result in the initiationand progression of HCC. Herein, we emphasize recent advances concerning thebiological function of lncRNAs as ceRNAs in HCC, with the aim of elucidating themolecular mechanism underlying these HCC-related RNA molecules andproviding novel insights into the diagnosis and treatment of HCC.

Circular RNA expression and the competitive endogenous RNA network in pathological,age-related macular degeneration events:A cross-platform normalization study

Age-related macular degeneration(AMD)causes irreversible blindness in people aged over 50 worldwide.The dysfunction of the retinal pigment epithelium is the primary cause of atrophic AMD.In the current study,we used the ComBat and Training Distribution Matching method to integrate data obtained from the Gene Expression Omnibus database.We analyzed the integrated sequencing data by the Gene Set Enrichment Analysis.Peroxisome and tumor necrosis factor-α(TNF-α)signaling and nuclear factor kappa B(NF-κB)were among the top 10 pathways,and thus we selected them to construct AMD cell models to identify differentially expressed circular RNAs(circRNAs).We then constructed a competing endogenous RNA network,which is related to differentially expressed circRNAs.This network included seven circRNAs,15 microRNAs,and 82 mRNAs.The Kyoto Encyclopedia of Genes and Genomes analysis of mRNAs in this network showed that the hypoxia-inducible factor-1(HIF-1)signaling pathway was a common downstream event.The results of the current study may provide insights into the pathological processes of atrophic AMD.

lncRNA介导的ceRNA网络在痛风性关节炎中的研究进展

长链非编码RNA(lncRNA)是长度大于200 nt的非编码RNA,近年来研究发现其可作为微小RNA(miRNA)的海绵而调控竞争性内源性RNA(ceRNA)网络。研究表明lncRNA在痛风性关节炎中存在异常表达,与Toll样受体和核苷酸结合寡聚化结构域样受体信号通路、嘌呤能离子通道型受体7信号通路等关系密切。lncRNA可通过多条lncRNA-miRNA-信使RNA轴影响痛风的发生发展。本文探讨lncRNA介导的ceRNA调控网络在痛风中的研究进展,加深对痛风的发病机制认识,为靶向干预痛风炎症以及预防骨侵蚀提供新思路。

ceRNA在动物低氧适应性中的研究进展

氧气是机体进行新陈代谢和维持生存的必要因素。低氧适应是机体为了适应缺氧这一生理或病理现象,降低缺氧带来的影响而发生的一系列局部性和系统性的改变。竞争性内源RNA(ceRNA)是指具有同种miRNA反应元件(MREs)的RNA分子,竞争性结合miRNA在转录后水平调控基因的表达,进而影响细胞的生物学功能。ceRNA是一种复杂的网络调节机制,在细胞增殖与凋亡、炎症反应、能量代谢、肌肉发育、脂肪沉积、脂质代谢等方面发挥作用。文章总结了长链非编码RNA(lncRNA)、环状RNA(circRNA)和假基因的生物学功能和特点,阐述经过验证的ceRNA参与动物低氧适应的生物学功能,为哺乳动物低氧适应性研究提供参考。

基于生物信息学构建膀胱尿路上皮癌的ceRNA网络以及关键mRNA与免疫功能分析

目的构建膀胱尿路上皮癌(bladder urothelial carcinoma,BLCA)具有预后价值的内源竞争性核糖核酸(competing endogenous RNA,ceRNA)调控网络,分析关键信使RNA(messenger RNA,mRNA)与免疫功能的关系。方法UCSC Xena数据库下载404例BLCA患者和28例正常人的mRNA表达数据,通过差异分析筛选关键mRNA。ENCORI数据库中查找与关键mRNA结合的微小核糖核酸(micro RNA,miRNA)以及与miRNA结合的长链非编码核糖核酸(long non-coding RNA,LncRNA)。TCGA数据库下载miRNA和LncRNA的表达数据,对关键mRNA与所有miRNA以及mi RNA与所有LncRNA进行共表达分析,筛选出关键的miRNA和LncRNA。根据关键mRNA,miRNA和LncRNA在肿瘤患者和正常人之间表达量的差异进行生存分析,最后构建了ceRNA调控网络。借助TIMER 2.0数据库,分析关键mRNA与免疫细胞、免疫检查点(CD274,PDCD1,CTLA4)以及免疫细胞标记基因(immunomarker genes,IG)的相关性。结果筛选出关键mRNA*共22个,其中差异显著性最高的是脯氨酸3-羟化酶4(proline3-hydroxylase 4,P3H4)。在BLCA中,P3H4表达高,在高表达组患者的生存时间较短。以关键mRNA为中心环节,共筛选出33个miRNA和14个LncRNA。经过共表达分析和生存分析后,筛选出具有预后价值的关键miRNA和关键LncRNA分别为hsa-miR-151a-3p和MIR100HG。上述分析结果差异具有统计学意义(均Ρ<0.05)。综合以上结果,构建了包含1个mRNA,1个miRNA和1个LncRNA的ceRNA调控网络。免疫分析首次在BLCA肿瘤微环境中发现了与P3H4表达量呈显著正相关的双阳性T细胞。此外还有3种免疫细胞(肿瘤相关性中性粒细胞、肿瘤相关巨噬细胞、树突状细胞)、3个免疫检查点(CD274,PDCD1,CTLA4)以及15个IG与P3H4相关度显著,这些差异具有统计学意义(均Ρ<0.01)。结论该研究有助于揭示BLCA的进展机制,构建的ceRNA网络及免疫分析,可为BLCA患者的诊断、治疗、预测提供新的生物学靶点和方向。

lncRNA作为ceRNA在多囊卵巢综合征中的作用

多囊卵巢综合征(polycystic ovary syndrome,PCOS)是一种常见的女性生殖内分泌疾病,受表观遗传和环境等多种因素影响。长链非编码RNA(long non-coding RNA,lncRNA)为不编码蛋白质且长度超过200个核苷酸的RNA分子,其可通过表观遗传修饰、转录及转录后调控等影响基因的表达。lncRNA可作为竞争性内源RNA(competing endogenous RNA,ceRNA)与微小RNA(microRNA,miRNA)竞争性结合,从而调控靶基因表达。作为一种新的调控机制,其可在细胞增殖分化、炎症反应及免疫应答等生物过程中发挥重要作用,并且与许多疾病密切相关。ceRNA假说的提出也使学者们对PCOS的发生发展机制有了进一步了解。近年来,ceRNA在PCOS中的研究也越来越多。在PCOS中差异表达的lncRNA可作为ceRNA调控靶基因进而影响卵巢颗粒细胞增殖、卵母细胞成熟以及激素合成,这对PCOS的发生发展起到重要作用。综述lncRNA作为ceRNA在PCOS发生发展中的作用。

新生儿缺血缺氧性脑病ceRNA调控网络构建分析

目的 分析并构建新生儿缺血缺氧性脑病(hypoxic-ischemic encephalopathy,HIE)竞争性内源RNA(competing endogenous RNA,ceRNA)的调控网络,筛选预测缺血缺氧性脑病诊治的潜在靶点。方法 通过TCGA和GEO数据库获取HIE的非编码RNA高通量测序数据,并进行差异基因分析。根据ceRNA理论构建出circRNA(circular RNA)-miRNA-mRNA网络,进行京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)信号通路和基因本体理论(Gene Ontology,GO)分享,探索和功能注释具有ceRNA潜在功能的circRNA。结果 对GSE121178数据集进行筛选,获得差异circRNAs165个,其中上调59个,下调106个;对GSE181127数据集进行筛选,获得差异miRNAs 63个,其中上调60个,下调3个。用miRecords、miRTarBase、TarBase数据库对获得差异miRNAs进行靶点mRNA预测,并对3个数据库预测结果取交集,共获得11个靶点mRNA(PIK3R1、BACE3、VEGFA、PPP2R2A、LATS2、WDR82、VEZT、TUBA1A、THBS1、SLC7A6、CDK6)。经阈值筛选,筛选了10个共表达circRNAs、4个共表达miRNAs和11个共表达mRNAs,构建circRNA-miRNA-mRNA网络。KEGG富集分析显示:HIE涉及的20个交集蛋白在信号通路中,较为靠前的10条信号通路包括T细胞受体信号通路、Ras信号通路、Rap1信号通路、PI3K-Akt信号通路、MAPK信号通路、FoxO信号通路、ErbB信号通路、胰岛素抵抗、酪氨酸激酶抑制作用、细胞衰老和细胞周期等靶点。说明这些信号通路或与HIE的发生有关。动物实验表明:模型组大鼠神经功能缺损评分高于空白组(P<0.001)。模型组miR-31-5p的mRNA表达水平明显低于空白组(P<0.05),模型组中miR-520g-3p,miR-30a-5p,miR-29a-3p表达水平明显高于空白组(P<0.05);WB显示,模型组中CDK6、THBS1和TUBA1的表达水平明显高于空白组(P<0.05),模型组中VEZT和WDR82的表达水平明显低于空白组(P<0.05)。结论 构建了HIE的circRNA-miRNA-mRNA调控网络,找到了疾病的潜在治疗靶点,为HIE的诊治提供了新方向。

Long noncoding RNA protein-disulfide isomerase-associated 3 regulated high glucose-induced podocyte apoptosis in diabetic nephropathy through targeting miR-139-3p

BACKGROUND Podocyte apoptosis plays a vital role in proteinuria pathogenesis in diabetic nephropathy(DN).The regulatory relationship between long noncoding RNAs(lncRNAs)and podocyte apoptosis has recently become another research hot spot in the DN field.AIM To investigate whether lncRNA protein-disulfide isomerase-associated 3(Pdia3)could regulate podocyte apoptosis through miR-139-3p and revealed the underlying mechanism.METHODS Using normal glucose or high glucose(HG)-cultured podocytes,the cellular functions and exact mechanisms underlying the regulatory effects of lncRNA Pdia3 on podocyte apoptosis and endoplasmic reticulum stress(ERS)were explored.LncRNA Pdia3 and miR-139-3p expression were measured through quantitative real-time polymerase chain reaction.Relative cell viability was detected through the cell counting kit-8 colorimetric assay.The podocyte apoptosis rate in each group was measured through flow cytometry.The interaction between lncRNA Pdia3 and miR-139-3p was examined through the dual luciferase reporter assay.Finally,western blotting was performed to detect the effect of lncRNA Pdia3 on podocyte apoptosis and ERS via miR-139-3p.RESULTS The expression of lncRNA Pdia3 was significantly downregulated in HG-cultured podocytes.Next,lncRNA Pdia3 was involved in HG-induced podocyte apoptosis.Furthermore,the dual luciferase reporter assay confirmed the direct interaction between lncRNA Pdia3 and miR-139-3p.LncRNA Pdia3 overexpression attenuated podocyte apoptosis and ERS through miR-139-3p in HG-cultured podocytes.CONCLUSION Taken together,this study demonstrated that lncRNA Pdia3 overexpression could attenuate HG-induced podocyte apoptosis and ERS by acting as a competing endogenous RNA of miR-139-3p,which might provide a potential therapeutic target for DN.

微环境下lncRNA介导miRNA调控牙周膜干细胞成骨分化的研究进展

研究牙周组织再生可为牙槽骨缺损提供可能的临床应对策略,牙周膜干细胞作为重要的种子细胞在牙槽骨修复中发挥着重要的作用。长链非编码RNA可作为竞争性内源性RNA在转录后水平发挥重要调控作用。该文就长链非编码RNA介导微小RNA对牙周膜干细胞在生理状态、炎症微环境以及力学刺激下的成骨分化机制进行综述。

Delineation of a SMARCA4-specific competing endogenous RNA network and its function in hepatocellular carcinoma

BACKGROUND Hepatocellular carcinoma(HCC)is a common malignancy worldwide,and the mortality rate continues to rise each year.SMARCA4 expression has been associated with poor prognosis in various types of cancer;however,the specific mechanism of action of SMARCA4 in HCC needs to be fully elucidated.AIM To explore the specific mechanism of action of SMARCA4 in HCC.METHODS Herein,the expression level of SMARCA4 as well as its association with HCC prognosis were evaluated using transcriptome profiling and clinical data of 18 different types of cancer collected from The Cancer Genome Atlas database.Furthermore,SMARCA4-high and-low groups were identified.Thereafter,gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to identify the function of SMARCA4,followed by construction of a SMARCA4-specific competing endogenous RNA(ceRNA)network using starBase database.The role of SMARCA4 in immunotherapy and its association with immune cells were assessed using correlation analysis.RESULTS It was observed that SMARCA4 was overexpressed and negatively correlated with prognosis in HCC.Further,SMARCA4 expression was positively associated with tumor mutational burden,microsatellite stability,and immunotherapy efficacy.The SNHG3/THUMP3-AS1-miR-139-5p-SMARCA4 ceRNA network was established and could be assumed to serve as a stimulatory mechanism in HCC.CONCLUSION The findings of this study demonstrated that SMARCA4 plays a significant role in progression and immune infiltration in HCC.Moreover,a ceRNA network was detected,which was found to be correlated with poor prognosis in HCC.The findings of this study could contribute towards the identification of predictive markers for immunotherapy and a novel mechanism of action for HCC treatment.

Analysis of long noncoding RNA-associated competing endogenous RNA network in glucagon-like peptide-1 receptor agonist-mediated protection inβcells

BACKGROUND Long noncoding RNAs(lncRNAs)and mRNAs are widely involved in various physiological and pathological processes.The use of glucagon-like peptide-1 receptor agonists(GLP-1RAs)is a novel therapeutic strategy that could promote insulin secretion and decrease the rate ofβ-cell apoptosis in type 2 diabetes mellitus(T2DM)patients.However,the specific lncRNAs and mRNAs and their functions in these processes have not been fully identified and elucidated.AIM To identify the lncRNAs and mRNAs that are involved in the protective effect of GLP-1RA inβcells,and their roles.METHODS Rat gene microarray was used to screen differentially expressed(DE)lncRNAs and mRNAs inβcells treated with geniposide,a GLP-1RA.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses were performed to assess the underlying functions of DE mRNAs.Hub mRNAs were filtered using the STRING database and the Cytoscape plugin,CytoHubba.In order to reveal the regulatory relationship between lncRNAs and hub mRNAs,their co-expression network was constructed based on the Pearson coefficient of DE lncRNAs and mRNAs,and competing endogenous RNA(ceRNA)mechanism was explored through miRanda and TargetScan databases.RESULTS We identified 308 DE lncRNAs and 128 DE mRNAs with a fold change filter of≥1.5 and P value<0.05.GO and KEGG pathway enrichment analyses indicated that the most enriched terms were G-protein coupled receptor signaling pathway,inflammatory response,calcium signaling pathway,positive regulation of cell proliferation,and ERK1 and ERK2 cascade.Pomc,Htr2a,and Agtr1a were screened as hub mRNAs using the STRING database and the Cytoscape plugin,CytoHubba.This result was further verified using SwissTargetPrediction tool.Through the co-expression network and competing endogenous(ceRNA)mechanism,we identified seven lncRNAs(NONRATT027738,NONRATT027888,NONRATT030038,etc.)co-expressed with the three hub mRNAs(Pomc,Htr2a,and Agtr1a)based on the Pearson coefficient of the expression levels.These lncRNAs regulated hub mRNA functions by competing with six miRNAs(rno-miR-5132-3p,rno-miR-344g,rno-miR-3075,etc.)via the ceRNA mechanism.Further analysis indicated that lncRNA NONRATT027738 interacts with all the three hub mRNAs,suggesting that it is at a core position within the ceRNA network.CONCLUSION We have identified key lncRNAs and mRNAs,and highlighted here how they interact through the ceRNA mechanism to mediate the protective effect of GLP-1RA inβcells.

肝细胞癌患者血液外泌体ceRNA调控网络的构建及生物信息学分析

目的基于肝细胞癌(hepatocellular carcinoma,HCC)患者血液外泌体中差异表达的长链非编码RNA(long non-cording RNA,lncRNA)、环状RNA(circular RNA,circRNA)和信使RNA(messenger RNA,mRNA),从竞争性内源性(competing endogenous RNA,ceRNA)调控网络角度出发,探索HCC的发病机制及潜在的分子标志物。方法通过exoRBase数据库获取HCC患者及健康对照者血液外泌体RNA的表达谱数据和注释文件,利用R软件进行数据处理和差异表达分析。使用Targetscan、miRanda、CSCD数据库预测可能与差异表达的lncRNA、circRNA、mRNA结合的miRNA,预测结果取交集后使用cytoscape3.9.1构建ceRNA调控网络。最后,对网络中的DEmRNA进行GO、KEGG富集分析及生存分析。结果共发现62个差异表达lncRNAs,18个差异表达circRNAs和160个差异表达mRNAs。经数据库分别预测其可能的结合靶点并将结果取交集后,共计20个DElncRNAs,16个DEcircRNAs,40个DEmRNAs,44个miRNAs被筛选出来构建ceRNA调控网络。GO富集分析显示网络中的DEmRNAs在生物学过程中主要富集在含核定位信号蛋白导入细胞核、肌管分化、RNA剪接调控等方面,细胞组分集中在核斑点、核膜孔、PML体等,分子功能主要表现在蛋白丝氨酸/苏氨酸激酶活性、蛋白激酶调节剂活性、GTP酶激活剂活性等方面。KEGG富集结果显示这些DEmRNAs与MAPK信号通路、癌症中的中心碳代谢、胰高血糖素信号通路等有密切关联。生存分析显示,12个基因(ADAMTS5、CDC42、HNRNPA3、LSM12、MOB1A、RBM39、SEPT7、SMARCA5、STK4、TUBB2A、UBC、VOPP1)与HCC患者的预后相关。结论HCC患者血液外泌体ceRNA网络的构建和生物信息学分析结果可为探讨HCC的发病机制及潜在生物标志物提供新的思路和理论依据。

CeRNA网络在糖尿病肾病发病中的作用及其中医药调控机制研究

糖尿病肾病作为糖尿病的微血管并发症之一,其发病率正在逐年攀升,而有关肾脏损伤发病机制的研究虽已逐渐深入,但尚未完全阐明。竞争性内源RNA(competing endogenous RNA,ceRNA)假说作为一种全新的基因表达调控模式,其机制是不同RNA之间的互作关系。作为ceRNA的环状RNA(circular RNA,circRNA)、长链非编码RNA(long non-coding RNA,lncRNA)、假基因等分子吸附微小RNA(microRNA,miRNA),参与转录后基因表达的调控。近来研究表明,ceRNA调控网络在糖尿病肾病发生发展进程中起重要作用,而中药及其有效成分在治疗糖尿病肾病方面亦有显著优势,因此,文章将就ceRNA网络参与糖尿病肾病的发病机制及其中医药调控作用进行综述,进而为糖尿病肾病的诊断和治疗提供新的研究方向。