Identification of potential biomarkers of genotoxicity and carcinogenicity in L5178Y mouse lymphoma cells by cDNA microarray analysis

In the present study, cDNA microarray analyses were performed with mouse cDNA chips in order to evaluate similarities and differences in the gene expression profiles for compounds differing in their genotoxic and carcinogenic potential. Eight test substances were evaluated, two each from four classes of compounds: genotoxic carcinogens (1,2-dibromoethane and glycidol), genotoxic noncarcinogens (8-hydroxyquinoline and emodin), nongenotoxic carcinogens (methyl carbamate and o-nitrotoluene), and nongenotoxic noncarcinogens (D-mannitol and 1,2-dichlorobenzene). Quadruplicate hybridization experiments were performed in order to identify a set of genes with significant expression changes for these four classes of substances. Twelve genes were consistently altered more than twofold by the genotoxic noncarcinogens while four genes were consistently regulated by the nongenotoxic carcinogens. One gene (Trp63) was identified whose expression was upregulated by all four genotoxic substances regardless of the presence or absence of carcinogenicity; this finding, however, was not confirmed by quantitative real-time RT-PCR. RT-PCR did confirm the change in expression of 9 of 15 genes (60%) identified by microarray analysis. Interestingly, the downregulated genes were least likely to be validated by real-time RT-PCR. Those genes showing more than a twofold change in expression level in response to at least one substance were further analyzed with hierarchical clustering after category assignment of each gene according to its main cellular function. Clustering revealed differences in the gene expression profiles between the genotoxic and nongenotoxic substances for genes involved in cell cycle control, the stress response, and the immune response. However, no clustering specific to all four carcinogenic substances was observed in any of the functional categories. Taken together, these results suggest that gene expression profiling in mouse lymphoma cells can provide valuable information for the evaluation of potential genotoxicity but may have limitations in predicting carcinogenicity.     

基因芯片技术检测子宫内膜异位症相关细胞因子及其受体基因的表达谱

目的:研究与子宫内膜异位症(EM)发生和发展相关的细胞因子(CK)基因的表达,进一步阐明子宫内膜异位症的发病机制。方法:应用含有1200条基因的基因芯片,用同位素探针标记,探讨EM组织与正常子宫组织相关CK基因的表达谱。结果:在3例EM组织与3例正常的子宫内膜组织中,共筛选出差异表达基因119条,其中CK及CKR基因表达上调15条,包括IL1、IL2、IL6、IL8、VEGFR、TGF、EGF、FGF和EPOR等。结论:表达差异基因有助于揭示EM发生发展的分子机制,基因表达谱芯片能有效地筛选EM相关的CK及CKR基因,为了解疾病发生机制提供了高效、准确的研究工具。     

Lipidomic analysis of the liver identifies changes of major and minor lipid species in adiponectin deficient mice

Adiponectin protects from hepatic fat storage but adiponectin deficient mice (APN−/−) fed a standard chow do not develop liver steatosis. This indicates that other pathways might be activated to compensate for adiponectin deficiency. An unbiased and comprehensive screen was performed to identify hepatic alterations of lipid classes in these mice. APN−/− mice had decreased hepatic cholesteryl esters while active SREBP2 and systemic total cholesterol were not altered. Upregulation of cytochromes for bile acid synthesis suggests enhanced biliary cholesterol excretion. Analysis of 37 individual fatty acid species showed reduced stearate whereas total fatty acids were not altered. Total amount of triglycerides and phospholipids were equally abundant. A selective increase of monounsaturated phosphatidylcholine and phosphatidylethanolamine which positively correlate with hepatic and systemic triglycerides with the latter being elevated in APN−/− mice, was identified. Stearoyl-CoA desaturase 1 (SCD1) is involved in the synthesis of monounsaturated fatty acids and despite higher mRNA expression enzyme activity was not enhanced. Glucosylceramide postulated to contribute to liver damage was decreased.     

胃癌基因表达谱的cDNA微阵列与聚类分析

目的 分析胃癌与非肿瘤胃组织中基因表达特征，探讨其生物学意义。方法 提取18例进展期胃癌患者术前未行治疗的新鲜肿瘤和非肿瘤胃组织总RNA，逆转录标记cy5和cy3制备cDNA探针，与148个基因组成的cDNA微阵列杂交，应用平均联接等级聚类和微阵列数据显著差异分析(significance analysis of microarrays，SAM)方法分析146个符合入选条件基因的实验数据。结果 胃癌与非肿瘤胃组织各被聚为一类，胃癌和非肿瘤胃组织又分别聚为两个亚类。基因在两种组织表达有3个特征，明显基因表达差异表现在特征B和特征C．特征B基因在胃癌组织呈低表达或不表达，特征C基因在胃癌组织呈高表达。在特征A，T2-S2亚类与T1和T2-S1亚类的基因表达存在差异性，然而13例患者的配对胃癌与非肿瘤胃组织有相似基因表达。结合SAM分析，从特征B和特征C分别检出19个和12个在两种组织间呈差异性表达基因。结论 cDNA微阵列实验结果客观地反映了胃癌和非肿瘤胃组织的基因表达特征，可以将胃癌与非肿瘤胃组织各聚为一类．胃癌组织之间基因表达既有相似性，又有异质性，反映了胃癌基因表达变异的复杂性．应用cDNA微阵列技术研究胃癌基因差异性表达特征，有助于阐明胃癌发生、发展的分子基础，为胃癌早期诊断和预后评估的生物标记物研究提供科学依据．     

Downregulation of apoptosis revealed by laser microdissection and cDNA microarray analysis of related genes in rat liver preneoplastic lesions

Regulation of cell proliferation and apoptosis plays a key role in tumor development. To elucidate mechanisms underlying hepatocarcinogenesis, patterns of gene expression, including apoptosis-related genes, were compared between glutathione S-transferase placental form (GST-P)-positive preneoplastic foci and surrounding tissue in the rat. Lesions were induced with a single intraperitoneal injection of diethylnitrosamine (DEN, 200mg/kgbw) and then 100ppm 2-acetylaminofluorene (2-AAF)-containing diet combined with two-thirds partial hepatectomy. Frozen sections of the livers were applied for immunohistochemical staining of GST-P, and both positive foci and surrounding negative areas were harvested by laser microdissection. Total RNAs were extracted and amplified with T7 polymerase to allow gene expression analysis by cDNA microarray assays. In the GST-P-positive foci, altered levels were observed for many genes, mostly related to metabolism or catalysis, with increased expression of testosterone-repressive prostate message-2 (TRPM-2), which is reported to act as a protective factor against apoptosis, and decreased expression of thymus-expressed acidic protein (TEAP), which is considered to promote apoptosis. The results indicate that rat liver preneoplastic lesions might be protected against apoptosis and that the approach adopted is useful for clarification of mechanisms underlying hepatocarcinogenesis.     

利用基因芯片研究六味地黄丸对老年大鼠基因表达的影响

目的:利用基因芯片研究六味地黄丸对老年大鼠基因表达的影响。方法:将40只20月龄SD雄性大鼠分成不用药与用六味地黄丸两组,用药5周后,通过检测相关生化指标,确定用药组与对照组之间具显著差异。提取20只4月龄SD雄性大鼠脾脏mRNA,平均分成两组,分别与老年用药组脾脏mRNA和老年对照组脾脏mRNA配对进行逆转录和芯片杂交实验,获得老年对照组和老年用药组分别和青年组相比,相关基因表达水平的差异,通过比较两组数据,评价六味地黄丸对与衰老相关的基因表达的调节作用。结果:芯片结果显示老年对照组与青年组相比有13个基因表达显著下调,1个基因表达显著上调。而在老年用药组中,14个相关基因的表达水平没有明显变化;而另有2序列与青年组相比表达显著上调。结论:通过基因芯片技术,发现16个基因的表达水平可受六味地黄丸用药的影响。通过深入研究对我们深入理解六味地黄丸抗衰老的分子机制可能有帮助。     

基因芯片在宫颈癌、卵巢癌和乳腺癌相关基因表达研究中的运用

目的 应用基因微矩阵芯片筛查妇科恶性肿瘤相关基因表达。方法 分别提取癌组织和正常对照组织mRNA，分别用Cv3—dCTP和Cy5—dCTP经反转录荧光标记cDNA，获得两组探针，将探针混合后与基因芯片H40s(基因点数为4096点，上海联合基因公司提供)杂交，经严格洗片后用GenePix4000B扫描仪进行扫描，获得荧光信号图像，GenePixPro3．0图像处理软件对图像进行处理，获得两种组织中差异表达的基因信息。结果 在子宫颈癌组织中差异表达的基因24．61％(1008／4096)，其中表达降低(下调趋势)占11．28％(462／4096)；表达增高(上调趋势)占13．32％(546／4096)。在卵巢癌组织中差异表达的基因24．02％(984／4096)，其中表达降低(下调趋势)占12．67％(519／4096)，表达增高(上调趋势)占11．35％(465／4096)；在乳腺癌组织中差异表达的基因占9．67％(396／4096)，其中表达降低(下调趋势)占4．59％(188／4096)，表达增高(上调趋势)的5．08％(208／4096)。在3种癌组织中同时出现表达差异的基因有1．37％。结论 子宫颈癌、卵巢癌和乳腺癌有多种基因表达失衡。     

BHA通过ERK信号转导途径促进小鼠胎肝细胞神经组织细胞特异基因表达的研究

目的：了解丁羟回香醚（BHA）对小鼠胎肝（FL）细胞神经组织特异基因表达的影响及其信号途径。 方法： 采用MACS试剂盒分离小鼠胚胎肝Sca-1+细胞，以DMEM+10%胎牛血清培养液培养；第4 d后，加入或者不加入细胞外信号调节蛋白激酶特异抑制剂PD98059 (25 μmol/L)处理24 h，再加入BHA处理24 h（0.2 mmol/L）。然后在无血清培养基中培养5 d。用Western blotting和半定量RT-PCR方法分析BHA处理前后基因表达。 结果： 经BHA诱导处理后，细胞表达神经组织细胞特异蛋白显著增加如神经丝轻链（NF-L）、神经丝重链（NF-H）、脑因子1（BF-1）和酪氨酸羟化酶（TH）。NF-L、NF-H、BF-1和TH分别增加6.32倍、2.73倍、3.37倍、2.68倍。而PD98059能明显抑制BHA诱导的神经组织细胞特异蛋白NF-L、NF-H、BF-1和TH的表达。 结论： BHA通过细胞外信号调节蛋白激酶途径促进小鼠FL Sca-1+细胞表达神经组织细胞特异抗原、结构和功能基因。     

Identification of key genes and pathways in castrate-resistant prostate cancer by integrated bioinformatics analysis

ObjectiveTo identify hub genes and pathways involved in castrate-resistant prostate cancer (CRPC).MethodsThe gene expression profiles of GSE70768 were downloaded from Gene Expression Omnibus (GEO) datasets. A total of 13 CRPC samples and 110 tumor samples were identified. The differentially expressed genes (DEGs) were identified, and the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analysis was performed. Protein-protein interaction (PPI) network module analysis was constructed and performed in Cytoscape software. Weighted correlation network analysis (WGCNA) was conducted to determine hub genes involved in the development and progression of CRPC. The gene expression profiles of GSE80609 were used for validation.ResultsA total of 1738 DEGs were identified, consisting of 962 significantly down-regulated DEGs and 776 significantly upregulated DEGs for the subsequent analysis. GO term enrichment analysis suggested that DEGs were mainly enriched in the extracellular matrix organization, extracellular exosome, extracellular matrix, and extracellular space. KEGG pathway analysis found DEGs significantly enriched in the focal adhesion pathway. PPI network demonstrated that the top 10 hub genes were ALB, ACACB, KLK3, CDH1, IL10, ALDH1A3, KLK2, ALDH3B2, HBA1, COL1A1. Also, WGCNA identified the top 5 hub genes in the turquoise module, including MBD4, BLZF1, PIP5K2B, ZNF486, LRRC37B2. Plus, the Venn diagram demonstrated that HBA1 was the key gene in both GSE70768 and GSE80609 datasets.ConclusionsThese newly identified genes and pathways could help urologists understand the differences in the mechanism between CRPC and PCa. Besides, it might be promising targets for the treatment of CRPC.     

Large-scale molecular and tissue microarray analysis of mesothelin expression in common human carcinomas

The 40-kilodalton processed glycoprotein, mesothelin, is highly expressed in epithelial mesotheliomas and adenocarcinomas of the ovary (serous papillary) and pancreas, but its expression in a large series of other common carcinomas has not been completely explored. In the present study, we used oligonucleotide and tissue microarrays to profile the expression of the mesothelin gene (MSLN) and encoded protein, respectively. Among 150 carcinomas of multiple anatomic sites, we found the highest average expression of MSLN in serous carcinomas of the ovary and adenocarcinomas of the pancreas, consistent with previous reports, as well as measurable but less-striking expression in pulmonary, gastric/esophageal, and colorectal adenocarcinomas. On tissue microarrays containing 621 carcinomas derived from the same and additional sites as those profiled by gene expression, mesothelin immunoreactivity was highest in cancers of the ovary (serous papillary, endometrioid, and undifferentiated) and pancreas, with less frequent staining seen in adenocarcinomas of the endometrium, lung, and stomach/esophagus. Some immunopositivity was observed in 42% of pulmonary adenocarcinomas, including 18% that had >50% of tumor cells that were immunoreactive. Some 14% of breast and 30% of colorectal adenocarcinomas showed immunopositivity, but no case contained >50% tumor cells that were immunoreactive. Mesothelin was either entirely absent or present in <5% of carcinomas of the prostate, bladder/ureter, liver, kidney, and thyroid. Overall, we observed good concordance between the results obtained by oligonucleotide and tissue microarrays. This large study of the MSLN gene and protein expression in common carcinomas provides data for future investigations that evaluate the utility of mesothelin/megakaryocyte potentiating factor as a potential serum tumor marker or target of immunotoxin-based therapy in human cancers.     

cDNA microarray analysis of differential gene expression and regulation in clinically drug-resistant isolates of Candida albicans from bone marrow transplanted patients

Fungi have emerged as the fourth most common pathogens isolated in nosocomial bloodstream infections, and Candida albicans is the most common human fungal pathogen. Only a few antibiotics are effective in the treatment of fungal infections. In addition, the repetition and lengthy duration of fluconazole therapy has led to an increased incidence of azole resistance and treatment failure associated with C. albicans. To investigate the mechanism of drug resistance and explore new targets to treat clinically resistant fungal pathogens, we examined the large-scale gene expression profile of two sets of matched fluconazole-susceptible and -resistant bloodstream C. albicans isolates from bone marrow transplanted (BMT) patients for the first time by microarray analysis. More than 198 differentially expressed genes were identified and they were confirmed and validated by RT-PCR independently. Not surprisingly, the resistant phenotype is associated with increased expression of CDR mRNA, as well as some common genes involved in drug resistance such as CaIFU5, CaRTA2 and CaIFD6. Meanwhile, some special functional groups of genes, including ATP binding cassette (ABC) transporter genes (IPF7530, CaYOR1, CaPXA1), oxidative stress response genes (CaALD5, CaGRP1, CaSOD2, IPF10565), copper transport and iron mobilization-related genes (CaCRD1/2, CaCTR1/2, CaCCC2, CaFET3) were found to be differentially expressed in the resistant isolates. Furthermore, among these differentially expressed genes, some co-regulated with CaCDR1, CaCDR2 and CaIFU5, such as CaPDR16 and CaIFD6, have a DRE-like element and may interact with TAC1 in the promoter region. These findings may shed light on mechanisms of azole resistance in C. albicans and clinical antifungal therapy.     

肝癌组织差异表达基因cDNA序列的筛选与鉴定

目的：筛选并鉴定肝癌组织特异表达基因。方法：通过菌落原位杂交技术筛选用抑制消减杂交法构建肝癌与癌旁肝组织差异表达基因消减cDNA文库，用PCR方法进一步筛选出有插入片段的阳性克隆，将阳性克隆进行DNA测序和同源性比较分析，用Northern印迹方法对新的cDNA序列进行初步鉴定。结果：从消减文库中随机挑取的100个白色克隆中筛选出13个阳性克隆，DNA测序获得11个不同的cDNA序列；同源性比较分析表明，6个cDNA片段与在基因高度同源，5个cDNA片段为新的序列。其长度大于300bp的3个新序列，Norther印迹证实它都来源于肝癌组织。结论：用抑制消减杂交方法构建的肝癌差异表达基因消减cDNA文库富含肝癌特异表达基因，经验证的3个新的cDNA序列可能为肝癌特异的基因序列。     

Expression profiles of proliferative and antiapoptotic genes in sporadic and colitis‐related mouse colon cancer models

Elevated levels of survivin, telomerase catalytic subunit (TERT), integrin‐linked kinase (ILK), cyclooxygenase 2 (COX‐2), inducible nitric oxide synthase (iNOS) and the regulatory factors c‐MYB and Tcf‐4 are often found in human cancers including colorectal cancer (CRC) and have been implicated in the development and progression of tumorigenesis. The aim of this study was to determine the expression of these genes in mouse models of sporadic and colitis‐associated CRC. To address these issues, we used qRT‐PCR approach to determine changes in gene expression patterns of neoplastic cells (high‐grade dysplasia/intramucosal carcinoma) and surrounding normal epithelial cells in A/J and ICR mouse strains using laser microdissection. Both strains were injected with azoxymethane and ICR mice were also given drinking water that contained 2% dextran sodium sulphate. In both sporadic (A/J mice) and colitis‐associated (ICR mice) models of CRC, the levels of TERT mRNA, COX‐2 mRNA and Tcf‐4 mRNA were higher in neoplastic cells than in surrounding normal epithelial cells. In contrast, survivin mRNA was upregulated only in neoplastic cells from A/J mice and ILK mRNA was upregulated only in neoplastic cells from ICR mice. However, the expression of iNOS mRNA was similar in normal and neoplastic cells in both models and c‐MYB mRNA was actually downregulated in neoplastic cells compared with normal cells in both models. These findings suggest that the genetic background and/or the molecular mechanisms of tumorigenesis associated with genotoxic insults and colonic inflammation influence the gene expression of mTERT, COX‐2, Tcf‐4, c‐MYB, ILK and survivin in colon epithelial neoplasia.