非特指型外周T细胞淋巴瘤microRNA的表达及其生物学信息分析

目的 探讨非特指型外周T细胞淋巴瘤中microRNA的特征性改变及其在发病机制中的作用.方法 应用高通量miRNA芯片技术对5例原发于淋巴结的非特指型外周T细胞淋巴瘤及5例反应性增生的淋巴结组织进行检测,筛选出特异性表达的miRNA,采用Targetscan、miRnada及mirdb软件对差异有统计学意义的miRNA进行靶基因预测,应用生物学信息方法对靶基因GO和信号通路进行分析.结果 miRNA表达谱分析显示,有20种miRNA在这两组样本中差异有统计学意义(P＜0.05),其中非特指型外周T细胞淋巴瘤组有13种miRNA明显上调,分别为kshv-miR-K12-12-5p,hsa-miR-1290,hsa-miR-5585-3p,hsa-miR-593-3p,hsa-miR-4763-3p,hsa-miR-3196,hsa-miR-4714-5p,hcmv-miR-UL148D,hsa-miR-4485,hsa-miR-4769-3p,hsvl-miR-H17,hsa-miR-1587,hsa-miR-4674,预测靶基因显著性GO有30个,信号通路30条;有7种miRNA明显下调,分别为hsa-miR-3913-5p,hsa-miR-614,hsa-miR-224-3p,hsa-miR-4694-3p,hsa-miR-513c-3p,hsa-miR-4677-3p,hsa-miR-218-2-3p,预测靶基因显著性GO有31个,信号通路4条.结论 有统计学意义的20种miRNA可能作为非特指型外周T细胞淋巴瘤与炎性反应性淋巴结增生鉴别指标.hsa-miR-1290、hsa-miR-4485、hsa-miR-3196、hsa-miR-614、hsa-miR-224-3p,可能参与非特指型外周T细胞淋巴瘤的发病机制,所涉及的靶基因有BCL2、C-myc、FOXA1、MAPT、NAT1、PSA、FUT4,影响的信号通路有MAPT通路、Wnt信号通路、NF-κB通路、Hippo信号通路、TGF-β信号通路、人类T淋巴细胞白血病病毒Ⅰ型(HTLV-1)感染相关信号通路.     

神经母细胞瘤血浆外泌体差异表达miRNA靶基因预测及生物信息学分析

目的通过生物信息学分析筛选出神经母细胞瘤外周血血浆外泌体中差异表达miRNA,并对其靶基因功能进行分析预测。方法从高通量基因表达数据库下载数据集GSE128004,分析神经母细胞瘤血浆外泌体中miRNA的差异表达;通过miRTarBase数据库筛选差异表达miRNA的靶基因;进一步通过运用clusterProfiler进行靶基因的基因本体(GO)功能富集与京都基因与基因组百科全书数据库(KEGG)通路富集。结果经筛选发现,数据集GSE128004包含41个表达差异在2倍以上的血浆外泌体miRNA。靶基因预测显示,hsa-miR-199a-3p, hsa-miR-196b-5p, hsa-miR-127-3p, hsa-miR-410-3p和hsa-miR-487b-3p为靶基因最多的前5个差异表达miRNA。GO功能分析发现,这些靶基因大都在细胞运动正调节、细胞迁移正调节、血管生成等生物过程富集;在膜侧、细胞-基底连接、细胞-基底黏附连接、焦点黏连等细胞组成富集;在蛋白丝氨酸/苏氨酸激酶活性、蛋白异二聚体化活性、转录因子活性和RNA聚合酶Ⅱ核心启动子近端区序列特异性结合等分子功能富集。KEGG分析显示:这些差异表达miRNA的靶基因主要参与磷脂酰肌醇3激酶-蛋白激酶B信号通路、癌症相关miRNA、丝裂原活化蛋白激酶信号通路等通路富集。结论 hsa-miR-199a-3p, hsa-miR-127-3p和hsa-miR-410-3p可能作为神经母细胞瘤的潜在生物标志物或治疗靶标,进一步为该病的发病机制提供研究思路。     

乳腺癌microRNA表达谱的初步研究

目的:探讨miRNA基因表达谱的筛选及其在乳腺癌发生发展中的作用.方法:收集8例患者的新鲜乳腺癌组织及配对癌旁组织,利用miRNA芯片对其进行实验分析, 并采用 real time-PCR验证芯片结果的准确性,生物信息学分析其作用靶点.结果:通过SAM软件,相对癌周组织在乳腺癌组织中查出上调的miRNA基因3个,下调的miRNA基因23个.其中显著上调的为hsa-miR-155和hsa-miR-193b.显著下调的为hsa-miR-145,hsa-miR-381,hsa-miR-132,rno-miR-10b,hsa-miR-199b-5p,hsa-miR-100,hsa-miR-335,hsa-miR-497和hsa-miR-99a.实时定量验证芯片结果准确可靠,生物信息学发现不同miRNA对应的靶基因分别为FOXA1、 HOXA1、SMAD7和PSTON等.结论:筛选得到乳腺癌miRNA的差异表达谱靶点非常广泛,涉及到细胞周期调控,转录调控等,可能在乳腺癌的发病机制中发挥潜在作用.     

不同转移潜能肝癌细胞株miRNAs表达谱的差异性研究

目的筛选不同转移潜能肝癌细胞株的microRNA(miRNA)差异表达谱,并预测分析差异表达miRNAs调控的靶基因与功能。方法提取总RNA进行miRNA芯片分析,通过分析MHCC-97H(高转移)、Hep3B(不转移)两种不同转移潜能肝癌细胞株与正常肝细胞L02比较,以及两种肝癌细胞株相互比较的miRNA差异表达谱,筛选出差异表达明显的miRNAs进行qRT-PCR验证,利用4个靶基因预测软件(Target Scan、miRanda、miRWalk、miRDB)进行靶基因预测,并通过生物信息学分析来探讨候选靶基因的生物学功能。结果与正常肝细胞L02相比,肝癌细胞株MHCC-97H、Hep3B中的miR-192-5p、miR-215-5p表达均明显上调,而miR-130a-3p、miR-196a-5p则明显降低;与不转移肝癌细胞株Hep3B相比,miR-224-5p在肝癌细胞株MHCC-97H中明显上调,而miR-146a-5p、miR-483-3p、miR-200b-3p则明显降低。qRT-PCR验证结果与芯片结果相一致。结论 MHCC-97H及Hep3B两种转移能力不同的肝癌细胞株的miRNAs存在差异表达,这些差异表达的miRNAs与肝细胞癌的发生发展、转移侵袭密切相关。     

CSC诱导BEAS-2B细胞恶性转化中miRNA表达谱变化

目的通过烟草烟雾凝集物(cigarette smoke condensate, CSC)慢性染毒永生化人支气管上皮细胞BEAS-2B体外构建恶性转化细胞模型,miRNA芯片技术筛选模型中差异表达的miRNAs,发现与恶性转化相关的miRNAs,为进一步研究CSC诱导恶性转化的作用机制提供实验基础。方法 CCK-8检测细胞存活率,确定CSC染毒终浓度。划痕实验、克隆形成实验、MTT实验及凋亡检测评估细胞恶性转化情况。MiRNAs芯片检测BEAS-2B和CSC30组细胞,明确差异表达谱。表达下调的hsa-miR-2115-3p和hsa-miR-4521进行RT-PCR验证。结果 CSC诱导的恶性转化细胞迁移能力、克隆形成能力和增殖活力明显增强,凋亡率明显下降。相对于BEAS-2B组,CSC30组细胞中有78种miRANs差异表达,其中52种表达上调,26种表达下调。RT-PCR验证hsa-miR-2115-3p和hsa-miR-4521表达下调与芯片结果一致。结论 CSC可诱导BEAS-2B细胞发生恶性转化,采用miRNA芯片技术筛选到miRNA差异表达谱,其可能与CSC诱导恶行转化的发生发展有关。     

子宫内膜异位症在位内膜中自噬相关基因及ceRNA网络的作用

目的 通过筛选子宫内膜异位症在位内膜中的自噬相关基因,明晰竞争性内源性RNA(ceRNA)网络在子宫内膜异位症中的作用。方法 从GEO数据库和Human Autophagy Database数据库分别获取子宫内膜异位症数据集和自噬相关基因列表,查找自噬相关基因,通过预测和相关性筛选miRNA和LncRNA并构建ceRNA网络。验证筛选得到的关键基因在其他子宫内膜异位症在位内膜数据集的表达及诊断效能。结果 子宫内膜异位症在位内膜中有39个自噬相关基因存在表达差异,通过PPI查找到7个关键基因,功能富集在巨自噬、线粒体自噬和激活转录因子等,信号通路主要涉及E2F、FOXO、DNA损伤修复、FAS信号通路、PI3K/Akt/mTOR等。构建11个ceRNA调控网络,包括4个mRNA(CASP3、HIF1A、CDKN1A、RPS6KB1)、7个miRNA(hsa-let-7e-5p、hsa-miR-124-3p、hsa-miR-199a-5p、hsa-miR-200c-3p、hsa-miR-24-3p、hsa-miR-30a-5p和hsa-miR-382-5p)和8个LncRNA(NORAD、...     

脑神经胶质瘤替莫唑胺耐药 circRNA-miRNA-mRNA调控网络的构建

目的 筛选脑神经胶质瘤替莫唑胺耐药细胞株U87/TR与亲本细胞株U87的环状RNA(circRNA)差异表达谱以及构建关键环状RNA(circRNA)-微小RNA(miRNA)-信使RNA(mRNA)调控网络.方法 2020年1—6月,应用circRNAs芯片检测神经胶质瘤替莫唑胺耐药细胞circRNAs差异表达谱,并进行RT-PCR验证.用miRanda数据库预测circRNA-miRNA靶向结合关系,通过miRanda v5、TargetScan、miBase数据库预测靶基因,Cytoscape软件构建circRNA-miRNA-mRNA调控网络.结果 circRNA芯片结果显示,与U87细胞比较,U87/TR细胞有313个差异有统计学意义表达的circRNAs(P<0.05),其中145个显著上调,168个明显下调;RT-qPCR验证结果与芯片结果相符.miRNA靶位点预测结果显示,关键上调人环状RNAhsa_circRNA_009054,hsa_circRNA_104338(n=3,t=12.09、9.52,P=0.007、0.011)以及下调hsa_circRNA_016459,hsa_circRNA_101975(n=3,t=13.86、7.75,P=0.005、0.016)可与hsa-miR-33a-5p,hsa-miR-15b-3p以及hsa-miR-193b-5p,hsa-miR-23a-5p等多个miRNAs靶向结合,关键circRNA-miRNA-mRNA调控网络包括4个关键circRNAs,20个关键miRNAs,以及278个关键mRNAs.结论 cir?cRNA在脑神经胶质瘤替莫唑胺耐药细胞中异常表达,hsa_circRNA_009054,hsa_circRNA_104338以及hsa_circRNA_016459,hsa_circRNA_101975等关键circRNA可能通过circRNA-miRNA-mRNA调控网络参与脑神经胶质瘤替莫唑胺的耐药过程.     

基于生物信息学分析关键miRNAs在肺鳞癌发生发展中的功能及意义

目的 应用生物信息学方法探究关键miRNAs在肺鳞癌发生发展中的功能及临床意义。方法 利用GEO2R在线工具分析GSE17681数据集中肺癌样本和对照样本的差异表达miRNA。利用miRTarBase数据库预测排在前3位的上调和下调miRNA的靶基因。利用DAVID数据库对靶基因进行GO和KEGG富集分析。通过STRING数据库构建靶基因间的蛋白互作网络及miRNA-基因互作网络，然后利用Cytoscape软件的cytoHubba插件分析关键miRNA及其调控的Hub靶基因。利用UALCAN数据库分析关键miRNA及其调控的Hub靶基因在肺鳞癌中的表达。最后利用Kaplan-Meier Plotter工具分析关键miRNA对肺鳞癌生存状况的影响。结果 共筛选出116个差异表达的miRNA,包括93个上调miRNA,23个下调miRNA。预测了前3位上调和下调miRNA的1282个靶基因，参与了肺鳞癌的相关通路，如癌症途径、MAPK信号通路等。通过miRNA-基因互作网络筛选到上调和下调的关键miRNA为hsa-miR-19a和hsa-miR-126,其调控的Hub靶基因分别为TNF、P...     

脂肪干细胞分化成血管内皮细胞前后miRNA的差异表达

目的：探讨人脂肪间充质干细胞向血管内皮细胞诱导分化前后microRNA （miRNA ）的差异表达,预测其靶基因。方法对人脂肪间充质干细胞诱导成的血管内皮细胞进行鉴定后,提取人脂肪间充质干细胞向血管内皮细胞诱导分化前后的 miRNA ,微阵列芯片检测表达谱的变化,对有显著差异的miRNA进行实时荧光定量PCR验证,通过TargetScan、Miranda、PITA 、RNAhybrid和microTar五个数据库预测靶基因。结果筛选、验证出四个显著差异表达的miRNA。其中,miR‐29b‐3p和miR‐5096为显著上调,miR‐143‐3p和 miR‐145‐5p为显著下调。预测到 OCT4、SOX2、KLF4、TGFB2、IGF1、TAF11、TMEM169、UHRF1和OSBPL6等相关靶基因。结论人脂肪间充质干细胞向血管内皮细胞诱导分化前后存在显著差异性表达的miRNA ,提示这些miRNA在其分化中有重要的调控作用。     

阴虚火旺型OLP差异表达miRNAs靶基因信号通路调控分析

目的:探索口腔扁平苔藓(Oral Lichen Panus,OLP)的中医证候研究方法,探寻阴虚火旺型OLP的miRNAs表达特征,分析实验获得的阴虚火旺型OLP差异表达miRNAs的靶基因信号通路。方法:选取3例阴虚火旺型口腔扁平苔藓患者及3例正常人血液,分离提取miRNA,荧光标记后与miRNA基因芯片杂交,SAM软件筛选阴虚火旺型OLP患者和正常人有表达差异的miRNA,运用Targetscan软件及Kegg和Biocarta数据库分析阴虚火旺型OLP差异表达miRNAs靶基因信号通路。结果:获得5个口腔扁平苔藓特异表达miRNA,3个下调,2个上调,其中hsa-miR-18a miRNA相关的有统计学意义的信号通路共12条(P<0.01);hsa-miR-99bmiRNA基因相关的有统计学意义的信号通路有2条(P<0.05)。结论:基因芯片技术可用于口腔扁平苔藓中医证候研究,hsa-miR-18a上调和hsa-miR-99b下调可能是阴虚火旺型口腔扁平苔藓的标志性mi RNA,并且hsa-miR-18a可能通过12条信号通路调控OLP的发生发展,以及hsa-miR-99b可能通过2条信号通路调控OLP的发生发展。     

A Non-invasive Liquid Biopsy Screening of Urine-Derived Exosomes for miRNAs as Biomarkers in Endometrial Cancer Patients

Exosomes have great potential to serve as a source of diagnostic and prognostic biomarkers for endometrial cancer (EC). Urine-derived exosomes from patients with EC and patients with symptoms of EC, but without established EC, were used to evaluate a unique miRNA expression profile. Of the 84 miRNA studied, 57 were amplified in qPCR, suggesting the differential packaging of miRNA in exosomes. Further, hsa-miR-200c-3p was identified to be enriched the most. Various bioinformatics and in silico tools were used to evaluate the biological significance of hsa-miR-200c-3p in EC. We conclude that differential miRNA in exosomes can be utilized for discovery of biomarker signatures and EC diagnosis; hsa-miR-200c-3p is one such candidate. Urine-derived exosomes pave the way for the development of non-invasive biomarkers.     

Mechanisms of migration and invasion promoted by NSCLC cells-derived exosomes

OBJECTIVE To explore the function and mechanism of exosomes from non-small cell lung cancer(NSCLC) in promoting the invasion and metastasis of lung cancer cel s. METHODS The exosomes were isolated and identified by differential centrifugation, nanosight,transmission electron microscope and Western blotting.Observation of the exosome uptake was applied by immune fluorescent confocal experiments. Scratch test was used to detect the influence of exosomes to tumor cells migration ability and transwell assay were carried out to investigate the effect of exosomes on migration and invasion. Total RNAs from exosomes were used for miRNA library preparation and sequencing. RT-Q-PCR was employed to detect the miRNA levels. Western blotting was adopted to detect the protein expression levels and dual luciferase reporter assay was used to verify the predict target site of miRNA. RESULTS The extracellular vesicles in the supernatant of NSCLC cells were isolated by the differential centrifugation and confirmed as exosomes by nanosight, transmission electron microscope and Western blotting. Exosomes from NSCLC can promote migration and invasion of non-small cell lung cancer cells showing concentration-and time-dependent manner. By analyzing the differential expression profile of exosomes miRNA of lung epithelial cells and lung cancer cell A549,30 miRNAs were screened out. Then, hsa-miR-34c-3p was selected in combination with clinical specimen detection. The expression level of miR-34c-3p in exosomes from lung cancer was lower than that of the normal one.CONCLUSION Exosomes from NSCLC cells can be uptaken by cells and promote cell migration and invasion in dose-dependent manner. The expression level of miR-34c-3p in exosomes from NSCLC is significantly lower than normal tissues. The level of miR-34c-3p was further declined after incubating with exosomes. Exosomes from NSCLC cells can deliver miR-34c-3p to recepted cells and up-regulate the protein level of integrin α2β1.     

Evaluation of microRNA responses in ARPE-19 cells against the oxidative stress

Purpose: This study aimed to determine microRNA (miRNA) expression profile of human retinal pigment epithelium cell (ARPE-19) against the oxidative stress induced by hydrogen peroxide (H₂O₂).

Methods: ARPE-19 cells were incubated with different concentrations of H₂O₂ (200, 600 and 800?μM) for 18?h, and then cell viability, vascular endothelial growth factor levels and total oxidant status were evaluated. Expressions of 1152 miRNA were determined by quantitative real-time PCR in each group.

Results: Expressions of 90 miRNA were significantly changed in the ARPE-19 cells incubated with H₂O₂ compared to control group. However, miR-143-3p was only found to be expressed in groups incubated with H₂O₂. While 24 miRNA (hsa-miR-200c-3p, miR-192-5p, miR-194-5p, miR-141-3p, miR-658, miR-18?b-5p, miR-486-5p, miR-525-3p, miR-493-3p, miR-518d-3p, miR-29?b-1-5p, miR-675-3p, miR-1238-3p, miR-195-3p, miR-1539, miR-490-5p, miR-3200-5p, miR-1273d, miR-130a-5p, miR-30?b-5p, miR-1247-5p, miR-1910-5p, miR27a-5p and miR-200?b-3p) upregulated due to the increased dose of H₂O₂, nine miRNA (hsa-miR-96-5p, miR-33a-5p, miR-345-5p, miR-106?b-3p, miR-1285-3p, miR-23?b-5p, miR-27?b-5p, miR-103a-3p and miR-4289) were also found to be downregulated.

Conclusion: This study suggests that oxidative stress may be an important factor on expression of miRNAs in ARPE-19 cells. These miRNAs may have a role in the pathogenesis of age-related macular degeneration related to oxidative stress. However, this relationship needs to be examined in new studies by evaluation of pathways and target genes.     

Integrated mRNA and micro RNA profiling reveals epigenetic mechanism of differential sensitivity of Jurkat T cells to AgNPs and Ag ions

In our previous in vitro study of the toxicity on silver nanoparticles (AgNPs), we observed a dramatically higher sensitivity of Jurkat T cells to AgNPs than to Ag ions, and DNA damage and apoptosis were found to be involved in that toxicity. In this study, to understand underlying mechanism of different sensitivity of Jurket T cells to AgNPs and Ag ions, mRNA microarray and micro RNA microarray were concomitantly conducted on AgNPs and Ag ions exposed Jurkat T cells. Surprisingly only a small number of genes were differentially expressed by exposure to each of the silver (15 altered mRNA by AgNPs exposure, whereas 4 altered mRNA by Ag ions exposure, as determined 1.5-fold change as the cut-off value). miRNA microarray revealed that the expression of 63 miRNAs was altered by AgNPs exposure, whereas that of 32 miRNAs was altered by Ag ions exposure. An integrated analysis of mRNA and miRNA expression revealed that the expression of hsa-miR-219-5p, was negatively correlated with the expression of metallothionein 1F (MT1F) and tribbles homolog 3 (TRIB3), in cells exposed to AgNPs; whereas, the expression of hsa-miR-654-3p was negatively correlated with the expression of mRNA, endonuclease G-like 1 (EDGL1) in cells exposed to Ag ions. Network analysis were further conducted on mRNA-miRNA pairs, which revealed that miR-219-5p–MT1F and –TRIB3 pairs by AgNPs are being involved in various cellular processes, such as, oxidative stress, cell cycle and apoptosis, whereas, miR-654-3p and ENDOGL1 pair by Ag ions generated a much simpler network. The putative target genes of AgNPs-induced miR-504, miR-33 and miR-302 identified by Tarbase 6.0 are also found to be involved in DNA damage and apoptosis. These results collectively suggest that distinct epigenetic regulation may be an underlying mechanism of different sensitivity of Jurkat T cells to AgNPs and Ag ion. Further identification of putative target genes of DE miRNA by AgNPs and Ag ions may provide additional clues for the mechanism of differential toxicity. Overall results suggest that epigenetic mechanism is involved in toxicity of AgNPs and Ag ions in Jurkat T cells.     

Effect of c-fos gene silence on PM2.5-induced miRNA alteration in human bronchial epithelial cells

Human bronchial epithelial (HBE) cells and c-fos-silenced HBE cells were first exposed to fine particulate matter (PM_2.5) and the resulting miRNA sequenced. Thereafter, a weighted gene co-expression network analysis was performed using Cytoscape software to visualize the interactions between identified hub miRNAs and their target genes. Nine differentially expressed miRNAs in hub miRNAs were identified in the different treatment groups, of which miR-25−3p, miR-215−5p, and miR-145−5p were selected for further study. Following qPCR validation, both miR-25−3p and miR-215−5p were found to be significantly up-regulated whilst, miR-145−5p was significantly down-regulated (p < 0.05) in the PM_2.5 group. Furthermore, miR-25−3p and miR-145−5p were also significantly down-regulated in the untreated group of c-fos silenced HBE cells. However, miR-215−5p was significantly down-regulated in both the untreated and PM_2.5-treated groups of c-fos silenced HBE cells. Subsequent analysis of their target genes also illustrated differential gene expression when comparing the treatment groups of the two cell types. The present data indicated that the c-fos gene has an important effect on the miRNA expression profiles and the related signaling pathways in PM_2.5-treated HBE cells. Therefore, each of miR-25−3p, miR-145−5p, and miR-215−5p may potentially provide future research information for additional exploration of a PM_2.5-induced carcinogenesis mechanism.     

Differential and unique patterns of synaptic miRNA expression in dorsolateral prefrontal cortex of depressed subjects

Altered synaptic plasticity is often associated with major depressive disorder (MDD). Disease-associated changes in synaptic functions are tightly correlated with altered microRNA (miRNA) expression. Here, we examined the role of miRNAs and their functioning at the synapse in MDD by examining miRNA processing machinery at synapse and sequencing miRNAs and analyzing their functions in synaptic and total tissue fractions obtained from dorsolateral prefrontal cortex (dlPFC) of 15 MDD and 15 matched non-psychiatric control subjects. A total of 333 miRNAs were reliably detected in the total tissue fraction. Multiple testing following the Benjamini–Hochberg false discovery rate [FDR] showed that 18 miRNAs were significantly altered (1 downregulated 4 up and 13 downregulated; p < 0.05) in MDD subjects. Out of 351 miRNAs reliably expressed in the synaptic fraction, 24 were uniquely expressed at synapse. In addition, 8 miRNAs (miR-215-5p, miR-192-5p, miR-202-5p, miR-19b-3p, miR-423-5p, miR-219a-2-3p; miR-511-5p, miR-483-5p showed significant (FDR corrected; p < 0.05) differential regulation in the synaptic fraction from dlPFC of MDD subjects. In vitro transfection studies and gene ontology revealed involvement of these altered miRNAs in synaptic plasticity, nervous system development, and neurogenesis. A shift in expression ratios (synaptic vs. total fraction) of miR-19b-3p, miR-376c-3p, miR-455-3p, and miR-337-3p were also noted in the MDD group. Moreover, an inverse relationship between the expression of precursor (pre-miR-19b-1, pre-miR-199a-1 and pre-miR-199a-2) and mature (miR-19b-3p, miR-199a-3p) miRNAs was found. Although not significantly, several miRNA processing enzymes (DROSHA [95%], DICER [17%], TARBP2 [38%]) showed increased expression patterns in MDD subjects. Our findings provide new insights into the understanding of the regulation of miRNAs at the synapse and their possible roles in MDD pathogenesis.Subject terms: Depression, Depression