决策森林法在胃癌基因信号通路分析中的应用

DNA微阵列分析为识别疾病类型及鉴别特征基因等生物研究提供了重要的研究手段,但目前大量使用的基于单基因的分析方法受样本数量和噪音的影响较大,无法呈现基因间的相互关系,而基因信号通路分析则是解决这一问题的一种有效方法。结合决策森林法对胃癌数据进行了基因通道分析,对所选择基因在基因信号通路中的作用以及通路中基因之间的相互作用进行了研究,为胃癌的研究提供了新的思路。     

Nrf2/ARE信号通路与胃癌耐药关系的研究进展

胃癌是癌症死亡的第二大原因。化疗是胃癌治疗的主要方法之一,胃癌化疗失败的主要原因是对化疗药物的耐受。Nrf2/ARE信号通路与肿瘤耐药的关系是当前的研究热点。转录因子Nrf2作为抗氧化反应中的关键转录因子,可以与抗氧化反应元件ARE结合,正向调节II相解毒酶、抗氧化酶及某些药物转运泵基因等靶基因的表达,诱导胃癌耐药性的产生。该综述整理归纳了Nrf2/ARE信号通路与胃癌耐药之间的关系。     

TRPS1在胃癌中的表达及生物信息学分析

目的探究转录抑制因子GATA结合基因1(TRPS1)在胃癌中的表达水平及其与表达相关基因的细胞功能及信号通路。方法通过筛选基因表达谱数据动态分析(GEPIA)、基因芯片表达谱公共数据库(GEO)数据,对TRPS1在胃癌组织中的数据进行Meta分析。采用实时荧光定量PCR技术(RT-qPCR)检测TRPS1在胃癌细胞中的表达水平。应用生物信息学分析TRPS1及表达相似基因的细胞功能和信号通路。结果在公共数据库中,TRPS1在胃癌组织中均呈高表达,合并标准均差SMD为0.40(95%CI:0.04～0.76,P=0.028),敏感性分析稳定,无发表偏倚。TRPS1在胃癌细胞HGC-27和MGC-803中呈高表达(均P0.01)。TRPS1和表达相关基因ESR1富集在多条功能通路中,与转录因子活性、序列特异性DNA结合等肿瘤相关通路密切相关;TRPS1与ESR1存在直接蛋白互作关联。结论 TRPS1在胃癌中可能是一个促癌因子,在胃癌的调控机制中有重要作用。     

NF-kB 通路中TAK1 靶点对胃癌细胞系AGS增殖的抑制作用

目的：探讨NF-kB信号传导通路中转化生长因子激活激酶1(TAK1)靶点对胃癌AGS 细胞系增殖的影响。方法：利用siRNA 沉默胃癌AGS细胞系中的TAK1 基因，通过Western Blot 验证细胞中TAK1 基因的沉默情况，双项荧光素酶报告基因系统检测 TAK1 基因沉默对AGS细胞系NF-资B信号传导通路活性的影响，软琼脂克隆形成实验检测沉默TAK1 基因对胃癌AGS 细胞系 成瘤能力的影响，MTT 法检测沉默TAK1 基因对胃癌AGS细胞系增殖能力的影响。结果：与对照组Sis-Con 细胞相比，TAK1 基 因沉默组Sir-TAK1-1/Sir-TAK1-2 细胞中NF-kB信号传导通路活性明显受抑制；TAK1 基因沉默组Sir-TAK1-1/Sir-TAK1-2 细胞 软琼脂克隆形成的集落数目明显减少，差异具有统计学意义(P＜0.05)，且细胞生长的速度明显减慢。结论：TAK1 是NF-kB信号 传导通路激活的关键因子，沉默TAK1 基因可以抑制AGS胃癌细胞系的成瘤性和增殖力。     

BATF2对Wnt信号通路影响的研究

摘要wnt信号通路在各种生物体内高度进化保守,与癌症的发生发展密切相关。BATF2是一个新近发现的基因,研究表明其具有抑癌基因的作用。目前,BATF2与wnt信号通路的关系尚不清楚,该文用荧光素酶报告基因检测、Real－timePCR和Western blot发现BATF2能影响wnt信号通路。过表达BArF2可明显下调TCF4／p－catenin的转录活性和Wnt信号通路下游基因的表达,可以下调细胞核中的β-caenin。推测BATF2可能通过下调细胞核中的p－catenin来实现对wnt信号通路的下调。上述结果为抑制Wnt信号通路用于肿瘤治疗提供了一定的依据。     

胃癌发生及其耐药性形成中的相关信号通路

胃癌是常见的消化道恶性肿瘤,而化疗药物的耐药性严重影响晚期胃癌患者的化疗效果。本文总结了多种与胃癌的发生及耐药性产生相关的信号通路,包括rnTOR、Nrf2-ARE、Notch、Hedgehog和Wnt。这些信号通路不仅决定着胃癌等恶性肿瘤的发生、分化与转移,更影响着恶性肿瘤耐药性的产生,而耐药性正是目前肿瘤化疗的最大障碍。研究这些信号通路可以从分子水平研究癌症发生的机理从而阻断肿瘤的生长,从这些肿瘤相关信号通路中亦能了解到肿瘤耐药性产生的机制,为胃癌等恶性肿瘤研究和治疗提供新的思路。     

胃癌多药耐药相关microRNA的筛选和鉴定

目的:研究胃癌多药耐药相关microRNA并对其进行鉴定、靶基因预测和预测靶基因的生物信息学分析。方法:运用microRNA芯片对胃癌多药耐药细胞SGC7901/ADR和其亲本细胞SGC7901进行microRNA表达谱分析;采用实时定量PCR的方法对差异表达的miRNA进行验证;再运用生物信息学方法对差异表达的miRNA进行靶基因预测;再对预测的靶基因进行GO和KEGG通路分析。结果:与SGC7901相比SGC7901/ADR表达上调超过2倍的miRNA有6个,表达下调超过2倍的有11个。实时定量PCR对共同差异表达的microRNA进行验证显示与芯片结果的一致性。对这17个差异表达的miRNA进行靶基因预测,再对预测得到的靶基因进行GO和KEGG通路分析显示预测的靶基因参与了肿瘤相关通路、MAPK通路、Focal Adhesion通路等。结论:我们初步筛选得到了胃癌多药耐药相关miRNA并对其进行了生物信息学分析,为进一步地探索miRNA在胃癌多药耐药中的作用及其分子机制奠定了基础。     

神经前体细胞表达发育性下调蛋白4在消化系统肿瘤发生中的作用

神经前体细胞表达发育性下调蛋白4(neural precursor cell expressed,developmentally down-regulated protein 4,NEDD4-1,部分文章也称NEDD4)是近年来才备受关注的肿瘤相关基因,属于E3 HECT(homologous to E6 associated protein C terminus,E6蛋白c端同源基因)泛素连接酶NEDD4样家族成员。泛素连接酶,能够参与多种蛋白质的泛素化、溶酶体及蛋白酶体的降解、胞核-胞质转位等,间接影响不同恶性肿瘤的多种信号通路。随着大量NEDD4-1与肿瘤相关实验的不断深入,目前已发现其可通过调控细胞周期、癌细胞侵袭转移、拮抗耐药性等许多途径影响肿瘤的生物学行为。在消化系统肿瘤中,NEDD4-1主要通过PTEN/PI3K/AKT、TGF-β、Hippo、LDLRAD4等多条通路促进肝细胞癌的增殖、侵袭和迁移能力;在胰腺癌中发现,NEDD4-1在PI3K/AKT信号通路中发挥癌基因作用,但在与Myc-SIRT2所形成的信号环路中,却发挥抑癌基因的作用;在胃癌和结直肠癌中,NEDD4-1所参与的信号通路与其他消化系统肿瘤均不相同,NEDD4-1能独立于PTEN/PI3K/AKT通路而发挥促进胃癌恶化、转移(EGFR信号通路)和抑制结直肠癌肿瘤生长(WNT信号通路)的作用。NEDD4-1已经成为人们治愈肿瘤的热门研究方向。本文通过系统总结NEDD4-1在不同消化系统肿瘤中的功能、信号通路和潜在抑制剂等,进行探讨NEDD4-1与不同信号通路的关系,旨为临床在癌症治疗领域提供重要的参考数据。     

癌相关通路在肺腺癌中的共扰动机制

肺腺癌的发生涉及多个生物学功能通路的扰动,其遗传改变频繁地发生于MAPK信号、p53信号、Wnt信号、细胞周期和mTOR等通路的基因中。解析癌相关通路间的共扰动机制对我们理解癌机制以及寻找诊断标记具有重要意义。因此,本文基于肺腺癌突变谱数据,研究上述癌相关通路在肺腺癌中的共扰动机制。结果发现:在肺腺癌发生的过程中,MAPK信号、p53信号、Wnt信号、细胞周期和mTOR等通路同时被扰动。在不同的癌样本中,一对通路可能通过以下三种方式被共同扰动:(1)在两条通路中的不同基因间的共突变;(2)两条通路相互交叠基因的突变;(3)与两条通路同时具有频繁的互作关系的蛋白质的编码基因的突变。该结果提示,癌相关通路对在不同的样本中可能通过不同的方式被共扰动,这也可能是造成癌症异质性的重要原因之一。     

山奈酚对胃癌细胞PARP1以及P53基因表达的影响研究

胃癌(GC)是最常见的恶性肿瘤之一,是人类健康的主要威胁,其发病机制是一个单基因或多基因逐步突变的过程,与细胞的侵袭、增殖和转移有关,包括癌基因遗传和表观遗传的突变、肿瘤抑制基因、DNA修复途径基因、细胞周期途径基因和幽门螺杆菌感染等。而山奈酚具有多种生物学活性,能够抑制多种肿瘤细胞的细胞周期,诱导肿瘤细胞凋亡从而抑制肿瘤细胞/组织的侵袭及转移。因此本研究用不同浓度的山奈酚处理胃癌细胞,并检测了胃癌细胞的形态变化情况、癌细胞凋亡相关因子P53和PARP1基因的表达水平和其对应的蛋白质表达变化。结果表明大于100μmol/L山奈酚处理后的胃癌细胞中P53基因和P53蛋白的表达水平被显著提高,而相反的PARP1基因和蛋白的表达则被显著抑制,且山奈酚处理后胃癌细胞的凋亡数目也明显增加,因此本实验结果表明,山奈酚能够有效的促进胃癌细胞凋亡的发生,以此来达到抑制癌细胞恶性增殖的作用。这一结果可以为后续针对胃癌新疗法的研究提供一些思路和理论支持。     

Transcriptome analysis reveals GPNMB as a potential therapeutic target for gastric cancer

Gastric cancer has the fifth highest incidence of disease and is the third leading cause of cancer-associated mortality in the world. The etiology of gastric cancer is complex and needs to be fully elucidated. Thus, it is necessary to explore potential pathogenic genes and pathways that contribute to gastric cancer. Gene expression profiles of the GSE33335 and GSE54129 datasets were downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) were compared and identified using R software. The DEGs were then subjected to gene set enrichment analysis and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. Survival analyses based on The Cancer Genome Atlas database were used to further screen the essential DEGs. A knockdown assay was performed to determine the function of the candidate gene in gastric cancer. Finally, the association between the candidate gene and immune-related genes was investigated. We found that GPNMB serves as an essential gene, with a high expression level, and predicts a worse outcome of gastric cancer. Knockdown of GPNMB inhibited gastric cancer cell proliferation and migration. In addition, GPNMB may augment the immunosuppressive ability of gastric cancer by recruiting immunosuppressive cells and promoting immune cell exhaustion through PI3K/AKT/CCL4 signaling axis. Collectively, these data suggest that GPNMB acts as an important positive mediator of tumor progression in gastric cancer, and GPNMB could exert multimodality modulation of gastric cancer-mediated immune suppression.     

Gene-expression signatures can distinguish gastric cancer grades and stages

Microarray gene-expression data of 54 paired gastric cancer and adjacent noncancerous gastric tissues were analyzed, with the aim to establish gene signatures for cancer grades (well-, moderately-, poorly- or un-differentiated) and stages (I, II, III and IV), which have been determined by pathologists. Our statistical analysis led to the identification of a number of gene combinations whose expression patterns serve well as signatures of different grades and different stages of gastric cancer. A 19-gene signature was found to have discerning power between high- and low-grade gastric cancers in general, with overall classification accuracy at 79.6%. An expanded 198-gene panel allows the stratification of cancers into four grades and control, giving rise to an overall classification agreement of 74.2% between each grade designated by the pathologists and our prediction. Two signatures for cancer staging, consisting of 10 genes and 9 genes, respectively, provide high classification accuracies at 90.0% and 84.0%, among early-, advanced-stage cancer and control. Functional and pathway analyses on these signature genes reveal the significant relevance of the derived signatures to cancer grades and progression. To the best of our knowledge, this represents the first study on identification of genes whose expression patterns can serve as markers for cancer grades and stages.     

Alterations of frizzled (FzE3) and secreted frizzled related protein (hsFRP) expression in gastric cancer.

Wnt signaling pathway is important for development and carcinogenesis. Alterations of this pathway, such as mutations in adenomatous polyposis coli (APC) gene and activation mutations of beta-catenin, would result in stabilization of beta-catenin and subsequent translocation to nucleus where genes are transcribed. Recently, a receptor of Wnt, FzE3 was found to be up-regulated in esophageal carcinoma while a non-receptor antagonist of Wnt, secreted frizzled related protein (hsFRP) was found to be down-regulated in some cancer. These findings suggested that FzE3 is a potential oncogene while hsFRP is a potential tumor suppressor gene. We aimed to investigate whether FzE3 and hsFRP were altered in gastric cancer. Twelve cases of gastric cancer, including 7 cases of intestinal type, 4 cases of diffuse type and I case of mixed type, were studied. FzE3 and hsFRP mRNAs were expressed in most of the paired normal gastric tissues. FzE3 was over-expressed in 9 cases (75%) of gastric carcinoma tissues while hsFRP was down-regulated in 2 cases (16%). Beta-catenin nuclear staining was identified in 3 cases (27%) and cyclin D1 was expressed in 5 cases (41%) of cancer samples. All these cases were associated with either up-regulation of FzE3 or down-regulation of hsFRP. Our results suggested that alterations of FzE3 or hsFRP were frequent in gastric cancer. These provide alternative mechanisms leading to activation of Wnt signaling pathway in gastric carcinogenesis.     

Characterization of Differentially Expressed Genes Involved in Pathways Associated with Gastric Cancer

To explore the patterns of gene expression in gastric cancer, a total of 26 paired gastric cancer and noncancerous tissues from patients were enrolled for gene expression microarray analyses. Limma methods were applied to analyze the data, and genes were considered to be significantly differentially expressed if the False Discovery Rate (FDR) value was < 0.01, P-value was <0.01 and the fold change (FC) was >2. Subsequently, Gene Ontology (GO) categories were used to analyze the main functions of the differentially expressed genes. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we found pathways significantly associated with the differential genes. Gene-Act network and co-expression network were built respectively based on the relationships among the genes, proteins and compounds in the database. 2371 mRNAs and 350 lncRNAs considered as significantly differentially expressed genes were selected for the further analysis. The GO categories, pathway analyses and the Gene-Act network showed a consistent result that up-regulated genes were responsible for tumorigenesis, migration, angiogenesis and microenvironment formation, while down-regulated genes were involved in metabolism. These results of this study provide some novel findings on coding RNAs, lncRNAs, pathways and the co-expression network in gastric cancer which will be useful to guide further investigation and target therapy for this disease.     

Integration of DNA copy number alterations and transcriptional expression analysis in human gastric cancer

Background

Genomic instability with frequent DNA copy number alterations is one of the key hallmarks of carcinogenesis. The chromosomal regions with frequent DNA copy number gain and loss in human gastric cancer are still poorly defined. It remains unknown how the DNA copy number variations contributes to the changes of gene expression profiles, especially on the global level.

Principal Findings

We analyzed DNA copy number alterations in 64 human gastric cancer samples and 8 gastric cancer cell lines using bacterial artificial chromosome (BAC) arrays based comparative genomic hybridization (aCGH). Statistical analysis was applied to correlate previously published gene expression data obtained from cDNA microarrays with corresponding DNA copy number variation data to identify candidate oncogenes and tumor suppressor genes. We found that gastric cancer samples showed recurrent DNA copy number variations, including gains at 5p, 8q, 20p, 20q, and losses at 4q, 9p, 18q, 21q. The most frequent regions of amplification were 20q12 (7/72), 20q12–20q13.1 (12/72), 20q13.1–20q13.2 (11/72) and 20q13.2–20q13.3 (6/72). The most frequent deleted region was 9p21 (8/72). Correlating gene expression array data with aCGH identified 321 candidate oncogenes, which were overexpressed and showed frequent DNA copy number gains; and 12 candidate tumor suppressor genes which were down-regulated and showed frequent DNA copy number losses in human gastric cancers. Three networks of significantly expressed genes in gastric cancer samples were identified by ingenuity pathway analysis.

Conclusions

This study provides insight into DNA copy number variations and their contribution to altered gene expression profiles during human gastric cancer development. It provides novel candidate driver oncogenes or tumor suppressor genes for human gastric cancer, useful pathway maps for the future understanding of the molecular pathogenesis of this malignancy, and the construction of new therapeutic targets.