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Mitochondria‐Specific Mouse Gene Array and its Application in Toxicogenomics 线粒体特异性小鼠基因阵列及其在毒物基因组学中的应用
Pub Date : 2011-09-15 DOI: 10.1002/9780470744307.GAT209
V. Desai
In recent years, mitochondria have gained significant attention in toxicology because of their involvement in several drug-induced toxicities and in the pathogenesis of a number of degenerative diseases. Thus far, numerous molecular and biochemical assays have been developed and utilized to understand the association between mitochondria and drug toxicities or disease processes. However, the knowledge gained by these assays is inadequate to obtain a comprehensive outlook of the mitochondrial activity during toxic exposures and the underlying pathologies. High-throughput technologies, such as DNA microarray, have great potential in advancing genomic research in toxicology. This technology allows expression profiling of thousands of genes in a single experiment. Building on this technology, a mitochondria-specific mouse oligonucleotide microarray (MitoChip) was developed, which is described in this review. This review also discusses results generated using the MitoChip in studies that were designed to elucidate the molecular mechanisms of altered mitochondrial function induced by anti-HIV drugs (zidovudine and lamivudine) and a weight-loss dietary supplement (usnic acid) in mice. The results from these studies clearly demonstrate that the MitoChip is a valuable genomic tool and can help unravel the underlying molecular basis of impaired mitochondrial function in drug-induced toxicities. Keywords: anti-HIV drugs; gene expression profiles; mitochondria; MitoChip; mouse; usnic acid
近年来,线粒体在毒理学中引起了极大的关注,因为它们参与了几种药物诱导的毒性和许多退行性疾病的发病机制。到目前为止,已经开发了许多分子和生化分析方法,并用于了解线粒体与药物毒性或疾病过程之间的关系。然而,通过这些检测获得的知识不足以全面了解毒性暴露期间的线粒体活性和潜在病理。DNA微阵列等高通量技术在推进毒理学基因组研究方面具有巨大潜力。这项技术允许在一次实验中对数千个基因进行表达谱分析。在此基础上,研制了线粒体特异性小鼠寡核苷酸微阵列(MitoChip)。本综述还讨论了使用MitoChip在研究中产生的结果,这些研究旨在阐明抗hiv药物(齐多夫定和拉米夫定)和减肥膳食补充剂(usnic酸)诱导小鼠线粒体功能改变的分子机制。这些研究的结果清楚地表明,MitoChip是一种有价值的基因组工具,可以帮助揭示药物诱导毒性中线粒体功能受损的潜在分子基础。关键词:抗hiv药物;基因表达谱;线粒体;MitoChip;鼠标;地衣酸
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引用次数: 0
Next-Generation Sequencing: A Revolutionary Tool for Toxicogenomics 新一代测序:毒物基因组学的革命性工具
Pub Date : 2011-09-15 DOI: 10.1002/9780470744307.GAT232
Z. Su, B. Ning, H. Fang, H. Hong, R. Perkins, W. Tong, Leming Shi
Over the past five years, DNA sequencing has been undergoing fundamental changes due to the rapid development of next-generation sequencing (NGS) technologies. NGS technologies have been offering unprecedented opportunities for high-throughput functional genomic research, and opening up new fields and novel applications in biology, life sciences, and biomedicine. The major advantages of NGS technologies over conventional Sanger sequencing include sequencing cost reduction from about 0.50 per kilobase to as little as 0.001 per kilobase, and massive parallelism that dramatically increases sequencing throughput. However, Sanger-based approaches provide advantages in terms of read-length and base call accuracy. In this chapter, we first describe the fundamental principles of four currently commercialized NGS platforms from Roche/454, Illumina, Life Technologies, and Helicos BioSciences. Next we discuss the challenges in analyzing short reads from NGS, and outline major applications of these new technologies. Finally, we compare data between NGS and microarrays with a toxicogenomics study aiming at gene expression profiling. Keywords: next-generation sequencing (NGS); ultra high-throughput sequencing; RNA-Seq; ChIP-Seq; transcriptome; toxicogenomics; sequence alignment
在过去的五年中,由于下一代测序技术的快速发展,DNA测序发生了根本性的变化。NGS技术为高通量功能基因组研究提供了前所未有的机遇,并在生物学、生命科学和生物医学领域开辟了新的领域和新的应用。与传统的Sanger测序相比,NGS技术的主要优势包括测序成本从每千碱基0.50降低到每千碱基0.001,以及大量并行性大大提高了测序吞吐量。然而,基于sanger的方法在读取长度和基本调用精度方面具有优势。在本章中,我们首先描述了四个目前商业化的NGS平台的基本原理,这些平台来自Roche/454、Illumina、Life Technologies和Helicos BioSciences。接下来,我们将讨论分析NGS短读数所面临的挑战,并概述这些新技术的主要应用。最后,我们通过针对基因表达谱的毒物基因组学研究比较了NGS和微阵列之间的数据。关键词:新一代测序;超高通量测序;RNA-Seq;ChIP-Seq;转录组;toxicogenomics;序列比对
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引用次数: 6
Biomarkers of System Response to Therapeutic Intervention 系统对治疗干预反应的生物标志物
Pub Date : 2011-09-15 DOI: 10.1002/9780470744307.GAT238
Ludmila V. Danilova, M. Ochs
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引用次数: 0
Use of Proteomic and Metabolomic Techniques in Ecotoxicological Research 蛋白质组学和代谢组学技术在生态毒理学研究中的应用
Pub Date : 2011-09-15 DOI: 10.1002/9780470744307.GAT215
M. Sepúlveda, K. Ralston-Hooper, Brian C. Sanchez, Amber Hopf-jannasch, S. D. Baker, N. Diaz, J. Adamec
Over the last decade, the environmental sciences have witnessed an incredible movement towards the utilization of high through-put molecular tools that are capable of detecting simultaneous changes of hundreds and even thousands of molecules and molecular components after exposure of organisms to different environmental stressors. These techniques have received lots of attention because they not only offer the potential to unravel novel mechanisms of physiological and toxic action, but they also are amenable for the discovery of biomarkers of exposure and effects. In this chapter we will review the state of knowledge of two of these holistic tools in ecotoxicological research: Proteomics and metabolomics. We will follow this review with a presentation of three of our own case studies utilizing proteomic and metabolomic tools: (i) Analysis of proteomic responses in fish exposed to different types of contaminants using GeneGo™; (ii) Comparison of proteomic and metabolomic responses in aquatic invertebrates exposed to herbicides; and (ii) Use of metabolomics to characterize egg quality in fish eating birds exposed to persistent organic pollutants. We will end with some ideas for future studies and research needs. Keywords: proteomics; metabolomics; ecotoxicology; fish; invertebrates; birds; aquatic; wildlife; biomarkers; contaminants; toxicity; pollution
在过去的十年中,环境科学在利用高通量分子工具方面取得了令人难以置信的进展,这些工具能够检测生物体暴露于不同环境压力后数百甚至数千个分子和分子成分的同时变化。这些技术受到了广泛的关注,因为它们不仅提供了揭示生理和毒性作用新机制的潜力,而且它们也适用于发现暴露和影响的生物标志物。在本章中,我们将回顾生态毒理学研究中两个整体工具的知识状况:蛋白质组学和代谢组学。接下来,我们将介绍我们自己使用蛋白质组学和代谢组学工具进行的三个案例研究:(i)使用GeneGo™分析暴露于不同类型污染物的鱼类的蛋白质组学反应;比较接触除草剂的水生无脊椎动物的蛋白质组学和代谢组学反应;(二)利用代谢组学表征暴露于持久性有机污染物的食鱼鸟类的蛋质量。最后,我们将对未来的研究和研究需求提出一些想法。关键词:蛋白质组学;代谢组学;生态毒理学;鱼;无脊椎动物;鸟类;水生的;野生动物;生物标志物;污染物;毒性;污染
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引用次数: 3
Application of Metabonomic Approach in Target Organ Toxicity 代谢组学方法在靶器官毒性中的应用
Pub Date : 2011-09-15 DOI: 10.1002/9780470744307.GAT220
Athina Zira, S. Theocharis
The report and understanding of interactions among genes, proteins and metabolites is of crucial importance in the classification of mechanisms involved in chemical/drug-induced toxicity. Consequently, the application of the “omics” technologies (genomics, proteomics and metabonomics), and mainly metabonomics, is imperative in toxicological studies. Metabonomics has been widely used in established models of target organ toxicity in order to monitor the effect of the toxic agents and possibly identify novel biomarkers of toxicity. In the present review, the applications of metabonomics in toxicological studies have been reported. Although limitations from the use of this technology in toxicology still exist, its combination with genomics and proteomics could provide valuable information for the underlying mechanisms of target organ toxicity. Keywords: brain; heart; kidney; liver; metabolomics; toxicity
基因、蛋白质和代谢物之间相互作用的报道和理解对于化学/药物诱导毒性的机制分类至关重要。因此,“组学”技术(基因组学、蛋白质组学和代谢组学),尤其是代谢组学在毒理学研究中的应用势在必行。代谢组学已广泛应用于已建立的靶器官毒性模型,以监测毒性药物的作用并可能识别新的毒性生物标志物。本文综述了代谢组学在毒理学研究中的应用。尽管该技术在毒理学中的应用仍然存在局限性,但它与基因组学和蛋白质组学的结合可以为靶器官毒性的潜在机制提供有价值的信息。关键词:大脑;心;肾脏;肝;代谢组学;毒性
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引用次数: 1
Implementing Systems Toxicology in Drug Development for Regulatory Decision Making 在药物开发中实施系统毒理学以进行监管决策
Pub Date : 2011-09-15 DOI: 10.1002/9780470744307.GAT248
J. Sina, F. Sistare
The concept of integrating molecular and biochemical data from new technologies with more traditional endpoints to develop a more complete understanding of risks and benefits in drug development has gained wide acceptance as a reasonable way to advance human health. However, actual implementation of this systems approach is not straightforward. While technology keeps advancing, our ability to accurately interpret the complexity of human biology has not kept pace. Indeed, sometimes the case seems to be one of the deeper we investigate, the more we realize what we do not understand. Additionally, in developing ethical pharmaceuticals, a major issue is establishing the necessary level of confidence to extrapolate from a series of endpoint measurements to accurately predict beneficial and/or potentially adverse responses in the diverse population of patients. The evidentiary standard for acceptance of new models and biomarkers in clinical practice is necessarily high, although the concept of “fit-for-purpose” may help expedite the application of new knowledge in specific clinical situations. This chapter will present a view of both the progress and hurdles to applying systems toxicology to drug development in a regulated environment. Keywords: systems toxicology; drug development; biomarkers; clinical translation; pre-clinical; pathways; review; genomics; metabolomics; proteomics
将来自新技术的分子和生化数据与更传统的端点相结合,以更全面地了解药物开发中的风险和益处,这一概念作为促进人类健康的合理途径已得到广泛接受。然而,这种系统方法的实际实现并不简单。虽然技术不断进步,但我们准确解释人类生物学复杂性的能力却没有跟上。的确,有时案件似乎是我们调查得越深,我们就越意识到我们不了解的东西。此外,在开发符合伦理的药物时,一个主要问题是建立必要的信心水平,以便从一系列终点测量中推断出准确预测不同患者群体的有益和/或潜在不良反应。在临床实践中接受新模型和生物标志物的证据标准必须很高,尽管“符合目的”的概念可能有助于加快新知识在特定临床情况下的应用。本章将介绍在监管环境下将系统毒理学应用于药物开发的进展和障碍。关键词:系统毒理学;药物开发;生物标志物;临床翻译;临床前;通路;审查;基因组学;代谢组学;蛋白质组学
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引用次数: 0
Systems Modeling in Developmental Toxicity 发育毒性的系统建模
Pub Date : 2011-09-15 DOI: 10.1002/9780470744307.GAT236
T. Knudsen, R. Dewoskin
High-throughput or high-content studies are now providing a rich source of data that can be applied to in vitro profiling of chemical compounds for biological activity and potential in vivo toxicity. EPA's ToxCast™ project, and the broader Tox21 consortium, as well as other projects worldwide, are providing high-throughput and high-content screening data (HTS-HCS) focusing on the in vitro targets and cellular bioactivity profiles for thousands of chemical compounds in commerce or entering the environment. A goal of chemical profiling is to rapidly identify and efficiently classify signatures of biological activity that are potentially diagnostic of in vivo toxicities using automated technologies. Predictive modeling of developmental toxicity faces several challenges: correlating in vitro concentration–response with internal dose–response kinetics; understanding how in vitro bioactivity profiles extrapolate from one cell-type or technology platform to another; and linking individual targets of in vitro bioactivity to complex signatures associated with pathways of in vivo toxicity. Toxicity in the intact organism is an expression of complex and interwoven events that follow from cellular perturbations. As such, multicellular computer models known as ‘virtual tissues’ that recapitulate developmental events can provide a technology platform to simulate non-linear behaviors of dynamical systems and to model perturbations. A virtual embryo, for example, might be envisaged as a toolbox of computational (in silico) models that execute morphogenetic programs to simulate developmental toxicity. Keywords: computational toxicology; high-throughput; screening; developmental toxicity; chemical profiling; toxicity pathways; predictive models; risk assessment; mechanistic models; systems biology; virtual tissues
高通量或高含量的研究现在提供了丰富的数据来源,可用于化合物的生物活性和潜在的体内毒性的体外分析。EPA的ToxCast™项目,以及更广泛的Tox21联盟,以及全球其他项目,正在提供高通量和高含量筛选数据(HTS-HCS),重点关注数千种商业或进入环境的化合物的体外靶点和细胞生物活性概况。化学分析的目标是使用自动化技术快速识别和有效分类生物活性的特征,这些特征可能用于体内毒性的诊断。发育毒性的预测建模面临几个挑战:将体外浓度-反应与体内剂量-反应动力学相关联;了解体外生物活性概况如何从一种细胞类型或技术平台推断到另一种;并将体外生物活性的单个目标与体内毒性途径相关的复杂特征联系起来。完整生物体的毒性是由细胞扰动引起的复杂和相互交织的事件的表达。因此,被称为“虚拟组织”的多细胞计算机模型概括了发育事件,可以提供一个技术平台来模拟动力系统的非线性行为和模拟扰动。例如,虚拟胚胎可以设想为一个计算(计算机)模型的工具箱,执行形态发生程序来模拟发育毒性。关键词:计算毒理学;高通量;筛选;发育毒性;化学分析;毒性通路;预测模型;风险评估;机械模型;系统生物学;虚拟组织
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引用次数: 5
Toxicity of Selenium Compounds and Nano‐Selenium Particles 硒化合物和纳米硒颗粒的毒性
Pub Date : 2011-09-15 DOI: 10.1002/9780470744307.GAT243
Jinsong Zhang, J. Spallholz
Selenium is a necessary dietary constituent of at least 25 human selenoproteins and enzymes all containing selenocysteine. In excessive amounts, all selenium compounds become toxic in a dose-dependent fashion to cells in vitro and to the primary target tissue of chronic selenium toxicity, the liver. Elemental selenium of zero valence state has long been considered to be biologically inert. With bovine serum albumin or other dispersant agents such as polysaccharide, biologically active nano-selenium particles (Nano-Se) are formed from sodium selenite and glutathione. Different from the biologically inert black elemental selenium with coarse size, red Nano-Se manifests toxicity which conforms to the concern of nanotoxicity. However, compared with selenium compounds such as sodium selenite, selenomethionine and Se-methylselenocysteine, Nano-Se is not compromised in increasing the activities of selenoenzymes including glutathione peroxidase and thioredoxin reductase at nutritional levels and phase 2 detoxification enzymes such as glutathione S-transferase at supranutritional levels, but exhibits much lower toxicities. Nano-Se is thus a potential selenium source with a prominent characteristic of lower toxicity for supplementation. Keywords: toxicity; selenite; selenomethionine; Se-methylselenocysteine; nano-selenium particles
硒是至少25种含硒半胱氨酸的人体硒蛋白和酶的必需膳食成分。在过量的情况下,所有硒化合物都以剂量依赖的方式对体外细胞和慢性硒毒性的主要靶组织——肝脏产生毒性。零价态硒一直被认为是生物惰性元素。用牛血清白蛋白或其他分散剂如多糖,亚硒酸钠和谷胱甘肽形成具有生物活性的纳米硒颗粒(纳米硒)。不同于黑色元素硒的生物惰性和粗粒度,红色纳米硒具有毒性,符合纳米毒性的关注。然而,与亚硒酸钠、硒代蛋氨酸和硒甲基硒半胱氨酸等硒化合物相比,纳米硒在营养水平上并不影响谷胱甘肽过氧化物酶和硫氧还蛋白还原酶等硒酶的活性,在超营养水平上也不影响谷胱甘肽s -转移酶等2期解毒酶的活性,但毒性要低得多。因此,纳米硒是一种潜在的硒源,具有补充毒性较低的突出特点。关键词:毒性;亚硒酸盐;硒代蛋氨酸;Se-methylselenocysteine;nano-selenium粒子
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引用次数: 34
Cardiac Toxicity of Anthracyclines 蒽环类药物的心脏毒性
Pub Date : 2009-12-15 DOI: 10.1002/9780470744307.GAT177
R. Olson, B. Cusack
Cardiotoxicity of anthracyclines limits their therapeutic potential. In the in vitro acute model, anthracyclines produce cardiotoxicity in minutes or hours at concentrations near 100 μM, through a mechanism involving impairment of sarcoplasmic reticulum (SR) function and requiring the quinone moiety, most likely through a non-free-radical process. The chronic cardiotoxicity is more complex, but may also involve SR. Additional mechanisms in the chronic model of anthracycline cardiotoxicity may include impairment of triiodothyronine function, cardiac protein degradation, free-radical generation, apoptosis, cardiac metabolite formation, impairment of iron metabolism and oestrogen-dependent up-regulation of nitric oxide synthase (NOS). Thus, prevention or attenuation of anthracycline cardiotoxicity may be achieved by favourably manipulating these mechanisms.Keywords:anthracyclines;cardiotoxicity;heart failure;calcium;free radicals;ageing
蒽环类药物的心脏毒性限制了其治疗潜力。在体外急性模型中,在浓度接近100 μM的情况下,蒽环类药物在几分钟或几小时内产生心脏毒性,其机制涉及肌浆网(SR)功能受损,并需要醌部分,最可能是通过非自由基过程。慢性心脏毒性更为复杂,但也可能涉及到衰老。蒽环类药物慢性心脏毒性模型的其他机制可能包括三碘甲状腺原氨酸功能损害、心脏蛋白质降解、自由基产生、细胞凋亡、心脏代谢物形成、铁代谢损害和雌激素依赖性一氧化氮合酶(NOS)上调。因此,通过控制这些机制可以预防或减轻蒽环类药物的心脏毒性。关键词:蒽环类药物;心脏毒性;心力衰竭
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引用次数: 1
Endocrine Disruption in Toxic Responses 毒性反应中的内分泌干扰
Pub Date : 2009-12-15 DOI: 10.1002/9780470744307.GAT018
S. Kitamura, K. Sugihara, Kazuo Nakamura, Y. Kotake, A. Kashiwagi, N. Fujimoto
Many endocrine-disrupting agents, including industrial materials, pesticides, pharmaceuticals and phytochemicals, have been identified with their use by in vitro assay systems and in vivo studies in laboratory animals. These chemicals are widely distributed in the environment, and are able to mimic or antagonize the biological functions of natural hormones. Indeed, abnormalities thought to be due to such agents have been found in animals throughout the world. There is also thought to be a risk to humans, for example, DES syndrome. Xenoestrogens can accumulate in our environment, and may play a role in the increasing incidences of breast cancer, testicular cancer and other problems of the reproductive system in humans. Risks due to endocrine disruptors in the environment are discussed in this chapter. Keywords: endocrine disrupting activity; oestrogen; antiandrogen; reproductive system; central nervous system; immune system
许多内分泌干扰剂,包括工业材料、杀虫剂、药物和植物化学物质,已经通过体外分析系统和实验室动物体内研究确定了它们的用途。这些化学物质广泛分布于环境中,能够模仿或对抗天然激素的生物功能。事实上,在世界各地的动物身上都发现了被认为是由这些药物引起的异常。也被认为对人类有风险,例如DES综合征。异种雌激素可以在我们的环境中积累,并可能在乳腺癌、睾丸癌和人类生殖系统其他问题的发病率上升中发挥作用。本章将讨论环境中内分泌干扰物的风险。关键词:内分泌干扰活性;雌激素;抗雄激素;生殖系统;中枢神经系统;免疫系统
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引用次数: 0
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General, Applied and Systems Toxicology
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