Micro RNAs（mi RNAs） are known to regulate post-transcriptional gene expression.They are involved in carcinogenesis and tumor progression.The aim of this study was to explore the micro RNA-m RNA regulatory network in...Micro RNAs（mi RNAs） are known to regulate post-transcriptional gene expression.They are involved in carcinogenesis and tumor progression.The aim of this study was to explore the micro RNA-m RNA regulatory network in esophageal squamous cell carcinoma（ESCC） using comprehensive computational approaches.In this study we have selected a total of 11 mi RNAs from one previously reported study in ESCC.The m RNA targets of these mi RNAs were predicted using various algorithms.The expression profiles of these m RNA targets were identified on DNA microarray experiment dataset across ESCC tissue samples.Based on the mi RNA-m RNA regulatory relationships,the network was inferred.A total of 23 mi RNA-m RNA regulatory interactions,with 11 mi RNAs and 13 m RNA targets,were inferred in ESCC.The mi RNA-m RNA regulatory network with increased confidence provides insights into the progression of ESCC and may serve as a biomarker for prognosis or the aggressiveness of ESCC.However,the results should be examined with further experimental validation.展开更多
目的通过microRNAs差异分析、网络药理学及分子对接技术,探讨益母草治疗宫腔粘连(intrauterine adhesion,IUA)的潜在作用靶点及相关机制。方法基于GEO(gene expression omnibus)数据库筛选IUA与健康者的差异miRNA,经multiMiR进行靶基因...目的通过microRNAs差异分析、网络药理学及分子对接技术,探讨益母草治疗宫腔粘连(intrauterine adhesion,IUA)的潜在作用靶点及相关机制。方法基于GEO(gene expression omnibus)数据库筛选IUA与健康者的差异miRNA,经multiMiR进行靶基因预测。通过TCMSP(traditional Chinese medicine systems pharmacology)数据库检索益母草有效活性成分及相关靶点,并与miRNA靶基因取交集。利用String平台进行蛋白质互作分析,利用cytoNCA筛选关键靶点。基于R语言进行基因本体(gene ontology,GO)和基因组百科全书(kyoto encyclopedia of genes and genomes,KEGG)富集分析。利用CB-dock2对关键靶点和活性成分进行分子对接。结果共筛选出与IUA相关的差异miRNA 43个,经靶基因预测后与IUA共有13个交集靶点,GO及KEGG富集分析结果显示,益母草治疗IUA作用机制主要与细胞衰老、丝裂原活化蛋白激酶(mitogen-activated protein kinase,MAPK)信号通路、PI3K-Akt信号通路等有关。益母草3个特征性活性成分是花生四烯酸、山奈酚、槲皮素,可与蛋白互作网络中相对应的靶点蛋白细胞周期蛋白依赖性激酶4(cyclin-dependent kinase 4,CDK4)、芳香烃受体(aryl hydrocarbon receptor,AHR)、原癌基因c-myc编码转录因子、血管内皮生长因子(vascular endothelial growth factor,VEGF)进行分子对接,主要活性成分能够与核心靶点结合,并展现出较好的亲和力。结论益母草治疗IUA是多成分、多靶点、多通路相互作用的结果,进一步证实了益母草治疗IUA的科学性及有效性,为后续实验提供了研究思路。展开更多
目的观察双相躁狂患者血浆中微小RNA-134(micro RNA-134)及LIM激酶-1(LIMK-1)m RNA的表达水平与双相躁狂之间的关系。方法 105例双相躁狂患者作为患者组,100例与患者组在年龄和性别上匹配的健康志愿者作为对照组,患者组常规应用情绪稳...目的观察双相躁狂患者血浆中微小RNA-134(micro RNA-134)及LIM激酶-1(LIMK-1)m RNA的表达水平与双相躁狂之间的关系。方法 105例双相躁狂患者作为患者组,100例与患者组在年龄和性别上匹配的健康志愿者作为对照组,患者组常规应用情绪稳定剂治疗1个月。患者组于入组时和治疗1个月时、对照组于入组时分别评定Bech-Rafaelsen躁狂量表(BRMS)评分表并收集血浆,采用实时荧光定量聚合酶链式反应(PCR)技术检测血浆micro RNA-134及LIMK-1 m RNA的表达水平,最后对检测结果及BRMS评分进行统计分析。结果治疗前,患者组血浆micro RNA-134及LIMK-1 m RNA表达水平分别为(1.17±0.02)、(0.37±0.02)显著低于对照组的(1.46±0.04)、(0.46±0.01),差异有统计学意义(P<0.05);治疗1个月后,患者组血浆micro RNA-134、LIMK-1 m RNA表达水平分别为(1.36±0.07)、(0.52±0.01)较治疗前显著升高,差异有统计学意义(P<0.05)。患者组治疗前及治疗后血浆micro RNA-134表达水平与BRMS评分之间均存在负相关(r=-0.48、-0.39,P<0.05)。结论血浆micro RNA-134、LIMK-1 m RNA的表达水平和双相障碍躁狂发作有关,有可能作为双相躁狂的生物标记物。展开更多
AIM To explore the expression profiles of microRNAs(miRNAs), long non-coding RNAs(lncRNAs), and mRNAs in oesophageal squamous cell carcinoma(ESCC) in order to construct an oesophageal cancer-specific competing endogen...AIM To explore the expression profiles of microRNAs(miRNAs), long non-coding RNAs(lncRNAs), and mRNAs in oesophageal squamous cell carcinoma(ESCC) in order to construct an oesophageal cancer-specific competing endogenous RNA(ceRNA) network.METHODS In this work, the expression data of miRNAs, lncRNAs, and mRNAs in ESCC were obtained. An oesophageal cancer-specific ceRNA network was then constructed and investigated.RESULTS CeRNAs have the ability to reduce the targeting activityof miRNAs, leading to the de-repression of specific mRNAs with common miRNA response elements. CeRNA interactions have a critical effect in gene regulation and cancer development.CONCLUSION This study suggests a novel perspective on potential oesophageal cancer mechanisms as well as novel pathways for modulating ceRNA networks for treating cancers.展开更多
Acute myocardial infarction(AMI)is a severe cardiovascular disease.This study aimed to identify crucial microRNAs(miRNAs)and mRNAs in AMI by establishing a miRNA-mRNA network.The microarray datasets GSE31568,GSE148153...Acute myocardial infarction(AMI)is a severe cardiovascular disease.This study aimed to identify crucial microRNAs(miRNAs)and mRNAs in AMI by establishing a miRNA-mRNA network.The microarray datasets GSE31568,GSE148153,and GSE66360 were downloaded from the Gene Expression Omnibus(GEO)database.We identified differentially expressed miRNAs(DE-miRNAs)and mRNAs(DE-mRNAs)in AMI samples compared with normal control samples.The consistently changing miRNAs in both GSE31568 and GSE148153 datasets were selected as candidate DE-miRNAs.The interactions between the candidate DE-miRNAs and DE-mRNAs were analyzed,and a miRNA-mRNA network and a protein-protein interaction network were constructed,along with functional enrichment and pathway analyses.A total of 209 DE-miRNAs in the GSE31568 dataset,857 DE-miRNAs in the GSE148153 dataset,and 351 DE-mRNAs in the GSE66360 dataset were identified.Eighteen candidate DE-miRNAs were selected from both the GSE31568 and GSE148153 datasets.Furthermore,miR-646,miR-127-5p,miR-509-5p,miR-509-3-5p,and miR-767-5p were shown to have a higher degree in the miRNA-mRNA network.THBS-1 as well as FOS was a hub gene in the miRNA-mRNA network and the protein-protein interaction(PPI)network,respectively.CDKN1A was important in both miRNA-mRNA network and PPI network.We established a miRNA-mRNA network in AMI and identified five miRNAs and three genes,which might be used as biomarkers and potential therapeutic targets for patients with AMI.展开更多
BACKGROUND： The integrative analysis of microRNA and mRNA expression profiles can elucidate microRNA-targeted gene function. We used this technique to elucidate insights into the immunological pathology of non-alcoho...BACKGROUND： The integrative analysis of microRNA and mRNA expression profiles can elucidate microRNA-targeted gene function. We used this technique to elucidate insights into the immunological pathology of non-alcoholic fatty liver disease （NAFLD）. METHODS： We analyzed differentially expressed microRNA and mRNA expression profiles of CD4＋ T lymphocytes from the liver and mesenteric lymph nodes （MLNs） of mice with NAFLD using microarrays and RNA sequencing. Normal mice were used as controls. The target genes of microRNAs were predicted by TargetScan. Integrative analysis showed that the mRNAs were overlapped with microRNAs. Furthermore, the Gene Ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） analyses were performed to predict the key genes and pathways. Then, 16 microRNAs and 10 mRNAs were validated by qRT-PCR. RESULTS： Microarray analysis suggested that 170 microRNAs were significantly de-regulated in CD4＋ T lymphocytes from the liver between the two groups. Eighty mRNAs corresponded with microRNA targeted genes. KEGG analysis indicated that the MAPK pathway was consistently augmented in the liver of NAFLD mice. miR-23b, let-7e, miR-128 and miR-130b possibly played significant parts in the MAPK pathways. Furthermore, between the two groups, 237 microRNAs were significantly deregulated in CD4＋ T lymphocytes from MLNs. 38 mRNAs coincided with microRNA target genes. The metabolic pathway was consistently enriched in the MLNs of NAFLD mice. miR- 206-3p, miR-181a-Sp, miR-29c-3p and miR-30d-5p likely play important roles in the regulation of metabolic pathways. CONCLUSION： The results of this study presented a new perspective on the application of integrative analysis to identify complex regulation means involved in the immunological pathogenesis of NAFLD.展开更多
基金supported by grants from Natural Science Foundation of Hubei Province,China(No.2010CDB09204)Youth Dawn Plan of Science and Technology in Wuhan,China(No.201150431137)
文摘Micro RNAs（mi RNAs） are known to regulate post-transcriptional gene expression.They are involved in carcinogenesis and tumor progression.The aim of this study was to explore the micro RNA-m RNA regulatory network in esophageal squamous cell carcinoma（ESCC） using comprehensive computational approaches.In this study we have selected a total of 11 mi RNAs from one previously reported study in ESCC.The m RNA targets of these mi RNAs were predicted using various algorithms.The expression profiles of these m RNA targets were identified on DNA microarray experiment dataset across ESCC tissue samples.Based on the mi RNA-m RNA regulatory relationships,the network was inferred.A total of 23 mi RNA-m RNA regulatory interactions,with 11 mi RNAs and 13 m RNA targets,were inferred in ESCC.The mi RNA-m RNA regulatory network with increased confidence provides insights into the progression of ESCC and may serve as a biomarker for prognosis or the aggressiveness of ESCC.However,the results should be examined with further experimental validation.
文摘目的通过microRNAs差异分析、网络药理学及分子对接技术,探讨益母草治疗宫腔粘连(intrauterine adhesion,IUA)的潜在作用靶点及相关机制。方法基于GEO(gene expression omnibus)数据库筛选IUA与健康者的差异miRNA,经multiMiR进行靶基因预测。通过TCMSP(traditional Chinese medicine systems pharmacology)数据库检索益母草有效活性成分及相关靶点,并与miRNA靶基因取交集。利用String平台进行蛋白质互作分析,利用cytoNCA筛选关键靶点。基于R语言进行基因本体(gene ontology,GO)和基因组百科全书(kyoto encyclopedia of genes and genomes,KEGG)富集分析。利用CB-dock2对关键靶点和活性成分进行分子对接。结果共筛选出与IUA相关的差异miRNA 43个,经靶基因预测后与IUA共有13个交集靶点,GO及KEGG富集分析结果显示,益母草治疗IUA作用机制主要与细胞衰老、丝裂原活化蛋白激酶(mitogen-activated protein kinase,MAPK)信号通路、PI3K-Akt信号通路等有关。益母草3个特征性活性成分是花生四烯酸、山奈酚、槲皮素,可与蛋白互作网络中相对应的靶点蛋白细胞周期蛋白依赖性激酶4(cyclin-dependent kinase 4,CDK4)、芳香烃受体(aryl hydrocarbon receptor,AHR)、原癌基因c-myc编码转录因子、血管内皮生长因子(vascular endothelial growth factor,VEGF)进行分子对接,主要活性成分能够与核心靶点结合,并展现出较好的亲和力。结论益母草治疗IUA是多成分、多靶点、多通路相互作用的结果,进一步证实了益母草治疗IUA的科学性及有效性,为后续实验提供了研究思路。
文摘目的观察双相躁狂患者血浆中微小RNA-134(micro RNA-134)及LIM激酶-1(LIMK-1)m RNA的表达水平与双相躁狂之间的关系。方法 105例双相躁狂患者作为患者组,100例与患者组在年龄和性别上匹配的健康志愿者作为对照组,患者组常规应用情绪稳定剂治疗1个月。患者组于入组时和治疗1个月时、对照组于入组时分别评定Bech-Rafaelsen躁狂量表(BRMS)评分表并收集血浆,采用实时荧光定量聚合酶链式反应(PCR)技术检测血浆micro RNA-134及LIMK-1 m RNA的表达水平,最后对检测结果及BRMS评分进行统计分析。结果治疗前,患者组血浆micro RNA-134及LIMK-1 m RNA表达水平分别为(1.17±0.02)、(0.37±0.02)显著低于对照组的(1.46±0.04)、(0.46±0.01),差异有统计学意义(P<0.05);治疗1个月后,患者组血浆micro RNA-134、LIMK-1 m RNA表达水平分别为(1.36±0.07)、(0.52±0.01)较治疗前显著升高,差异有统计学意义(P<0.05)。患者组治疗前及治疗后血浆micro RNA-134表达水平与BRMS评分之间均存在负相关(r=-0.48、-0.39,P<0.05)。结论血浆micro RNA-134、LIMK-1 m RNA的表达水平和双相障碍躁狂发作有关,有可能作为双相躁狂的生物标记物。
基金Supported by the National Natural Science Foundation of China,No.31670895 and No.71673254
文摘AIM To explore the expression profiles of microRNAs(miRNAs), long non-coding RNAs(lncRNAs), and mRNAs in oesophageal squamous cell carcinoma(ESCC) in order to construct an oesophageal cancer-specific competing endogenous RNA(ceRNA) network.METHODS In this work, the expression data of miRNAs, lncRNAs, and mRNAs in ESCC were obtained. An oesophageal cancer-specific ceRNA network was then constructed and investigated.RESULTS CeRNAs have the ability to reduce the targeting activityof miRNAs, leading to the de-repression of specific mRNAs with common miRNA response elements. CeRNA interactions have a critical effect in gene regulation and cancer development.CONCLUSION This study suggests a novel perspective on potential oesophageal cancer mechanisms as well as novel pathways for modulating ceRNA networks for treating cancers.
基金supported by the funds from the National Natural Science Foundation of China(Grant No.81871359 and No.81800445).
文摘Acute myocardial infarction(AMI)is a severe cardiovascular disease.This study aimed to identify crucial microRNAs(miRNAs)and mRNAs in AMI by establishing a miRNA-mRNA network.The microarray datasets GSE31568,GSE148153,and GSE66360 were downloaded from the Gene Expression Omnibus(GEO)database.We identified differentially expressed miRNAs(DE-miRNAs)and mRNAs(DE-mRNAs)in AMI samples compared with normal control samples.The consistently changing miRNAs in both GSE31568 and GSE148153 datasets were selected as candidate DE-miRNAs.The interactions between the candidate DE-miRNAs and DE-mRNAs were analyzed,and a miRNA-mRNA network and a protein-protein interaction network were constructed,along with functional enrichment and pathway analyses.A total of 209 DE-miRNAs in the GSE31568 dataset,857 DE-miRNAs in the GSE148153 dataset,and 351 DE-mRNAs in the GSE66360 dataset were identified.Eighteen candidate DE-miRNAs were selected from both the GSE31568 and GSE148153 datasets.Furthermore,miR-646,miR-127-5p,miR-509-5p,miR-509-3-5p,and miR-767-5p were shown to have a higher degree in the miRNA-mRNA network.THBS-1 as well as FOS was a hub gene in the miRNA-mRNA network and the protein-protein interaction(PPI)network,respectively.CDKN1A was important in both miRNA-mRNA network and PPI network.We established a miRNA-mRNA network in AMI and identified five miRNAs and three genes,which might be used as biomarkers and potential therapeutic targets for patients with AMI.
基金supported by a grant from the National Natural Science Foundation of China(81170375)
文摘BACKGROUND： The integrative analysis of microRNA and mRNA expression profiles can elucidate microRNA-targeted gene function. We used this technique to elucidate insights into the immunological pathology of non-alcoholic fatty liver disease （NAFLD）. METHODS： We analyzed differentially expressed microRNA and mRNA expression profiles of CD4＋ T lymphocytes from the liver and mesenteric lymph nodes （MLNs） of mice with NAFLD using microarrays and RNA sequencing. Normal mice were used as controls. The target genes of microRNAs were predicted by TargetScan. Integrative analysis showed that the mRNAs were overlapped with microRNAs. Furthermore, the Gene Ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） analyses were performed to predict the key genes and pathways. Then, 16 microRNAs and 10 mRNAs were validated by qRT-PCR. RESULTS： Microarray analysis suggested that 170 microRNAs were significantly de-regulated in CD4＋ T lymphocytes from the liver between the two groups. Eighty mRNAs corresponded with microRNA targeted genes. KEGG analysis indicated that the MAPK pathway was consistently augmented in the liver of NAFLD mice. miR-23b, let-7e, miR-128 and miR-130b possibly played significant parts in the MAPK pathways. Furthermore, between the two groups, 237 microRNAs were significantly deregulated in CD4＋ T lymphocytes from MLNs. 38 mRNAs coincided with microRNA target genes. The metabolic pathway was consistently enriched in the MLNs of NAFLD mice. miR- 206-3p, miR-181a-Sp, miR-29c-3p and miR-30d-5p likely play important roles in the regulation of metabolic pathways. CONCLUSION： The results of this study presented a new perspective on the application of integrative analysis to identify complex regulation means involved in the immunological pathogenesis of NAFLD.
