Profiling of microRNA-mRNA reveals roles of microRNAs in cervical cancer

Background  Cervical cancer is one of the most common malignant tumors in women. This study was designed to explore the expression profiles of microRNAs (miRNAs) and mRNAs and the gene regulation network in cervical tumorigenesis and to find candidate molecular markers and key tumorigenic genes in cervical cancer.

Methods  miRNAs and mRNAs expression microarrays were used to detect the expression of miRNAs and mRNAs in normal and cancer cervical tissues. TargetScan 5.0 database (UK) was used to predict the target genes of the miRNAs, analyze their intersection with differentially expressed mRNAs and negatively correlate the intersection with miRNAs. Bioinformatic approaches were used to analyze functions and pathways of the target genes and establish miRNA-gene network.

Results  Twenty-nine miRNAs and 2036 mRNAs were differentially expressed in normal and cervical tumor tissues. Among them, 13 miRNAs and 754 mRNAs were up-regulated in cervical tumor tissues and 16 miRNAs and 1282 RNA were down-regulated. The 327 target genes negatively related to miRNAs in the intersection were involved in functions and signal pathways. Down-regulated miRNAs targeted genes and up-regulated miRNAs targeted genes were involved in 415 and 163 functions, respectively, and in 37 and 17 significant pathways, respectively (P <0.05, false discovery rate (FDR) <0.05). We constructed the miRNAs-gene network and found that hsa-miR-15a, hsa-miR-106b and hsa-miR-20b were key nodes in the network.

Conclusions  The differentially expressed miRNAs and mRNAs in cervical cancer and related miRNA-gene network have been identified. They play important roles in cervical tumorigenesis and are involved in many important biological functions and signal transduction pathways. These findings lay a foundation for research on the molecular mechanism of miRNAs in the pathogenesis of cervical cancer.

     

Detection of microvesicle miRNA expression in ALL subtypes and analysis of their functional roles

Microvesicles （MVs） are the heterogeneous mixtures of vesicles. MVs released by leukemia cells constitute an important part of the leukemia microenvironment. MVs might act as important reser- voirs of microRNAs （miRNAs）. It is worth evaluating whether MVs possess some unique miRNA con- tents that are valuable in understanding the pathogenesis. In this study, we investigated the miRNA ex- pression patterns of Nalm-6-derived MVs, Jurkat-derived MVs and normal cell-derived MVs using miRNA microarrays. The potential target genes regulated by differentially expressed miRNAs were also predicted and analyzed. Results demonstrated that 182 miRNAs and 166 miRNAs were differentially expressed in Nalm-6-MVs and Jurkat-MVs, respectively. Many oncogenes, tumor suppressors and sig- nal pathway genes were targeted by these aberrantly expressed miRNAs, which might contribute to the development of B-ALL or T-ALL. Our findings expanded the potential diagnostic markers of ALL and provided useful information for ALL pathogenesis.     

Relationship between magnetic resonance imaging features and miRNA gene expression in patients with glioblastoma multiforme

Background Magnetic resonance imaging (MRI) is commonly utilized as part of the diagnostic workup for the clinical diagnosis of glioblastoma multiforme (GBM), further guiding the clinical treatment of this aggressive cancer. Recent research has shown that microRNAs (miRNAs) may act as oncogenes, or in some cases, tumor suppressor genes that in turn may reflect the genotypic features of GBM. This study aimed to investigate the relationship between MRI features and miRNA gene expression in patients with glioblastoma multiforme.

Methods In order to identify the relationship between the radiographic findings of MRI and those identified changes in miRNA gene expression of GBM, we reviewed the MRI images of GBM patients and compared them with the identified miRNA expression profiles utilizing microarray analysis of paired GBM tumor samples. We chose five MRI imaging features: (1) contrast tumor enhanced/necrosis ratio, (2) contrast tumor enhanced/T2 ratio, (3) multiple lesions, (4) hemorrhage, and (5) necrotic volume. The relationship between these five imaging features and miRNA expression was studied using significance analysis of microarrays analysis.

Results We found that the expression of miRNAs such as hsa-miR-892b, hsa-miR-892a, and hsa-miR-888 was inversely correlated with an enhanced/necrosis ratio ≥1. The miRNAs such as hsa-miR-95, hsa-miR-498, and hsa-miR-1300 were associated with a contrast tumor enhanced/T2 ratio ≥1. The miRNAs such as hsa-miR-612, hsa-miR-524-3, and hsa-miR-1282 were associated with multiple lesions identified on MRI and the expression of miR-221 was associated with hemorrhage by GBM. The expression of miR-let-7, including miR-let-7f, miR-let-7i, and miR-let-7f-1*, was downregulated in the hemorrhage group. The gene expression of miRNAs such as hsa-miR-140-5p, hsa-miR-30e, and hsa-miR-301a was relatively low when compared with the larger necrotic volume group as identified by MRI.

Conclusions The miRNA gene expression profiles correlate with several selected MRI features of patients with GBM. Further analysis of key imaging features of MRI with correlation with miRNA gene expression patterns may help to guide treatment decisions based on these unique correlative profiles of GBM.

     

MiR-503 regulates cisplatin resistance of human gastric cancer cell lines by targeting IGF1R and BCL2

Background Studies have shown that the drug resistance of gastric cancer cells can be modulated by abnormal expression of microRNAs （miRNAs）.We investigated the role of miR-503 in the development of cisplatin resistance in human gastric cancer cell lines.Methods MiR-503 expression was measured by quantitative real-time PCR.MTT （3-（4,5-dimethylthiazol-2-yl）-2,5-diphenyltetrazolium bromide） and clonogenic assays were used to examine changes in cell viability and the drug resistance phenotype of cancer cells associated with upregulation or downregulation of the miRNA.A dual-luciferase activity assay was used to verify target genes of miR-503.Immunohistochemistry,Western blotting analysis,and a flow cytometric apoptosis assay were used to elucidate the mechanism by which miR-503 modulates drug resistance in cancer cells.Results MiR-503 was significantly downregulated in gastric cancer tissues and several gastric cancer cell lines.Additionally,downregulation of miR-503 in the cisplatin （DDP）-resistant gastric cancer cell line SGC7901/DDP was concurrent with the upregulation of insulin-like growth factor-1 receptor （IGF1R） and B-cell lymphoma 2 （BCL2） expression compared with the parental SGC7901 cell line.An in vitro drug sensitivity assay showed that overexpression of miR-503 sensitized SGC7901/DDP cells to cisplatin.The luciferase activity of reporters driven by IGF1R and BCL2 3＇-untranslated regions in SGC7901/DDP cells suggested that IGF1R and BCL2 were both direct target genes of miR-503.Enforced miR-503 expression in SGC7901/DDP cells reduced expression of the target proteins,inhibited proliferation,and sensitized the cells to DDP-induced apoptosis.Conclusion Our findings suggest that hsa-miR-503 modulates cisplatin resistance of human gastric cancer cells at least in part by targeting IGF1R and BCL2.     

宫颈鳞状细胞癌组织中miRNA差异性表达及其靶基因作为诊断标志物的意义

目的: 采用生物信息学方法研究宫颈鳞状细胞癌(CESC)组织中差异性表达的miRNA并预测其靶基因,以期找到影响CESC发生发展及可用于肿瘤标志物的miRNA。 方法: 癌症基因组图谱 (TCGA)数据库中下载3例CESC组织及3例配对正常组织,用统计学方法对差异性表达的基因及miRNA进行筛选,通过靶基因预测网站对差异性表达的miRNA进行靶基因预测,运用KEGG数据库分析靶基因参与的肿瘤相关信号通路。 结果: 与同源正常组织比较,CESC组织有18个miRNA和1180个基因有差异性表达(P<0.05),其中有15个miRNA和411个基因上调,3个miRNA和770个基因下调,采用靶基因预测网站有7个miRNA与预测到的靶基因呈负向调控关系,6个上调miRNA的靶基因下调,1个下调miRNA的靶基因上调,靶基因集中在Wnt、MAPK、P53和cAMP等肿瘤相关信号通路。 结论: 差异性表达的miRNA包括hsa-miR-27a、hsa-miR-148b、hsa-miR-185、hsa-miR-200a、hsa-miR-200b、hsa-miR-221和hsa-mir-133b,差异性表达的miRNA及其靶基因在CESC的发生发展过程中起重要作用,有可能成为诊断CESC的肿瘤标志物。     

Relationship between MRI features and miRNA gene expression in patients with glioblastoma multiforme

BACKGROUND: Magnetic resonance imaging (MRI) is commonly utilized as the part of the diagnostic workup for the clinical diagnosis of glioblastoma multiforme (GBM), further guiding the clinical treatment of this aggressive cancer. Recent research has shown that micro RNA’s (miRNAs) may act as oncogenes, or in some cases, tumor suppressor genes that in turn may reflect the genotypic features of GBM. METHODS: In order to identify the relationship between the radiographic findings of MRI with those identified changes in miRNA gene expression of GBM, we reviewed the MRI images of GBM patients and compared them to the identified miRNA expression profiles utilizing microarray analysis of paired GBM tumor samples. We chose five MRI imaging features: 1. contrast tumor enhanced/necrosis ratio, 2. contrast tumor enhanced/T2 ratio, 3. multiple lesions, 4. hemorrhage and 5. necrotic volume. The relationship between these five imaging features and miRNA expression was studied using Significance Analysis of Microarrays (SAM) analysis. RESULTS: We found that the expression of miRNA’s hsa-miR-892b, hsa-miR-892a, hsa-miR-888 was inversely correlated with a enhanced/necrosis ratio ≥ 1. The miRNA’s hsa-miR-95, hsa-miR-498 and hsa-miR-1300 were associated with a contrast tumor enhanced/T2 ratio ≥ 1. The miRNA’s hsa-miR-612,hsa-miR-524-3 and hsa-miR-1282 were associated with multiple lesions identified on MRI and the expression of miR-221 was associated with hemorrhage in GBM. The expression of miR-let-7, including miR-let-7f, miR-let-7i, miR-let-7f-1*, were down-regulated in the hemorrhage group. The gene expression of of miRNA’s hsa-miR-140-5p, hsa-miR-30e and hsa-miR-301a was relatively low when compared with the larger necrotic volume group as identified by MRI. CONCLUSION: The miRNA gene expression profiles correlate with several select MRI features of patients with GBM. Further analysis of key imaging features of MRI with correlation with miRNA gene expression patterns may help to guide treatment decisions based upon these unique correlative profiles of GBM.     

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...     

不同腹膜后淋巴结转移能力的卵巢癌细胞小RNA（miRNA）表达差异

 目的  筛选具有腹膜后高淋巴结转移能力的浆液性卵巢癌细胞株,并分析其导致淋巴高转移的相关小RNA (microRNA,miRNAs)。方法   接种人卵巢癌细胞株SKOV-3于BALB/c裸鼠腹腔,从腹膜后淋巴结中筛选出卵巢癌细胞,再次接种于裸鼠腹腔,重复分选4次后获得了稳定的高腹膜后淋巴结转移细胞株SKOV-3/LN403。对比SKOV-3和SKOV-3/LN403细胞的形态、增殖和侵袭能力,应用miRCURYTM LNA Array技术对两者的miRNA进行差异分析,通过real-time PCR验证差异表达的miRNAs。结果  稳定筛选的腹膜后高淋巴结转移卵巢癌细胞株SKOV 3/LN403,淋巴转移率高达90% (n=10),并能成功模拟卵巢癌淋巴转移患者的临床表现。SKOV-3/LN403具有比SKOV-3更强的增殖(P<0.05)和侵袭能力(P<0.01)。miRNA的表达谱提示14种miRNA表达差异明显,包括3种miRNA上调(hsa-miR-886 5p,hsa-miR-640,hsa-miR-801),11种miRNA下调(hsa-let-7a,hsa-miR-30a,hsa-miR-491-3p,hsa-let-7i,hsa-miR-125b-1,hsa-miR-27a,hsa-miR-24,hsa-let 7b,hsa-miR-16,hsa-miR-20a,hsa-miR-26b)。Real time PCR结果和芯片结果一致。结论  SKOV-3/LN403可用于构建卵巢癌腹膜后淋巴结转移模型,其高腹膜后淋巴结转移力与miRNA分子的调控相关,为卵巢癌腹膜后淋巴结转移机制提供潜在研究靶点。     

Unique MicroRNAs Signature of Lymphocyte of Yang and Yin Syndromes in Acute Ischemic Stroke Patients

Objective: To identify the differentially expressed microRNAs (miRNAs) profiles of yang and yin syndromes in patients with acute ischemic stroke, and to provide the molecular basis of the classification of these two syndrome types in acute ischemic stroke patients. Methods: A microarray assay was performed to assess the expression pattern of miRNAs in the lymphocyte of acute ischemic stroke patients. Target genes for the deregulated miRNAs were predicated using the online bioinformatic algorithms and functional annotation via Kyoto encyclopedia of genes and genomes pathway analysis for miRNAs predicted targets was carried out. Based on the predicted target genes of differentially expressed miRNAs, the miRNA-gene-network and miRNA-pathway network were constructed. Results: Yang score based on tongue texture, urine, dejecta, and appearance, etc. showed that clinical symptoms were distinct between yang and yin syndromes. There were significantly higher total leukocyte number and lower total protein level in patients with yang syndrome compared with those in patients with yin syndrome (P<0.05). Comprehensive miRNA analysis identified 36 unique down-regulated miRNAs in yang syndrome group, and 20 unique down-regulated and 2 unique up-regulated miRNAs in yin syndrome group. The key regulatory miRNAs, gene, and pathways in the yang syndrome were hsa-miR-93-5p and -320b, enabled homolog, the metabolic pathways and mitogen-activated protein kinase signaling pathways, respectively, while those in the yin syndrome were hsa-miR-424-5p and -106b-5p, CNOT4, hepatitis B and pathways in cancer, respectively. Conclusion: These results offered insight into the molecular basis underlying the different pathogenesis of yang or yin syndrome, providing clues for the individualized therapeutic strategies of acute ischemic stroke.     

MiRNA异常表达对肥胖儿童代谢综合征发生发展的影响

目的探讨微小RNA（microRNA,miRNA）异常表达对肥胖儿童代谢综合征发生发展的影响。方法应用miRNA表达谱芯片检测肥胖合并代谢综合征患儿、单纯性肥胖患儿及正常体重儿童血清中miRNA的表达谱;利用实时定量PCR技术检测其差异表达的miRNA,验证miRNA芯片结果的可靠性;应用软件对筛选出的显著差异表达miRNA的靶基因进行预测。结果单纯性肥胖患儿血清中,上调表达超过1.5倍的miRNA有15个,下调表达超过1.5倍的有11个。肥胖合并代谢综合征患儿血清中9个上调miRNA,7个下凋miRNA。其中肥胖合并代谢综合征患儿hsa-miR-143、hsa-miR-24、hsa-miR-34a和has-miR-29a表达高于单纯性肥胖患儿,下调表达中有hsa-miR-192和hsa-miR-23a表达低于单纯性肥胖儿童。通过生物信息学分析发现了表达显著改变miRNA的共同作用的靶基因。结论筛选出肥胖合并代谢综合征患儿的差异表达miRNA,可能参与其对应共同靶基因,具有调控肥胖儿童合并代谢综合征发生发展的作用。     

左向右分流型肺动脉高压大鼠肺组织中microRNA的表达谱及初步分析

目的检测晚期肺动脉高压(pulmonary hypertension,PH)大鼠肺组织中microRNA(miRNA)的表达,初步预测差异表达的microRNA调控的靶基因。方法 4～5周龄健康雄性SPF级SD大鼠20只,体质量90～110 g,按完全随机分组法分成分流组(n=10)和对照组(n=10)。分流组采用套管法行右侧颈总动脉-颈外静脉分流术以建立左向右分流型肺动脉高压模型,对照组行假手术,建立左向右分流型肺动脉高压大鼠模型。12周后,取大鼠外周肺组织,运用microRNA表达谱芯片检测分流组和对照组大鼠肺组织microRNA的差异性表达。运用Miranda、TargetScan、PicTar软件预测可能调控的靶基因,实时定量PCR验证miR-98、miR-130b和miR-127等的表达。结果平均肺动脉压(mPAP)、肺动脉中膜厚度百分比(MT%)及右心室肥厚指数(RVHI)均明显高于对照组(P<0.01),microRNA芯片结果提示:与对照组相比,在分流组大鼠肺组织中表达明显上调的miRNA有30个(miR-122、miR-130b、miR-146b等),明显下的miRNA有7个(miR-382、miR-192、miR-29c等),RT-PCR结果与芯片结果一致。结论 microRNA在左向右分流型肺动脉高压大鼠中表达存在差异,microRNA可能参与肺动脉高压大鼠肺血管的重构。     

基于TCGA数据库应用生物信息学方法分析和挖掘肺腺癌预后和诊断miRNA研究

目的基于TCGA数据库,应用生物信息学方法分析和挖掘肺腺癌预后和诊断miRNA生物学标志物。方法数据下载:从TCGA下载获取肺腺癌miRNA表达谱数据,包括miRNAseq和临床数据。筛选差异表达miRNAs:应用R-version 3.6.2软件中的edgeR包筛选肺腺癌组织和正常肺组织的差异基因,以│logFC│>2,P<0.05为筛选条件。筛选与预后相关miRNAs:应用R-version 3.6.2软件中的survival包绘制KM生存曲线,筛选与预后相关的miRNAs。筛选可作为肺腺癌诊断的miRNAs:应用R-version 3.6.2软件中的pROC包制作受试者工作特征曲线(ROC)评价与预后相关miRNAs诊断肺腺癌的特异性和敏感性。结果共识别到肺腺癌与正常肺组织差异表达的miRNA 144个,其中上调表达119个,下调表达25个。通过K-M生存曲线筛选出与预后显著相关(P<0.05)的miRNA共13个,分别为hsa-miR-139-3p、hsa-miR-328-3p、hsa-let-7g-3p、hsa-miR-142-3p、hsa-miR-147b、hsa-miR-31-5p、hsa-miR-548v、hsa-miR-188-3p、hsa-miR-31-3p、hsa-miR-490-3p、hsa-miR-4664-3p、hsa-miR-1293、hsa-miR-615-3p,其中hsa-miR-147b、hsa-miR-4664-3p、hsa-miR-1293、hsa-miR-615-3p与预后呈负相关,其他呈正相关。应用ROC评价上述与预后相关miRNAs诊断肺腺癌的特异性和敏感性,其中hsa-miR-147b、hsa-miR-142-3p、hsa-let-7g-3p、hsa-miR-139-3p 4个miRNA的AUC曲线>0.9,分别为0.904、0.927、0.945、0.965,提示具有较高诊断价值及准确性。结论 hsa-miR-147b、hsa-miR-142-3p、hsalet-7g-3p、hsa-miR-139-3p可作为肺腺癌预后评估和诊断miRNA的生物学标志物,具有重要的临床价值。     

甲状腺乳头状癌组织中差异表达miRNA及其靶基因的筛选和预测

目的：分析甲状腺乳头状癌组织中差异表达小分子RNA（miRNAs）并预测其靶基因,寻找影响甲状腺乳头状癌（PTC）发生发展及可用于生物标志物的miRNAs。方法：选取经病理证实的甲状腺乳头状癌组织及配对正常组织切除标本,运用高通量基因芯片的方法对差异表达的基因和miRNAs进行筛选,采用KEGG通路分析差异表达基因的功能,通过预测网站对差异表达miRNA进行靶基因预测,并对分析结果进行qRT-PCR验证。结果：与同源正常组织比较,基因芯片检测出PTC组织有248个miRNAs（ P<0.01）和3 631个基因差异表达（P<0.05）。hsa-miR-101［靶基因：整合素3(ITGA3）］已验证,癌组织中hsa-miR-101表达(59.8%)低于正常甲状腺组织, ITGA3表达（100%）高于正常甲状腺组织,并且与正常组织比较,59.8%PTC组织hsa-miR -101表达下调,同时ITGA3表达上调。结论：hsa-miR-101的靶基因可能为ITGA3,两者在PTC的发生发展中可能发挥重要作用。     

基于生物信息学的乳腺癌miRNA生物标志物的筛选

目的 筛选与乳腺癌相关的miRNA生物标志物,为乳腺癌的早期诊断、预后评估以及药物靶点的研究提供参考.方法 从TCGA数据库中收集乳腺癌相关基因芯片数据,将肿瘤组织与正常组织样本数据进行对比分析,筛选差异miRNA与mRNA;预测差异miRNA的潜在靶基因并与差异mRNA取交集,进一步对miRNA进行筛选;采用ROC曲线分析对筛选得到的miRNA进行评价.结果 筛选得到9个差异miRNA,对肿瘤样本和正常样本分类良好.分别为6个上调miRNA:hsa-miR-141、hsa-miR-182、hsa-miR-183、hsa-miR-200a、hsa-miR-200b、hsa-miR-21;3个下调miRNA:hsa-let-7c、hsa-miR-125b-1、hsa-miR-145.结论 筛选得到的差异miRNA可作为乳腺癌的生物标志物,可对乳腺癌的发生进行预测.