基于TCGA和GEO数据库的胃癌lncRNA筛选与ceRNA网络构建

胃癌(gastric cancer,GC)是我国最常见的恶性肿瘤之一,严重危害人类健康。胃癌发病机制复杂,缺乏特异性预后生物标志物。长链非编码RNA (long non-coding RNA,lncRNA)可作为竞争性内源RNA (competing endogenous RNA,ceRNA),影响microRNA (miRNA)与mRNA的结合,从而影响胃癌的发生、发展。基于TCGA和GEO数据库的转录组数据,筛选GC 中差异表达的 lncRNAs,并构建基于 6 条 lncRNAs(HAGLROS、TMEM92-AS1、LINC01745、HOXC-AS3、SEMA3B-AS1、FEZF1-AS 1)的lncRNA-miRNA-mRNA网络。网络核心基因的KEGG/GO富集和蛋白质互作分析结果显示,lncRNA可能通过miRNA海绵吸附作用,调控胃癌的发生、发展与转移。AC011352.1、AC087636.1、AC093627.1、GAS1RR与胃癌患者的预后相关性具有统计学意义(P<0.05),并可能成为胃癌患者潜在的预后生物标志物。     

基于ceRNA网络识别登革热诊断标志物

通过比较登革热患者和健康人群转录组数据,识别差异基因,构建失调ceRNA网络,筛选关键基因富集分析,解析潜在生物学功能,助力登革热诊断标志物的研究。从GEO数据库下载登革热外周血芯片数据,识别差异基因并进行富集分析。结合miRNA-mRNA互作数据,利用超几何算法和皮尔森相关性计算方法识别登革热失调ceRNA互作对,使用Cytoscape软件可视化ceRNA网络与模块挖掘,对网络模块进行功能富集及外部数据验证表达模式。筛选出251个差异基因,发现其富集在细胞周期等生物学通路中。经外部数据验证,网络模块基因的表达趋势与训练集数据大致相同,表明模块基因在登革热疾病中的潜在诊断效能。本研究可为确定有效的疾病诊断分子标志物提供思路。     

PTEN蛋白在子宫内膜癌中的表达及其临床意义

目的　探讨抑癌基因PTEN产物PTEN蛋白在由正常子宫内膜过渡至子宫内膜癌过程中的表达缺失情况及其临床意义。方法　用SP免疫组化法测定 73例子宫内膜癌、 2 5例子宫内膜非典型增生、 71例子宫内膜增殖症和 31例正常子宫内膜组织中PTEN蛋白的表达 ,并与组织学类型、组织学分级、肌层浸润深度和临床分期等生物学行为进行相关分析。结果　PTEN蛋白在子宫内膜腺癌和癌前病变中的表达缺失率分别为 6 6 6 7%和 76 0 0 % ,表达缺失率与组织学类型(P <0 0 0 5 )和组织学分级有关 (P <0 0 5 ) ,与子宫内膜癌肌层浸润深度和临床分期无关 (P >0 0 5 )。结论　PTEN表达缺失是子宫内膜癌发生的早期分子事件 ,PTEN蛋白表达缺失是早期诊断子宫内膜癌及癌前病变较好的生物标志。     

ceRNA竞争性网络在三阴性乳腺癌中的研究进展

三阴性乳腺癌(triple negative breast cancer,TNBC)的特征是缺乏雌激素受体(estrogen receptor,ER)、孕激素受体(progesterone receptor,PR)和人表皮生长因子受体2(human epidermal growth factor receptor 2,...     

联合TCGA和GEO数据库构建和分析胃癌中circRNA相关的ceRNA网络

环状RNA (circular RNA, circRNA)是一类呈闭环状结构的竞争性内源RNA (competing endogenous RNA, ceRNA),其通过竞争性地吸附微RNA (microRNA, mi RNA)来调节基因表达。circRNA失调与癌细胞的增殖、分化和侵袭等密切相关。本研究基于生物信息学分析和多数据库的联合应用,以ceRNA为切入点探析胃癌中circRNA潜在的致病机制,以期为胃癌提供潜在的临床诊疗靶点,并为胃癌的科学研究提供新思路。首先,通过挖掘胃癌差异表达的circRNA、mi RNA和m RNA构建circRNA-miRNA-mRNA ceRNA网络;随后,利用网络拓扑属性分析确定核心的节点,并根据这些核心的节点从原始的ceRNA网络中提取子网;最后,对子网进行功能学分析和生存分析,分析网络行使的生物学功能并挖掘预后相关的基因。结果显示:共挖掘了6个核心节点(hsa_circ_0008468、hsa_circ_0005822、hsa_circ_0025842、hsa-miR-940、hsa-miR-944及hsa-miR-515-5p);从原始的ceRNA网络中提取了包含8对circRNA-miRNA和539个mi RNA-m RNA关系对的子网络。功能富集结果表明子网涉及癌症相关的多个生物学过程,包括代谢途径、cAMP信号通路、pathways in cancer信号通路等,生存分析发现子网中ACO2、E2F8、GHR、ITIH5等14基因与预后显著相关,这表明3个核心circRNA介导的ceRNA网络与胃癌的发生发展及预后密切相关。     

分子标志物在子宫内膜癌中的表达分析

目的:探讨EGFR、HER-2、P53、ER、Ki-67、PR、VEGF、TopⅡα、PDGFR-β、PDGFR-α十种分子标志物在子宫内膜癌肿瘤细胞中的表达情况。方法:利用免疫组织化学的方法研究解放军总医院病理科2010年到2012年199例子宫内膜癌中EGFR、HER-2、P53、ER、Ki-67、PR、VEGF、TopⅡα、PDGFR-β、PDGFR-α十种分子标志物的表达,表达结果使用x2检验进行统计。结果:分子标志物EGFR、HER-2、PDGFR-α在子宫内膜癌肿瘤细胞中的表达与临床手术分期相关;ER、PR在子宫内膜癌肿瘤细胞中的表达与病理分级、临床手术分期及肌层浸润程度均相关。P53、Ki-67、VEGF、TopⅡα、PDGFR-β五个分子标记物与病理分级、临床手术分期及肌层浸润程度无明显相关性。结论:对十种分子标志物在子宫内膜癌肿瘤细胞中的表达分析,以及与病理分级、临床手术分级和肌层浸润程度关系的研究,有助于预测子宫内膜癌的发生、发展、转移及预后。     

MIF和CerbB-2在子宫内膜癌中的表达及临床意义

目的:探讨MIF和Cerb B-2的表达与子宫内膜癌的关系,进一步探讨其表达与子宫内膜癌的发生、发展的关系,为早期诊断子宫内膜癌,判断预后和寻找子宫内膜癌的新的治疗方法奠定基础。方法:应用实时荧光定量RT-PCR和免疫组织化学技术检测正常子宫内膜、不典型增生和子宫内膜癌组织中MIF m RNA、Cerb B-2 m RNA和MIF蛋白、Cerb B-2蛋白的表达,其中免疫组化中子宫内膜癌组根据临床病理特征,如年龄,临床分期,组织学分级,肌层浸润深度和有无淋巴结转移进行分组。结果:正常子宫内膜、不典型增生内膜和子宫内膜癌组织中都有MIF和Cerb B-2的表达,子宫内膜癌中MIF m RNA和Cerb B-2 m RNA扩增含量显示高水平,其阳性表达率随着病变程度的加重而逐渐升高,差异具有统计学意义(P=0.037);MIF主要表达于子宫内膜腺上皮的细胞质中,少量表达于细胞质,在阳性表达的子宫内膜癌组织中,蛋白含量在I期(P=0.033)、G1期(P=0.034)、无淋巴结转移的组织中水平较高(P=0.041),差异具有统计学意义。Cerb B-2蛋白主要表达在子宫内膜的细胞质,少量在细胞膜中表达,阳性表达率子宫内膜癌不典型增生正常子宫内膜,差异具有统计学意义(P=0.013);Cerb B-2蛋白在III-IV(P=0.009)、G2-3期(P=0.033),有淋巴结转移(P=0.018)的子宫内膜癌中表达含量较高,与年龄和肌层浸润深度无关。结论:MIF和Cerb B-2在正常子宫内膜、不典型增生和子宫内膜癌中都有表达,提示着MIF和Cerb B-2与子宫内膜癌的发生和发展有关,MIF在子宫内膜癌的早期表达含量较高,可以作为子宫内膜癌的早期诊断指标,Cerb B-2在子宫内膜癌的晚期表达含量较高,可以促进肿瘤的侵袭转移,可作为判断疾病的严重程度和预后的指标之一。     

环氧合酶-2在子宫内膜癌中上调表达的临床意义

目的　探讨环氧合酶 2与子宫内膜癌发生、发展中的关系。方法　研究对象分为 5组 ,增生期组 2 5例 ,分泌期组 2 5例 ,内膜炎组 2 5例 ,非典型性增生组 2 3例 ,子宫内膜癌组 34例 ,应用免疫组化和定量RT PCR方法 ,检测其中Cox 2蛋白和mRNA水平表达。结果　 6 7%的子宫内膜癌表达Cox 2 ,在转录和蛋白水平子宫内膜癌组的Cox 2表达强度明显高于其它四组 (免疫组化评分分别为 :增生期组 5 4 6± 0 12 3,分泌期组 3 2 0± 0 176 ,内膜炎组 4 78± 0 12 ,非典型性增生组 6 10±0 2 5 ,子宫内膜癌组 8 70± 0 93,相应mRNA含量依次为 92 8± 8 2 2fpg/ μg ,6 4 9± 11 0 8fpg/ μg ,79 4± 5 83fpg/ μg ,2 99 3± 10 6 8fpg/ μg ,4 93 0± 2 9 5 8fpg/ μg) ,差异有显著性 (P <0 0 5 ) ,内膜癌中 ,高分化细胞Cox 2表达高于低分化细胞 ,差异有显著性 (P <0 0 5 )。非典型性增生组Cox 2表达显著高于正常内膜和内膜炎组 ,增殖期组Cox 2表达高于分泌期组 ,差异有显著性 (P <0 0 5 )。结论　Cox 2可能在子宫内膜癌发生发展中起重要作用 ,可为子宫内膜癌的化学预防和化疗的辅助治疗提供新靶点     

腹腔镜早期子宫内膜癌手术临床疗效分析

目的:探讨腹腔镜下早期子宫内膜癌分期手术与开腹手术的临床疗效的差异.方法:回顾性研究2008年1月～2012年10月在我院行子宫内膜癌分期手术的84例患者临床资料,手术病理分期为ⅠA～Ⅱ期.其中腹腔镜分期手术40例,开腹分期手术44例,比较2组手术时间、术中出血量、淋巴结清扫数目、术后胃肠功能恢复时间、并发症、术后住院时间.结果:腹腔镜组手术时间长于开腹组,两者相比具有统计学意义(P＜0.05);腹腔镜组术中出血量显著少于开腹组(P＜0.05);淋巴结清扫总数显著多于开腹组(P＜0.05);腹腔镜组在排气时间、尿管拔除时间、术后出院时间均显著早于开腹组(P＜0.05);两者并发症方面无统计学差异(P＞0.05).结论:腹腔镜分期手术较开腹手术更具微创价值,是治疗早期子宫内膜癌稳妥可行的选择.     

系统性淋巴结清扫术对子宫内膜癌患者预后的影响及安全性分析*

目的:分析系统性淋巴结清扫术对子宫内膜癌患者预后的影响及安全性。方法:选择2010年6月~2012年6月我院收治的68例子宫内膜癌患者作为研究对象,将其随机分为研究组与对照组。对照组行两侧附件+全子宫切除+盆腔淋巴结清扫术,研究组行两侧附件+全子宫切除+系统性腹腔、盆腔主动脉旁淋巴结清扫术。观察和比较两组患者术后3年内的生存率、疾病复发转移率以及并发症的发生率。结果:研究组检出阳性淋巴结15枚,发现4例患者淋巴结转移;对照组患检出阳性淋巴结3枚,发现1例患者淋巴结转移。两组阳性淋巴结检出率及淋巴结转移发现率比较差异无统计学意义(P0.05)。研究组3年内生存率为88.24%,显著高于对照组的67.65%(P0.05);复发转移率为14.71%,显著高于对照组的35.29%(P0.05)。研究组患者术后发生不全性肠梗阻发生率为17.65%,显著高于对照组(P0.05);但两组术后下肢水肿、深静脉血栓、淋巴囊肿、输尿管尿瘘、体温转复时间5 d的发生率对比差异均无统计学意义(P0.05)。结论:系统性淋巴结清扫术可以延长子宫内膜癌患者的3年生存率,降低病灶的复发及转移率,虽然术后不全性肠梗阻的发生率有所增加,但仍在可控范围内。     

A 7-lncRNA signature predict prognosis of Uterine corpus endometrial carcinoma

Current research indicate that long noncoding RNAs (lncRNAs) are associated with the progression of various cancers and can be used as prognostic biomarkers. This study aims to construct a prognostic lncRNA signature for the risk assessment of Uterine corpus endometrial carcinoma (UCEC). The RNA-Seq expression profile and corresponding clinical data of UCEC patients obtained from The Cancer Genome Atlas database. First, some prognosis-related lncRNAs were obtained by univariate Cox analysis. The minimum absolute contraction and selection operator (LASSO) regression and the Cox proportional hazard regression method were used to further identify the lncRNA prognostic model. Finally, seven lncRNAs (AC110491.1, AL451137.1, AC005381.1, AC103563.2, AC007422.2, AC108025.2, and MIR7-3HG) were identified as potential prognostic factors. According to the model constructed by the above analysis, the risk score of each UCEC patient was calculated, and the patients were classified into high and low-risk groups. The low-risk group had significant survival benefits. Moreover, we constructed a nomogram that incorporated independent prognostic factors (age, tumor stage, tumor grade, and risk score). The c-index value for evaluating the predictive nomogram model was 0.801. The area under the curve was 0.797 (3-year survival). The calibration curve also showed that there was a satisfactory agreement between the predicted and observed values in the probability of 1-, 3-, and 5-year overall survival. On the basis of the coexpression relationship, we established a coexpression network of lncRNA-messenger RNA (mRNA) of the 7-lncRNA. The Kyoto Encyclopedia of Genes and Genomes analysis of the coexpressing mRNAs showed that the main pathways related to the 7-lncRNA signature were neuroactive ligand-receptor interaction, serotonergic synapse, and gastric cancer pathway. Therefore, our study revealed that the 7-lncRNA could be used to predict the prognosis of UCEC and for postoperative treatment and follow-up.     

PPP1R14B is a diagnostic prognostic marker in patients with uterine corpus endometrial carcinoma

Uterine corpus endometrial carcinoma (UCEC) is one of the most common malignancies of the female genital tract. A recently discovered protein-coding gene, PPP1R14B, can inhibit protein phosphatase 1 (PP1) as well as different PP1 holoenzymes, which are important proteins regulating cell growth, the cell cycle, and apoptosis. However, the association between PPP1R14B expression and UCEC remains undefined. The expression profiles of PPP1R14B in multiple cancers were analysed based on TCGA and GTE databases. Then, PPP1R14B expression in UCEC was investigated by gene differential analysis and single gene correlation analysis. In addition, we performed gene ontology term analysis, Kyoto Encyclopedia of Genes and Genomes pathway analysis, gene set enrichment analysis, and Kaplan–Meier survival analysis to predict the potential function of PPP1R14B and its role in the prognosis of UCEC patients. Then, a tool for predicting the prognosis of UCEC, namely, a nomogram model, was constructed. PPP1R14B expression was higher in UCEC tumour tissues than in normal tissues. The results revealed that PPP1R14B expression was indeed closely associated with tumour development. The results of Kaplan–Meier plotter data indicated that patients with high PPP1R14b expression had poorer overall survival, disease-specific survival, and progression-free interval than those with low expression. A nomogram based on the results of multifactor Cox regression was generated. PPP1R14B is a key player in UCEC progression, is associated with a range of adverse outcomes, and can serve as a prognostic marker in the clinic.     

MCM10: An effective treatment target and a prognostic biomarker in patients with uterine corpus endometrial carcinoma

Molecular profiling has been applied for uterine corpus endometrial carcinoma (UCEC) management for many years. The aim of this study was to explore the role of MCM10 in UCEC and construct its overall survival (OS) prediction models. Data from TCGA, GEO, cbioPotal and COSMIC databases and the methods, such as GO, KEGG, GSEA, ssGSEA and PPI, were employed to bioinformatically detect the effects of MCM10 on UCEC. RT-PCR, Western blot and immunohistochemistry were used to validate the effects of MCM10 on UCEC. Based on Cox regression analysis using the data from TCGA and our clinical data, two OS prediction models for UCEC were established. Finally, the effects of MCM10 on UCEC were detected in vitro. Our study revealed that MCM10 was variated and overexpressed in UCEC tissue and involved in DNA replication, cell cycle, DNA repair and immune microenvironment in UCEC. Moreover, silencing MCM10 significantly inhibited the proliferation of UCEC cells in vitro. Importantly, based on MCM10 expression and clinical features, the OS prediction models were constructed with good accuracy. MCM10 could be an effective treatment target and a prognostic biomarker for UCEC patients. The OS prediction models might help establish the strategies of follow-up and treatment for UCEC patients.     

Comprehensive analysis of partial epithelial mesenchymal transition-related genes in hepatocellular carcinoma

Increasing evidence has revealed that cancer cells undergoing an intermediate state, partial epithelial mesenchymal transition (p-EMT), tend to metastasize rather than complete EMT. We performed a comprehensive analysis of E-cadherin and 25 p-EMT-related genes in HCC to explore the roles and regulatory mechanisms of them in HCC. We analysed E-cadherin and 25 p-EMT-related genes in HCC and constructed an mRNA-miRNA-lncRNA ceRNA subnetwork containing p-EMT-related genes by bioinformatic approaches. IHC was used to identify the protein expression of key p-EMT-related genes, P4HA2, ITGA5, MMP9, MT1X and SPP1. Complete EMT is not necessary for HCC progression. Overexpression of P4HA2, ITGA5, MMP9, SPP1 and down-regulation of MT1X were found in HCC tissues, which were significantly associated with poor prognosis of HCC patients. By means of stepwise reverse prediction and validation from mRNA to lncRNA, an mRNA-miRNA-lncRNA ceRNA subnetwork correlated with HCC prognosis was identified by expression and survival analysis. This study implied that key p-EMT-related genes P4HA2, ITGA5, MMP9, MT1X, SPP1 could be prognostic biomarkers and potential targets of therapy for HCC patients. We constructed an mRNA-miRNA-lncRNA subnetwork containing p-EMT-related genes successfully, among which each component might be utilized as a prognostic biomarker of HCC.     

Construction and analysis of dysregulated lncRNA-associated ceRNA network in colorectal cancer

Colorectal cancer (CRC) is one of the most frequently diagnosed digestive system cancer. The aim of the present study was to investigate the interactions among messenger RNAs (mRNAs), microRNAs (miRNAs), and long noncoding RNAs (lncRNAs) in CRC to reveal the mechanisms of CRC. Differentially expressed genes (DEGs) were identified from public gene expression data sets. One thousand eighty-one common dysregulated mRNAs in two data sets were identified. Gene function analysis and protein-protein interaction network analysis indicated that these DEGs might play important roles in CRC. LINC00365 was selected through coding- noncoding network analysis and its expression was validated upregulated in 22 paired clinical samples and four CRC cell lines. A competing endogenous RNA network composed of 70 miRNAs, nine mRNAs, and LINC00365 was constructed. Eight of nine mRNAs were validated upregulated in The Cancer Genome Atlas data set. Our results suggested that LINC00365 was an oncogene in CRC and it could regulate the expression of several mRNAs through sponging miRNAs.     

Construction and analysis of the abnormal lncRNA–miRNA–mRNA network in hypoxic pulmonary hypertension

The incidence of hypoxic pulmonary hypertension (HPH) is increasing. Accumulating evidence suggests that long noncoding RNAs (lncRNAs) play an important role in HPH, but the functions and mechanism have yet to be fully elucidated. In the present study, we established a HPH rat model with 8 h of hypoxia exposure (10% O₂) per day for 21 days. High-throughput sequencing identified 60 differentially expressed (DE) lncRNAs, 20 DE miRNAs and 695 DE mRNAs in rat lung tissue. qRT-PCR verified the accuracy of the results. The DE mRNAs were significantly enriched in immune response, inflammatory response, leukocyte migration, cell cycle, cellular response to interleukin-1, IL-17 signalling pathway, cytokine–cytokine receptor interaction and Toll-like receptor signalling pathway. According to the theory of competing endogenous RNA (ceRNA) networks, lncRNA–miRNA–mRNA network was constructed by Cytoscape software, 16 miRNAs and 144 mRNAs. The results suggested that seven DE lncRNAs (Ly6l, AABR07038849.2, AABR07069008.2, AABR07064873.1, AABR07001382.1, AABR07068161.1 and AABR07060341.2) may serve as molecular sponges of the corresponding miRNAs and play a major role in HPH.     

Integrated analysis of a competing endogenous RNA network reveals key long noncoding RNAs as potential prognostic biomarkers for hepatocellular carcinoma

Growing evidence has revealed that long noncoding RNAs (lncRNAs) have an important impact on tumorigenesis and tumor progression via a mechanism involving competing endogenous RNAs (ceRNAs). However, their use in predicting the survival of a patient with hepatocellular carcinoma (HCC) remains unclear. The aim of this study was to develop a novel lncRNA expression–based risk score system to accurately predict the survival of patients with HCC. In our study, using expression profiles downloaded from The Cancer Genome Atlas database, the differentially expressed messenger RNAs (mRNAs), lncRNAs, and microRNAs (miRNAs) were explored in patients with HCC and normal liver tissues, and then a ceRNA network constructed. A risk score system was established between lncRNA expression of the ceRNA network and overall survival (OS) or recurrence-free survival (RFS); it was further analyzed for associations with the clinical features of patients with HCC. In HCC, 473 differentially expressed lncRNAs, 63 differentially expressed miRNAs, and 1417 differentially expressed mRNAs were detected. The ceRNA network comprised 41 lncRNA nodes, 12 miRNA nodes, 24 mRNA nodes, and 172 edges. The lncRNA expression–based risk score system for OS was constructed based on six lncRNAs (MYLK-AS1, AL359878.1, PART1, TSPEAR-AS1, C10orf91, and LINC00501), while the risk score system for RFS was based on four lncRNAs (WARS2-IT1, AL359878.1, AL357060.1, and PART1). Univariate and multivariate Cox analyses showed the risk score systems for OS or RFS were significant independent factors adjusted for clinical factors. Receiver operating characteristic curve analysis showed the area under the curve for the risk score system was 0.704 for OS, and 0.71 for RFS. Our result revealed a lncRNA expression–based risk score system for OS or RFS can effectively predict the survival of patients with HCC and aid in good clinical decision-making.     

Long noncoding RNA HOXA-AS2 regulates the expression of SCN3A by sponging miR-106a in breast cancer

Breast cancer is the most commonly diagnosed cancer that affects women worldwide. This study aimed to investigate the competing endogenous RNAs (ceRNAs) mechanism in breast cancer. Microarray data were downloaded from the University of California Santa Cruz (UCSC) Xena database. The limma package was used to screen the differentially expressed messenger RNAs (DEMs) and differentially expressed long noncoding RNAs (DELs). Subsequently, functional analysis was performed using DAVID tool. After constructing the protein-protein interaction (PPI) network, we identified the major gene modules using the Cytoscape software. Univariate survival analysis in the survival package was performed. Finally, the ceRNA regulatory network was constructed to identify the critical genes. A total of 1380 DEMs and 345 DELs were identified in breast cancer samples compared with normal samples. Functional enrichment analysis showed that DEMs were mainly involved in cell division, and cell cycle. We screened four major gene modules and identified the hub nodes in these functional modules. Several DEMs (including FABP7, C4BPA, and LAMB3) and three long noncoding RNAs (lncRNAs) (LINC00092, SLC26A4.AS1, and COLCA1) exhibited significant correlation with patients' survival outcomes. In the ceRNA network, the lncRNA HOXA-AS2 regulated the expression level of SCN3A by interacting with hsa-miR-106a-5p. Thus, our study investigated the ceRNA mechanism in breast cancer. The results showed that lncRNA HOXA-AS2 might modulate the expression of SCN3A by sponging miR-106a in breast cancer.