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Application of toxicogenomic analysis to risk assessment of delayed long-term effects of multiple chemicals, including endocrine disruptors in human fetuses. 毒物基因组学分析在多种化学物质(包括人类胎儿内分泌干扰物)延迟长期影响风险评估中的应用。
Chisato Mori, Masatoshi Komiyama, Tetsuya Adachi, Kenichi Sakurai, Daisuke Nishimura, Kyoka Takashima, Emiko Todaka

Our previous studies analyzing umbilical cords show that human fetuses in Japan are exposed to multiple chemicals. Because of these findings, we believe it is necessary to establish a new strategy for examining the possible delayed long-term effects caused by prenatal exposure to multiple chemical combinations and evaluating the health risk to human fetuses. In this commentary we describe our attempts to apply toxicogenomic analysis of umbilical cords, using DNA microarray for future risk assessment. Because the umbilical cord is part of the fetal tissue, it is possible to estimate the effects of chemicals on the fetus by analyzing alteration of the gene expression. This type of toxicogenomic analysis could be a powerful and effective tool for developing a new risk assessment strategy to help investigators understand and possibly prevent long-term effects caused by fetal exposure to multiple chemicals. Worldwide cooperation is needed to establish a new stragegy for risk assessment using toxicogenomic analysis that focuses on the human fetus.

我们之前对脐带的分析研究表明,日本的人类胎儿暴露在多种化学物质中。由于这些发现,我们认为有必要建立一种新的策略来检查产前暴露于多种化学物质组合可能造成的延迟长期影响,并评估对人类胎儿的健康风险。在这篇评论中,我们描述了我们使用DNA微阵列对脐带进行毒性基因组分析的尝试,以进行未来的风险评估。由于脐带是胎儿组织的一部分,因此可以通过分析基因表达的变化来估计化学物质对胎儿的影响。这种类型的毒物基因组分析可能是一种强大而有效的工具,可以开发一种新的风险评估策略,帮助调查人员了解并可能防止胎儿接触多种化学物质造成的长期影响。需要世界范围的合作来建立一种新的战略,利用侧重于人类胎儿的毒物基因组分析进行风险评估。
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引用次数: 0
Expression profiling of estrogenic compounds using a sheepshead minnow cDNA macroarray. 用羊头鲦鱼cDNA大阵列分析雌激素化合物的表达谱。
Patrick Larkin, Leroy C Folmar, Michael J Hemmer, Arianna J Poston, Nancy D Denslow

A variety of anthropogenic compounds are capable of binding to the estrogen receptor (ER) of vertebrate species. Binding of these chemicals to the ER can interfere with homeostasis by altering normal gene expression patterns. The purpose of this study was to characterize the expression of 30 genes using a sheepshead minnow (Cyprinodon variegatus) cDNA macroarray. Many of the genes on the array were previously identified by differential display reverse transcriptase-polymerase chain reaction to be upregulated or downregulated in sheepshead minnows treated through aqueous exposure to known or suspected estrogenic chemicals. The results of this study show that 17 beta-estradiol (E2), 17 alpha-ethinyl estradiol (EE2), diethylstilbestrol (DES), and methoxychlor (MXC) have similar genetic signatures for the 30 genes examined. The genetic signature of fish treated with p-nonylphenol was identical in pattern to that in fish treated with E2, EE2, DES, and MXC except for the additional upregulation of a cDNA clone that shares similarity to ubiquitin-conjugating enzyme 9. Endosulfan produced results that resembled the gene expression patterns of untreated control fish with exception of the upregulation of estrogen receptor alpha and the downregulation of a cDNA clone that shares similarity to 3-hydroxy-3-methylglutaryl-coenzyme A reductase. We show that our estrogen-responsive cDNA macroarray can detect dose-dependent changes in gene expression patterns in fish treated with EE2.

多种人为化合物能够与脊椎动物的雌激素受体(ER)结合。这些化学物质与内质网的结合可以通过改变正常的基因表达模式来干扰体内平衡。本研究的目的是利用羊头鲦鱼(Cyprinodon variegatus) cDNA宏阵列对30个基因的表达进行表征。阵列上的许多基因先前通过差异显示逆转录-聚合酶链反应被鉴定为在羊头鲦鱼通过暴露于已知或可疑的雌激素化学物质的水处理中上调或下调。本研究结果表明,17 -雌二醇(E2)、17 -乙炔雌二醇(EE2)、己烯雌酚(DES)和甲氧基氯(MXC)在30个基因中具有相似的遗传特征。对壬基酚处理的鱼的遗传特征与E2、EE2、DES和MXC处理的鱼的遗传特征是相同的,除了一个与泛素结合酶9相似的cDNA克隆的额外上调。硫丹产生的结果与未经处理的对照鱼的基因表达模式相似,除了雌激素受体α上调和与3-羟基-3-甲基戊二酰辅酶a还原酶相似的cDNA克隆下调。我们发现我们的雌激素响应性cDNA大阵列可以检测EE2处理后鱼类基因表达模式的剂量依赖性变化。
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引用次数: 0
Development of a DNA microarray for toxicology based on hepatotoxin-regulated sequences. 基于肝毒素调控序列的毒理学DNA芯片的开发。
Jeffrey F Waring, Guy Cavet, Robert A Jolly, Jeff McDowell, Hongye Dai, Rita Ciurlionis, Chunsheng Zhang, Roland Stoughton, Pek Lum, Allan Ferguson, Christopher J Roberts, Roger G Ulrich

Toxicogenomics is an emerging field combining genomics and bioinformatics to identify and characterize mechanisms of toxicity of compounds. One of the main tools used in toxicogenomics is DNA microarrays. We have used a novel strategy to create a library highly enriched for genes expressed in the liver under hepatotoxic conditions. Using this library, we have created a new oligonucleotide microarray dedicated to the study of rat liver function. Oligonucleotide probes for these genes were designed and used in experimental hybridization studies to deduce the correct sequence orientation and to determine those sequences exhibiting differential regulation under a variety of toxicity-related treatments and conditions. The final array was benchmarked on treatments with 3-methylcholanthrene, Aroclor 1254, and cyclopropane carboxylic acid. Our results showed that the subtractive hybridization greatly enriched for genes regulated during a hepatotoxic response. Overall, our strategy for design of a new rat toxicology microarray can be applied to other systems as well and should aid greatly in the development of microarrays targeted for specific scientific areas.

毒物基因组学是一门将基因组学和生物信息学相结合的新兴领域,旨在识别和表征化合物的毒性机制。在毒物基因组学中使用的主要工具之一是DNA微阵列。我们使用了一种新的策略来创建一个高度丰富的库,用于肝毒性条件下肝脏中表达的基因。利用这个库,我们创建了一个新的寡核苷酸微阵列,专门用于大鼠肝功能的研究。这些基因的寡核苷酸探针被设计并用于实验杂交研究,以推断正确的序列方向,并确定在各种毒性相关处理和条件下表现出差异调控的序列。最后的阵列以3-甲基胆蒽、Aroclor 1254和环丙烷羧酸处理为基准。我们的结果表明,减法杂交极大地丰富了在肝毒性反应中调节的基因。总的来说,我们设计的一种新的大鼠毒理学微阵列的策略也可以应用于其他系统,并且应该有助于开发针对特定科学领域的微阵列。
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引用次数: 0
EHP Toxicogenomics: a publication forum in the postgenome era. EHP毒理学基因组学:后基因组时代的出版论坛。
Kenneth S Ramos
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引用次数: 3
Intrinsic hepatic phenotype associated with the Cyp1a2 gene as shown by cDNA expression microarray analysis of the knockout mouse. 基因敲除小鼠的cDNA表达芯片分析显示与Cyp1a2基因相关的内在肝脏表型。
Andrew G Smith, Reginald Davies, Timothy P Dalton, Marian L Miller, David Judah, Joan Riley, Timothy Gant, Daniel W Nebert

Several forms of cytochrome P450 (CYP) appear to metabolize principally pharmaceutical agents, as well as other dietary and plant chemicals. Other CYP forms have major roles in steroid, sterol, and bile acid metabolism. CYP1A2 expression is constitutively high in mouse liver and is well known for metabolizing several drugs and many procarcinogens to reactive intermediates that can cause toxicity or cancer. CYP1A2 is also known to carry out several endogenous functions such as uroporphyrinogen and melatonin oxidation and the 2- and 4-hydroxylations of estradiol. We have used cDNA microarray analysis of the untreated Cyp1a2(-/-) knockout mouse to search for changes in gene expression that might indicate important intrinsic roles for this enzyme. For 15 of the up- or downregulated genes, these increases or decreases were corroborated by reverse-transcription real-time polymerase chain reaction. Other than upregulation of the Hprt gene (used in the selection procedure for disrupting the Cyp1a2 gene), we found several genes upregulated that are associated with cell-cycle regulation and lipid metabolism. Besides Cyp1a2, the gene exhibiting the greatest downregulation was Igfbp1 (insulin-like growth factor binding protein-1), showing only 12% expression of that in the Cyp1a2(+/+) wild-type liver. Recurrent themes between both up- and downregulated genes include cell-cycle control, insulin action, lipogenesis, and fatty acid and cholesterol biosynthetic pathways. Histologically, the Cyp1a2(-/-) mouse exhibited an approximately 50% decrease in lipid stored in hepatocytes, and 50% increase in lipid present in interstitial fat-storing cells compared with that in the Cyp1a2(+/+) wild-type. These data suggest that the CYP1A2 enzyme might perform additional hepatic endogenous functions heretofore not appreciated.

几种形式的细胞色素P450 (CYP)似乎主要代谢药物,以及其他膳食和植物化学物质。其他形式的CYP在类固醇、固醇和胆汁酸代谢中起主要作用。在小鼠肝脏中,CYP1A2的表达量是组成性高的,众所周知,CYP1A2可以将几种药物和许多前致癌物代谢为可引起毒性或癌症的活性中间体。CYP1A2还具有多种内源性功能,如氧化尿卟啉原和褪黑素,以及雌二醇的2-羟基化和4-羟基化。我们对未经处理的Cyp1a2(-/-)敲除小鼠进行了cDNA微阵列分析,以寻找可能表明该酶重要内在作用的基因表达变化。对于15个上调或下调的基因,逆转录实时聚合酶链反应证实了这些增加或减少。除了Hprt基因上调(用于破坏Cyp1a2基因的选择过程),我们还发现了几个与细胞周期调节和脂质代谢相关的基因上调。除Cyp1a2外,下调幅度最大的基因是Igfbp1(胰岛素样生长因子结合蛋白-1),在Cyp1a2(+/+)野生型肝脏中表达量仅为其12%。在上调和下调基因之间反复出现的主题包括细胞周期控制、胰岛素作用、脂肪生成、脂肪酸和胆固醇生物合成途径。组织学上,与Cyp1a2(+/+)野生型相比,Cyp1a2(-/-)小鼠肝细胞中储存的脂质减少了约50%,而间质脂肪储存细胞中的脂质增加了50%。这些数据表明,CYP1A2酶可能具有其他的肝脏内源性功能,迄今为止尚未被认识到。
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引用次数: 0
Exploiting genome data to understand the function, regulation, and evolutionary origins of toxicologically relevant genes. 利用基因组数据了解毒理学相关基因的功能、调控和进化起源。
Nazzareno Ballatori, James L Boyer, John C Rockett

The wealth of new information coming from the many genome sequencing projects is providing unprecedented opportunities for major advances in all areas of biology, including the environmental health sciences. To facilitate this discovery process, experts in the fields of functional genomics and informatics and the emerging field of toxicogenomics recently gathered at the Mount Desert Island Biological Laboratory in Salisbury Cove, Maine, site of a National Institute of Environmental Health Sciences Marine and Freshwater Biomedical Science Center, to share their ideas and latest research findings. The goal of the symposium was to highlight approaches that may be used to identify and characterize toxicologically relevant genes being discovered in the genome sequencing projects. Many of the approaches rely heavily on comparative models as a way of identifying gene homology, ontology, and physiologic function, and on the availability of databases that facilitate storage, analysis, interpretation, and widespread dissemination of relevant data.

来自许多基因组测序项目的大量新信息为包括环境健康科学在内的所有生物学领域的重大进展提供了前所未有的机会。为了促进这一发现过程,功能基因组学和信息学领域的专家以及新兴的毒物基因组学领域的专家最近聚集在缅因州索尔兹伯里湾的Mount Desert Island生物实验室,该实验室是国家环境健康科学研究所海洋和淡水生物医学科学中心的所在地,分享他们的想法和最新的研究成果。研讨会的目的是强调可用于鉴定和描述基因组测序项目中发现的毒理学相关基因的方法。许多方法严重依赖比较模型作为识别基因同源性、本体论和生理功能的方法,并依赖于数据库的可用性,以促进相关数据的存储、分析、解释和广泛传播。
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引用次数: 0
The new biology. 新生物学。
Tina Adler
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引用次数: 0
Systems toxicology and the Chemical Effects in Biological Systems (CEBS) knowledge base. 系统毒理学和生物系统中的化学效应(CEBS)知识库。
Michael Waters, Gary Boorman, Pierre Bushel, Michael Cunningham, Rick Irwin, Alex Merrick, Kenneth Olden, Richard Paules, James Selkirk, Stanley Stasiewicz, Brenda Weis, Ben Van Houten, Nigel Walker, Raymond Tennant

The National Center for Toxicogenomics is developing the first public toxicogenomics knowledge base that combines molecular expression data sets from transcriptomics, proteomics, metabonomics, and conventional toxicology with metabolic, toxicologcal pathway, and gene regulatory network information relevant to environmental toxicology and human disease. It is called the Chemical Effects in Biological Systems (CEBS) knowledge base and is designed to meet the information needs of "systems toxicology," involving the study of perturbation by chemicals and stressors, monitoring changes in molecular expression and conventional toxicological parameters, and iteratively integrating biological response data to describe the functioning organism. Based upon functional genomics approaches used successfully in analyzing yeast gene expression data sets, relational and descriptive compendia will be assembled for toxicologically important genes, groups of genes, single nucleotide polymorphisms (SNPs), and mutant and knockout phenotypes. CEBS data sets will be fully documented in the experimental protocol and therefore searchable by compound, structure, toxicity end point, pathology and point, gene, gene group, SNP, pathway, and network as a function of dose, time, and the phenotype of the target tissue. A knowledge base is being developed by assimilating toxicological, biological, and chemical information from multiple public domain databases and by progressively refining that information about gene, protein, and metabolite expression for classes of chemicals and their biological effects in various species. By analogy to the GenBank database for genome sequences, researchers will globally query (or BLAST) CEBS using a transcriptome of a tissue of interest (or a list of outliers) to have the knowledge base return information on genes, groups of genes, metabolic and toxicological pathways, and contextually associated phenotypic information for compounds that display similar response profiles. With high-quality data content, CEBS will ultimately become a resource to support hypothesis-driven and discovery research that contributes effectively to drug safety and the improvement of risk assessments for chemicals in the environment. The CEBS development effort will span a decade or more.

国家毒理学基因组学中心正在开发第一个公共毒理学基因组学知识库,该知识库将转录组学、蛋白质组学、代谢组学和传统毒理学的分子表达数据集与与环境毒理学和人类疾病相关的代谢、毒理学途径和基因调控网络信息相结合。它被称为生物系统中的化学效应(CEBS)知识库,旨在满足“系统毒理学”的信息需求,涉及化学物质和应激源的扰动研究,监测分子表达和常规毒理学参数的变化,并迭代整合生物反应数据以描述功能生物体。基于在分析酵母基因表达数据集中成功使用的功能基因组学方法,将为毒理学上重要的基因、基因群、单核苷酸多态性(SNPs)以及突变和敲除表型组装相关和描述性纲要。CEBS数据集将在实验方案中完整记录,因此可以根据化合物、结构、毒性终点、病理和点、基因、基因组、SNP、途径和网络作为剂量、时间和靶组织表型的函数进行搜索。通过吸收来自多个公共领域数据库的毒理学、生物学和化学信息,并逐步提炼关于各类化学品及其在不同物种中的生物效应的基因、蛋白质和代谢物表达的信息,正在建立一个知识库。通过类比GenBank基因组序列数据库,研究人员将使用感兴趣组织的转录组(或异常值列表)全局查询(或BLAST) CEBS,以使知识库返回有关基因、基因组、代谢和毒理学途径的信息,以及显示相似反应概况的化合物的上下文相关表型信息。有了高质量的数据内容,CEBS最终将成为支持假设驱动和发现研究的资源,有效地促进药物安全和改进环境中化学品的风险评估。CEBS开发工作将跨越十年或更长时间。
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引用次数: 0
HapMap: building a database with blocks. HapMap:用块构建数据库。
Charles W Schmidt
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引用次数: 12
National Center for Toxicogenomics: an introduction. 国家毒物基因组学中心:简介。
James K Selkirk
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引用次数: 0
期刊
EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences
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