应用基因芯片检测喉鳞状细胞癌甲醛固定石蜡包埋组织microRNA表达谱

目的 建立以甲醛固定石蜡包埋组织为材料、基于基因芯片技术的microRNA(miRNA)表达谱的分析方法 ;筛选与喉鳞状细胞癌(简称喉癌)生物学特征密切相关的差异表达miRNA.方法 从喉癌甲醛固定石蜡包埋组织中制备总RNA,经质量鉴定后进行荧光标记.采用Agilent公司的容纳723条人类miRNA探针的基因芯片完成杂交实验,以获得喉癌的miRNA表达谱.以GeneSpring GX和R-Project软件处理分析基因芯片实验数据,筛选与喉癌转移相关的差异表达miRNA.结果 从24例甲醛固定石蜡包埋组织标本中获得了符合基因芯片实验质量标准的RNA样品,并完成了基因芯片杂交及数据分析.从中共鉴定到319个miRNA,有96个miRNA在24例喉癌中均有表达,其中与淋巴结转移密切相关的(检错率<0.05)差异表达miRNA有5个,分别为miR-23a* 、miR-28-5p、miR-15a、miR-16和miR-425.结论 甲醛固定石蜡包埋组织可以提供符合基因芯片分析质量要求的miRNA,是研究miRNA的重要样品资源.从喉癌的miRNA表达谱中筛选出的转移相关差异表达miRNA(miR-23a*、miR-28-5p、miR-15a、miR-16和miR-425)有可能成为评估喉癌转移风险的新型分子标志.     

应用基因芯片检测喉鳞状细胞癌甲醛固定石蜡包埋组织microRNA表达谱

目的 建立以甲醛固定石蜡包埋组织为材料、基于基因芯片技术的microRNA(miRNA)表达谱的分析方法 ;筛选与喉鳞状细胞癌(简称喉癌)生物学特征密切相关的差异表达miRNA.方法 从喉癌甲醛固定石蜡包埋组织中制备总RNA,经质量鉴定后进行荧光标记.采用Agilent公司的容纳723条人类miRNA探针的基因芯片完成杂交实验,以获得喉癌的miRNA表达谱.以GeneSpring GX和R-Project软件处理分析基因芯片实验数据,筛选与喉癌转移相关的差异表达miRNA.结果 从24例甲醛固定石蜡包埋组织标本中获得了符合基因芯片实验质量标准的RNA样品,并完成了基因芯片杂交及数据分析.从中共鉴定到319个miRNA,有96个miRNA在24例喉癌中均有表达,其中与淋巴结转移密切相关的(检错率<0.05)差异表达miRNA有5个,分别为miR-23a* 、miR-28-5p、miR-15a、miR-16和miR-425.结论 甲醛固定石蜡包埋组织可以提供符合基因芯片分析质量要求的miRNA,是研究miRNA的重要样品资源.从喉癌的miRNA表达谱中筛选出的转移相关差异表达miRNA(miR-23a*、miR-28-5p、miR-15a、miR-16和miR-425)有可能成为评估喉癌转移风险的新型分子标志.     

喉癌组织中的microRNA差异表达谱及miR-125a-5p抑制喉癌细胞增殖的初步研究

 目的：筛选并分析喉癌组织与周围正常喉黏膜的微小RNA(microRNAs,miRNAs) 之间的表达谱差异,为进一步研究miRNA与喉癌发生、发展的关系提供线索。方法：收集喉癌组织和癌旁正常喉黏膜标本共42对,随机选取10对标本进行miRNA微阵列基因芯片分析, 另选取32对标本进行实时荧光定量PCR （qRT-PCR）验证,获得喉癌组织中的miRNA差异表达谱。应用MTT法和克隆形成实验检测miR-125a-5p对喉癌Hep2细胞增殖的影响。结果：喉癌组织中的let-7f-5p、miR-10a-5p、miR-125a-5p、miR-144-3p、miR-195-5p、miR-203等6个miRNA在基因芯片以及qRT-PCR中表达均显著下调。与对照组相比,转染miR-125a-mimics组的喉癌Hep2细胞增殖能力受到抑制,而转染miR-125a-inhibitor组Hep2细胞增殖能力增强。结论：基因芯片与qRT-PCR结果一致;喉癌与正常喉黏膜之间存在明显的miRNA差异表达,这些miRNA的差异性表达可能与喉癌的发病、侵袭等相关。miR-125a可以抑制喉癌Hep2细胞的增殖,可能作为喉癌生物治疗的新靶点。     

新鲜冷冻和福尔马林固定石蜡包埋胃黏液腺癌组织中miRNA表达谱的比较

目的通过miRNA芯片对比分析新鲜冷冻与福尔马林固定石蜡包埋的胃黏液腺癌组织中miRNAs的表达谱,初步探讨大量存档且有完整病理资料的福尔马林固定石蜡包埋样本能否很好的应用于miRNA的表达分析。方法选取6例2017年术前未行放、化疗的胃黏液腺癌患者手术切除同一组织的新鲜冷冻标本和福尔马林固定石蜡包埋样本,进行镜下形态学观察并提取总RNA、质检,然后芯片杂交、信号扫描、数据转换后进行对比、相关性及表达谱的主成分分析。结果新鲜冷冻标本中提取的总RNA质量相对较高,保存度比较完整,从福尔马林固定石蜡包埋组中提取的总RNA有不同程度的降解。芯片杂交后统计结果显示两组样本中miRNA的表达谱差异有显著性,以fold_change(差异倍数log2)的绝对值≥2为标准,分别有76个(P0.05)和14个(P0.01)miRNA呈差异表达,但配对标本之间均有较好的相关性。结论配对的新鲜冷冻与福尔马林固定石蜡包埋的胃黏液腺癌组织中miRNAs的表达谱差异有显著性,所以用福尔马林固定石蜡包埋组织分析miRNA基因的绝对表达值,结果可能不准确,能否反映全部miRNA基因的相对表达也需进一步的实验去证实。     

肝癌耐药细胞的形态学及微小RNA表达谱分析

目的 比较3株肝癌耐药细胞(Huh-7/ADM、Huh-7/CBP、Huh-7/MMC)与亲本肝癌细胞Huh-7的形态学差异;分析这3株肝癌耐药细胞及Huh-7的miRNA表达谱,筛选3株耐药细胞中异常表达的微小RNA(miRNA).方法 光学显微镜下观察各细胞株细胞形态学特点、透射电镜下观察各细胞株细胞内超微结构特点.miRNA芯片检测各细胞株miRNA表达谱,real-time定量PCR(qPCR)法验证芯片结果.结果 镜下见肝癌耐药细胞比亲本肝癌细胞Huh-7更具多形性,核异型性亦增加;细胞周边微绒毛减少;胞质增多,胞质内细胞器含量增加,并出现脂滴、糖原等成分.miRNA表达谱分析显示:与Huh-7相比,有32个miRNA在3种肝癌耐药细胞株中表达同时上调,有22个miRNA在3种耐药细胞株中表达同时下调.real-time qPCR检测证实miR-15a、miR-16、miR-27b、miR-30b、miR-146a、miR-146b-5p、miR-181a、miR-181d、miR-194在各肝癌耐药细胞中表达同时上调.结论 耐药细胞异型性增加,筛选出的肝癌耐药细胞中异常表达miRNA,可为研究肝癌多药耐药与miRNA的相关性提供依据.     

永久性房颤的转录组分析及miRNA调控网络的建立

目的探索永久性房颤(p AF)发病相关的关键miRNAs及其调控的靶基因。方法联合应用表达谱芯片和miRNA芯片分析p AF患者(n=7)和健康成人(n=4)的左房组织,筛选p AF相关差异表达的miRNAs,进行靶基因预测后,与表达谱芯片的筛选结果进行负相关分析后的基因集合进行显著性功能分析(GO-analysis);利用miRNA与靶基因之间的靶向调控关系,构建差异miRNA与交集靶基因的调控网络(miRNA-gene-network),得到网络中起核心调控作用的miRNA和被调控的关键靶基因;采用RT-q PCR方法检验另一组p AF患者(n=5)和健康成人(n=4)的左房组织标本。结果表达谱基因芯片发现610个mRNA有显著性改变(fold change2,P0.05),miRNA-靶基因调节网络发现与p AF显著相关的20个miRNAs和107个靶基因,相关度最高的是miR-144、miR-1284、miR-1827、miR-1、miR-3613-3p和miR-101;其调控的重要靶基因包括CACNB2、EFNB1、PTEN、TAOK1、RUNX1和TPM3等;RT-q PCR验证结果显示这些miRNAs和靶基因密切相关。结论通过表达谱基因芯片与miRNAs芯片联合分析p AF左房组织标本,构建miRNA调控网络,发现p AF重要的miRNA-靶基因调控及功能,结果更加准确。     

喉癌相关miRNA的研究进展

喉癌是耳鼻咽喉头颈外科常见的肿瘤之一,其发病机制尚未完全明确。研究发现,微小RNA(miRNA)在喉癌的发生过程中发挥着重要的作用。miRNA的表达异常(如miR-106b-25和miR-21等的上调,miR-375和let-7a等的下调)与喉癌的发生有关。在喉癌组织中异常表达的miRNA为喉癌的诊断提供了新标志物,而相关miRNA更是为喉癌治疗提供了潜在的靶点。     

基质细胞衍生因子1诱导骨关节炎软骨细胞的miRNA表达谱分析

背景:骨关节炎是多因素介导的复杂疾病,发病机制尚待挖掘,随着基因层面的不断深入研究,非编码核糖核酸调控作用显现并得以研究。通过检测软骨细胞退变miRNA表达谱变化有助于更好地理解骨软骨细胞退变的分子机制,并为骨关节炎的诊断和治疗开辟新的途径。目的:探讨基质细胞衍生因子1刺激骨关节炎软骨细胞后miRNA表达谱变化,为基因层面延缓关节软骨退变提供实验基础。方法:对10例膝关节骨关节炎患者于全膝关节置换手术过程中截骨后残留的软骨组织进行软骨细胞培养,随机分为实验组与对照组,两组细胞培养基为含体积分数10%胎牛血清及青链霉素双抗的高糖DMEM培养基。实验组培养基中另外加入100μg/L基质细胞衍生因子1,对照组不做任何处理。两组软骨细胞培养48 h后,进行下一步实验用于miRNA芯片筛选和实时定量PCR验证。软骨组织标本取材前皆告知患者并征得同意,该研究符合《医疗机构管理条例》相关要求,获得昆明医科大学第一附属医院伦理委员会批准。结果与结论:miRNA基因芯片初筛共有84个miRNAs发生变化,其中70个miRNAs上调,14个miRNAs下调。通过基因芯片筛选差异变化的miRNA,对变化显著的7个miRNA(miR-146a-5p、miR-124-3p、miR-130a-3p、miR-185-5p、miR-221-3p、miR-126-3p)进行qRT-PCR实验验证,其中miR-146a-5p、miR-124-3p及miR-126-3p的qRT-PCR结果与基因芯片结果一致。结果表明,基质细胞衍生因子1刺激骨关节炎软骨细胞后循环miRNA表达谱出现明显变化,miR-146a-5p、miR-124-3p及miR-126-3p可能与基质细胞衍生因子1刺激骨关节炎SDF-1/CXCR4信号通路反应有关。     

基于microRNA差异表达探讨恶性纤维组织细胞瘤致病机制

目的 应用芯片表达分析技术探讨miRNA在恶性纤维组织细胞瘤发病机制中的作用.方法 利用miRCURYTM LNA miRNA表达谱芯片技术高通量筛选NMFH1与MSC、HSF、MRC-5和HT-1080细胞系差异表达miRNA,筛选靶基因,分析调控作用机制.结果 筛查NMFH1与4种对照组细胞系差异表达miRNA,选取与所有正常样本对比均下调miR-222、miR-186及miR-933,均上调miR-886-3p、miR-886-5p、miR-183、miR-340及miR-BART7进行qRT-PCR实验,验证芯片数据可靠性.基于生物信息学方法挖掘miRNA靶基因,构建基因调控网络,基于功能组注释信息分析NMFH1风险疾病基因及通路,揭示MFH恶性病变机制.结论 miRNA在肿瘤样本与正常细胞系间显著差异表达,是参与MFH发生发展过程的重要调控因子,发挥负调控基因表达作用,使肿瘤细胞逃避正常生长调控机制,无限增殖和转移,出现恶性表型.     

肠道病毒71型感染人神经母细胞瘤细胞(SH-SY5Y)的miRNA表达谱

目的 研究肠道病毒71型(EV71)感染神经细胞的miRNA表达谱,探讨miRNA在病毒感染神经细胞中的可能作用.方法 建立EV71感染人神经母细胞瘤细胞(SH-SY5Y)模型,收集感染后48 h细胞.以Taqman低密度芯片检测miRNA表达谱,使用实时RT-PCR对芯片结果进行验证并在TargetScan和miRanda网站预测靶基因,采用GO和KEGG分析靶基因功能.结果 成功建立EV71感染SH-SY5Y细胞模型,通过低密度芯片筛选出215种显著升高的miRNA和25种显著下调的miRNA.经过RT-PCR验证,3种miRNA(MiR-10a*、miR-15b*和miR-195)显著下调,7种miRNA(miR-10a、miR-342-5p、miR-483-5p、Let-7b、miR-99a、miR-140-5p和miR-21)显著上调,与芯片结果相符.GO分析显示发展进程和信号调节条目最富集靶基因.KEGG路径分析显示靶基因在肿瘤路径、蛋白水解、Wnt信号传导、黑素形成、粘附连接、MAPK信号通道最富集.结论 EV71感染神经细胞48 h后miRNA表达谱发生改变,10种变化的miRNA靶基因预测在发展进程、信号传导及凋亡中起着重要的作用,可为后期机制研究提供参考.     

Identification of microRNA expression signature for the diagnosis and prognosis of cervical squamous cell carcinoma

Cervical cancer is the fourth leading cause of cancer death among women globally. The prognosis of cervical cancer patients differs considerably, and clinical outcomes are difficult to predict. Given the significant roles of miRNAs in human cancers, identification of novel and reliable miRNA biomarkers is important for targeted cervical cancer therapy. In the present study, we aimed to reveal biological significance of miR-200a, miR-423, miR-34a, miR-193a, and miR-455 for the prognosis and diagnosis of cervical cancer and their association with the clinical outcomes of patients. Distinct expression profiles of miRNAs in formalin-fixed paraffin-embedded tissue samples of patients and healthy controls were evaluated using qRT-PCR. We identified miR-200a, miR-455, and miR-34a were significantly downregulated in cervical squamous cell carcinoma tissues compared to normal cervix tissue from healthy controls. Both miR-455 and miR-34a confer a promising diagnostic factor for the cervical cancer while miR-200a showed no significance in ROC analysis. Notably, low expression of miR-34a was markedly associated with the poor overall survival of cervical cancer patients as revealed by Kaplan-Meier survival analysis. Also, univariate and multivariate analysis indicated miR-34a expression as an independent prognostic factor. Consequently, our results underline the importance of distinct expression miRNAs in cervical squamous cell carcinoma.     

MicroRNA Expression Profiling Outperforms mRNA Expression Profiling in Formalin-fixed Paraffin-embedded Tissues

microRNAs (miRNAs) are ∼22nt RNAs that regulate target gene expression. Altered expression of miRNAs has been demonstrated in many different human cancers. Many studies using microarray technologies to characterize miRNA expression profiles have relied on fresh tissue to determine the miRNA signatures. In this study, we prepared total RNA from paired samples of formalin-fixed paraffin-embedded (FFPE) and fresh frozen malignant melanoma, and used that in microarray experiments to compare miRNA expression profiles between FFPE and fresh tissue with corresponding mRNA expression profiles from the same tissue sources. We demonstrate that miRNA expression profile from FFPE tissues closely resembles that from fresh tissues, and the correlation is significantly better than that for mRNA profiles from FFPE and fresh tissues. These results underscore the suitability of FFPE tissues as appropriate resources for molecular expression analyses and support the notion that miRNAs are more vigorous analytes for this purpose than mRNAs.     

Deep sequencing of small RNAs from human skin reveals major alterations in the psoriasis miRNAome

Psoriasis is a chronic and complex inflammatory skin disease with lesions displaying dramatically altered mRNA expression profiles. However, much less is known about the expression of small RNAs. Here, we describe a comprehensive analysis of the normal and psoriatic skin miRNAome with next-generation sequencing in a large patient cohort. We generated 6.7 × 10(8) small RNA reads representing 717 known and 284 putative novel microRNAs (miRNAs). We also observed widespread expression of isomiRs and miRNA*s derived from known and novel miRNA loci, and a low frequency of miRNA editing in normal and psoriatic skin. The expression and processing of selected novel miRNAs were confirmed with qRT-PCR in skin and other human tissues or cell lines. Eighty known and 18 novel miRNAs were 2-42-fold differentially expressed in psoriatic skin. Of particular significance was the 2.7-fold upregulation of a validated novel miRNA derived from the antisense strand of the miR-203 locus, which plays a role in epithelial differentiation. Other differentially expressed miRNAs included hematopoietic-specific miRNAs such as miR-142-3p and miR-223/223*, and angiogenic miRNAs such as miR-21, miR-378, miR-100 and miR-31, which was the most highly upregulated miRNA in psoriatic skin. The functions of these miRNAs are consistent with the inflammatory and hyperproliferative phenotype of psoriatic lesions. In situ hybridization of differentially expressed miRNAs revealed stratified epidermal expression of an uncharacterized keratinocyte-derived miRNA, miR-135b, as well as the epidermal infiltration of the hematopoietic-specific miRNA, miR-142-3p, in psoriatic lesions. This study lays a critical framework for functional characterization of miRNAs in healthy and diseased skin.     

头颈部鳞状细胞癌预后相关的miRNAs的生物信息学分析

目的 利用癌症基因组图谱（TCGA）数据库微小核糖核酸（miRNAs）表达谱数据分析头颈部鳞状细胞癌（HNSCC）与癌旁正常组织间差异表达的miRNAs,结合临床信息寻找与HNSCC预后相关的miRNAs。方法 从TCGA中下载miRNAs表达数据,包括39例HNSCC患者和39个肿瘤邻近正常组织样本筛选差异表达的miRNAs,应用481例HNSCC患者的miRNAs表达谱和临床信息来评估找到的差异表达miRNAs的预后作用。结果 共筛选出114个差异表达的miRNAs,包括60个上调和54个下调的miRNAs。Kaplan-Meier生存分析显示miR-4652-5p和miR-99a-3p与HNSCC患者预后相关,单因素和多因素Cox回归分析显示,miR-4652-5p和miR-99a-3p是HNSCC的重要预后因素。结论 miR-4652-5p和miR-99a-3p与HNSCC患者预后相关,但miR-4652-5p和miR-99a-3p在头颈鳞状细胞癌发生发展中的分子机制仍需更全面的基础和临床研究进行探讨。     

Overexpression of heat shock protein 27 in squamous cell carcinoma of the uterine cervix: a proteomic analysis using archival formalin-fixed, paraffin-embedded tissues

Proteomic analysis of squamous cell carcinoma of the uterine cervix was performed using total protein from archival formalin-fixed, paraffin-embedded tissues. A wide range of proteins with molecular weights of 10 to greater than 200 kd was extracted from formalin-fixed, paraffin-embedded tissues using a recently developed protocol based on the heat-induced antigen retrieval technique. The extracted proteins from normal squamous epithelium (n = 53) and squamous cell carcinoma (n = 21) were fluorescently labeled and separated using 2-dimensional gel electrophoresis. We identified 728 differentially expressed proteins, with 144 up-regulated and 584 down-regulated as compared with normal squamous epithelial tissue samples. Nine proteins showing pronounced up-regulation in squamous cell carcinoma were analyzed on liquid chromatography-tandem mass spectrometry. Among the candidate proteins identified, minichromosome maintenance 8, a disintegrin and metalloproteinase domain 18, and heat shock protein 27 were analyzed in Western blotting, resulting in significant overexpression of heat shock protein 27 in squamous cell carcinoma over normal mucosa (P < .05). Furthermore, immunostaining revealed heat shock protein 27 overexpression not only in squamous cell carcinoma but in various stages of cervical intraepithelial neoplasia (grades 1-3, n = 90), including dysplasia and carcinoma in situ. The expression levels of heat shock protein 27 in cervical intraepithelial neoplasia grades 1 to 3 and squamous cell carcinoma were significantly higher than that in normal mucosa (P < .05). In the neoplastic lesions, heat shock protein 27 expression levels in cervical intraepithelial neoplasia grade 3 and squamous cell carcinoma were significantly higher than that in cervical intraepithelial neoplasia grade 1 (P < .05). These results may suggest a role of heat shock protein 27 in tumor development and progression in the cervical intraepithelial neoplasia-squamous cell carcinoma sequence. Future experiments using formalin-fixed, paraffin-embedded tissue-based proteomic analysis will be a powerful tool for various pathologic studies.     

Angiotensin II induced differentially expressed microRNAs in adult rat cardiac fibroblasts

Angiotensin II (Ang II) plays a pivotal role in cardiac fibrosis, and microRNAs (miRNAs) have been shown to participate in diverse pathological processes. Our aim is to identify the Ang II-induced miRNAs in cardiac fibroblasts (CFs). The miRNA array was used to analyze the miRNA expression profile in CFs treated by Ang II and control cells. Stem-loop real-time PCR was performed to re-measure the levels of the differentially expressed miRNAs. Analysis of miRNA arrays showed that 33 miRNAs were differentially expressed (13 up- and 20 downregulated) in response to Ang II (100 nM) for 24 h as compared to control cells. Quantitative PCR revealed that Ang II upregulated the levels of miR-132, -125b-3p and miR-146b but downregulated the levels of miR-300-5p, -204* and miR-181b in CFs. The trend of miRNA change is consistent with microarray and qRT-PCR. Bioinformatic analysis revealed that MMP9 as the target of miR-132, MMP16 as the target of miR-146b and TIMP3 as the target of miR-181b have been listed in the miR database with experimentally validated targets, indicating the potential role of those miRNAs in cardiac fibrosis. Our results demonstrated that we did identify a subset of miRNAs that was differentially expressed in Ang II-treated CFs, which provide a starting point to explore their potential roles in cardiac fibrosis and hypertension.     

食管鳞癌组织中miRNAs差异表达谱的筛选及研究

目的 筛选并鉴定在食管鳞癌（ESCC）及癌旁组织中miRNAs的差异表达,为进一步阐明其在ESCC发病机制中的作用奠定基础。方法 选取在邯郸市第一医院行食管癌切除术患者新鲜的鳞癌组织及癌旁正常组织,各3例,抽提总RNA,利用miRNAs芯片筛选其中差异表达的miRNAs,并对miR-106b-3p通过进一步RT-qPCR 技术进行验证。结果 miRNAs芯片从配对组织中共筛检出62个差异表达的miRNAs,其中41个miRNAs表达上调,21个miRNAs表达下调,鳞癌组织与癌旁正常组织中差异表达的miRNAs比较,差异有统计学意义（P＜0.05）。miR-106b-3p在ESCC组织中的表达高于癌旁组织,差异有统计学意义（P＜0.05）,与芯片结果一致。结论 食管鳞癌组织中miRNAs的差异表达为进一步研究miRNAs在ESCC发病中的作用奠定了基础;miR-106b-3p的高表达可能与ESCC的发生、发展有关。