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Systems biology approaches to interpreting genomic data 解释基因组数据的系统生物学方法
IF 4.6 Pub Date : 2019-12-01 DOI: 10.1016/j.cotox.2019.02.004
Twan van den Beucken

Technological developments in genome-wide analysis have accelerated the generation of large, complex data sets characterizing human biology at the molecular level. Integration of data from different molecular levels holds great promise for gaining understanding of complex biological systems. Toxicogenomics aims to obtain a comprehensive mechanistic map of cellular processes that drive adverse outcomes. Such an integrated approach relies on combining various genome-wide profiles (DNA, RNA, protein, and metabolite) and linking these to functional endpoints to allow the identification of relevant biological pathways. Here, current strategies for generating multiomic data within the domain of toxicogenomics are highlighted, and current strategies for multiomic data integration are discussed.

全基因组分析的技术发展加速了在分子水平上表征人类生物学的大型、复杂数据集的产生。整合来自不同分子水平的数据对于理解复杂的生物系统大有希望。毒物基因组学旨在获得驱动不良结果的细胞过程的综合机制图。这种综合方法依赖于结合各种全基因组图谱(DNA、RNA、蛋白质和代谢物),并将它们与功能端点连接起来,从而识别相关的生物学途径。在这里,毒物基因组学领域内生成多组数据的当前策略被强调,并讨论了多组数据集成的当前策略。
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引用次数: 3
Microphysiological systems in the evaluation of hematotoxicities during drug development 药物开发过程中评估血液毒性的微生理系统
IF 4.6 Pub Date : 2019-10-01 DOI: 10.1016/j.cotox.2019.09.008
Eva-Maria Dehne, Annika Winter, Uwe Marx

Microphysiological systems are progressively entering the pharmaceutical industry, and various systems have already proven to be highly valuable at different stages of the drug development process. The field of hematotoxicity research has so far received only minor attention, even though microphysiological systems might provide key benefits over current assays. In this review, we will highlight the need for more complex human in vitro assays, and how emerging technologies such as microphysiological systems present novel solutions for the study of adverse hematologic effects.

微生理系统正逐步进入制药行业,各种系统已被证明在药物开发过程的不同阶段具有很高的价值。迄今为止,血液毒性研究领域只受到很少的关注,尽管微生理系统可能比目前的检测方法提供关键的好处。在这篇综述中,我们将强调对更复杂的人体体外检测的需求,以及微生理系统等新兴技术如何为血液不良反应的研究提供新的解决方案。
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引用次数: 4
Biomarkers of platelet dysfunction in non-clinical safety studies and humans 血小板功能障碍的生物标志物在非临床安全性研究和人类
IF 4.6 Pub Date : 2019-10-01 DOI: 10.1016/j.cotox.2019.11.001
James D. Smith , Padmakumar Narayanan , Nianyu Li

Platelets are small, anuclear, cellular components of blood with a primary role in hemostasis but emerging roles in tissue homeostasis, immunity and disease. Established clinical evaluations of platelets monitor and characterize certain risks of platelet dysfunction but only yield limited understanding of the mechanism underlying the dysfunction. Here we evaluate technically feasible and accessible biomarkers of platelet function with the potential to sensitively and specifically monitor platelet biology complementing standard platelet indices. These biomarkers are also discussed in the context of their usefulness to monitor platelet–tissue interactions beyond hemostasis. Tools available to evaluate pharmaceutical-induced platelet risks in the clinic and in preclinical animal studies are also introduced.

血小板是血液中小的、无核的细胞成分,主要作用是止血,但在组织稳态、免疫和疾病中也有新的作用。已建立的血小板临床评估监测和表征血小板功能障碍的某些风险,但对功能障碍的机制了解有限。在这里,我们评估技术上可行和可获得的血小板功能生物标志物,具有敏感性和特异性监测血小板生物学的潜力,补充标准血小板指标。这些生物标志物也在其有用性的背景下进行了讨论,以监测止血之外的血小板-组织相互作用。还介绍了在临床和临床前动物研究中评估药物诱导血小板风险的工具。
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引用次数: 0
Drug-induced thrombocytopenia: mechanisms and relevance in preclinical safety assessment 药物诱导的血小板减少症:临床前安全性评估的机制和相关性
IF 4.6 Pub Date : 2019-10-01 DOI: 10.1016/j.cotox.2019.10.002
Padma Kumar Narayanan , Scott Henry , Nianyu Li

Thrombocytopenia is one of the most commonly observed drug-induced adverse hematologic toxicities in the clinic. Therefore, in vitro and in vivo evaluations of effect of drugs on platelets are an important component in preclinical safety assessment in drug development. To date, a number of mechanisms have been identified to be associated with drug-mediated thrombocytopenia. Amongst these, some are conserved across species whereas others are not. Therefore, a case-by-case approach is needed to assess drug-induced thrombocytopenia at preclinical stages to understand translatability to humans. The present chapter reviews mechanisms in drug-mediated thrombocytopenia with a focus on nonimmune (direct myelotoxicity) as well as immune-mediated thrombocytopenia by both small and large molecule therapeutics. Several in vitro and in vivo models as well as challenges in assessing drug-mediated thrombocytopenia in preclinical stages will also be discussed.

血小板减少症是临床上最常见的药物引起的不良血液学毒性之一。因此,体外和体内评价药物对血小板的影响是药物开发临床前安全性评估的重要组成部分。迄今为止,许多机制已确定与药物介导的血小板减少症有关。其中,有些是跨物种保守的,而另一些则不是。因此,在临床前阶段评估药物诱导的血小板减少症,以了解对人类的可转译性,需要具体情况具体分析。本章回顾了药物介导的血小板减少的机制,重点是小分子和大分子治疗的非免疫性(直接骨髓毒性)和免疫介导的血小板减少。几个体外和体内模型以及评估药物介导的血小板减少症在临床前阶段的挑战也将被讨论。
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引用次数: 5
Methods for measurement of platelet function in the assessment of nonclinical drug safety and implications for translatability 血小板功能在非临床药物安全性评估中的测量方法及其可翻译性
IF 4.6 Pub Date : 2019-10-01 DOI: 10.1016/j.cotox.2019.10.005
David Ledieu, Serge Côté

Platelets play a pivotal role in normal hemostasis. Drug-induced derangement of platelet function can lead to either an increased bleeding risk when platelet function is inhibited or a proaggregant state that can manifest as thrombosis when it is exacerbated. In both cases, drug-induced platelet dysfunction can lead to serious adverse events in patients that can limit drug prescription or ultimately lead to the withdrawal of the drug from the market. Despite those risks, drug-induced platelet function defects do not appear to be highlighted during drug development; rather they are reported at the postapproval stage indicating that current preclinical assays and clinical development studies are failing to capture these liabilities. However, significant progresses have been made in platelet function testing and clinically useful methods now exist for the measurement of platelet function. This review article discusses these methods and describes their advantages and disadvantages in the setting of nonclinical drug safety to assess drug-induced platelet dysfunction and on the translatability of these tests to predict thrombosis and bleeding in patients.

血小板在正常止血中起关键作用。药物引起的血小板功能紊乱,当血小板功能受到抑制时,可导致出血风险增加;当血小板功能紊乱加剧时,可导致凝血状态,表现为血栓形成。在这两种情况下,药物引起的血小板功能障碍都可能导致患者发生严重的不良事件,从而限制药物处方或最终导致药物退出市场。尽管存在这些风险,但药物诱导的血小板功能缺陷在药物开发过程中似乎并未得到重视;相反,它们是在批准后阶段报告的,这表明目前的临床前分析和临床开发研究未能捕捉到这些责任。然而,血小板功能的检测已经取得了重大进展,目前已有临床有用的血小板功能检测方法。这篇综述文章讨论了这些方法,描述了它们在评估药物性血小板功能障碍的非临床药物安全性方面的优缺点,以及这些测试在预测患者血栓和出血方面的可翻译性。
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引用次数: 1
Off-target drug effects on platelet function: Protecting an Achilles heel of drug development 脱靶药物对血小板功能的影响:保护药物开发的致命弱点
IF 4.6 Pub Date : 2019-10-01 DOI: 10.1016/j.cotox.2019.09.004
James D. McFadyen , Himawan Fernando , Karlheinz Peter

The development of new drugs is often limited or even halted by their side effects on platelet number or function. This review introduces the signalling pathways and the role of various platelet receptors, such as GPIIb/IIIa, GPIb-IX-V, GPVI and P-selectin. The large scope of platelet function tests are described, including aggregometry, flow cytometry, VerifyNow, adhesion and in vivo thrombosis and haemostasis assays. Several important examples of drugs that have off-target effects influencing platelet function are discussed, including GPIIb/IIIa inhibitors, oligonucleotides, BH3 mimetics and Bruton tyrosine kinase inhibitors. Finally, challenges for future drug development with regards to platelet function are outlined, including the conclusion that no single assay can fully predict drug effects and thus a combination of platelet function tests is often required to assess platelet function in the context of newly developed therapeutics.

新药的开发常常因其对血小板数量或功能的副作用而受到限制甚至停止。本文综述了血小板受体GPIIb/IIIa、GPIb-IX-V、GPVI和p -选择素等的信号通路及其作用。描述了大范围的血小板功能测试,包括聚集、流式细胞术、VerifyNow、粘连和体内血栓形成和止血试验。本文讨论了几种具有脱靶效应影响血小板功能的药物,包括GPIIb/IIIa抑制剂、寡核苷酸、BH3模拟物和布鲁顿酪氨酸激酶抑制剂。最后,概述了未来药物开发中血小板功能方面的挑战,包括没有单一的检测方法可以完全预测药物作用的结论,因此在新开发的治疗方法中,通常需要结合血小板功能测试来评估血小板功能。
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引用次数: 1
Organs-on-Chips: a new paradigm for safety assessment of drug-induced thrombosis 芯片上的器官:药物诱导血栓形成安全性评估的新范式
IF 4.6 Pub Date : 2019-10-01 DOI: 10.1016/j.cotox.2019.08.004
Patrick Ng , Chaitra Belgur , Sonalee Barthakur , Andries D. van der Meer , Geraldine A. Hamilton , Riccardo Barrile

Blood hypercoagulability and thrombosis have been observed in patients during clinical trials of candidate drugs, yet these safety risks are seldom identified during preclinical testing, leading to increased mortality and morbidity, and increased attrition rates in the clinic. Current preclinical models — standard cell cultures, flow chambers, and animal models — are often ill-equipped to predict thrombosis in the clinic. In vitro models are typically assembled without critical biomechanical forces, such as shear stress and mechanical strain, or relevant cytoarchitecture, such as interactions between different tissue types, which are essential to physiological function. In addition, animal models not only are expensive and costly but also possess inherent cross-species biological differences that are difficult, if not impossible, to reconcile for accurate human predictions. As a preclinical platform with a potentially higher predictive value, organs-on-chips are fluidic systems that reproduce organ-level function via cellular components of human origin, tissue–tissue interfaces, and dynamic mechanical forces. Compared with other current preclinical models, organs-on-chips combine the advantages of tunability and ease of biochemical, histological, and image analysis, while bypassing difficulties in cross-species translation. In this review, we delineate the limitations of current preclinical models, which are often unable to predict drug-induced thrombosis, and report some recent advancements in Organs-on-Chips technology that represent a promising alternative for modeling tissue-specific thrombotic events and derisking next-generation drug discovery.

在候选药物的临床试验中,已经观察到患者的血液高凝性和血栓形成,但在临床前试验中很少发现这些安全风险,导致死亡率和发病率增加,增加了临床的损耗率。目前的临床前模型——标准细胞培养、流动室和动物模型——在临床预测血栓形成方面往往装备不足。体外模型通常没有关键的生物力学力,如剪切应力和机械应变,或相关的细胞结构,如不同组织类型之间的相互作用,这是生理功能所必需的。此外,动物模型不仅昂贵昂贵,而且具有固有的跨物种生物学差异,即使不是不可能,也很难调和这些差异以进行准确的人类预测。作为一个具有潜在更高预测价值的临床前平台,芯片上的器官是一种流体系统,它通过人类起源的细胞成分、组织-组织界面和动态机械力来重现器官水平的功能。与目前其他临床前模型相比,器官芯片结合了生物化学、组织学和图像分析的可调性和易用性的优势,同时绕过了跨物种翻译的困难。在这篇综述中,我们描述了目前临床前模型的局限性,这些模型通常无法预测药物引起的血栓形成,并报告了器官芯片技术的一些最新进展,这些技术代表了组织特异性血栓形成事件建模和降低下一代药物发现风险的有前途的替代方案。
{"title":"Organs-on-Chips: a new paradigm for safety assessment of drug-induced thrombosis","authors":"Patrick Ng ,&nbsp;Chaitra Belgur ,&nbsp;Sonalee Barthakur ,&nbsp;Andries D. van der Meer ,&nbsp;Geraldine A. Hamilton ,&nbsp;Riccardo Barrile","doi":"10.1016/j.cotox.2019.08.004","DOIUrl":"10.1016/j.cotox.2019.08.004","url":null,"abstract":"<div><p><span>Blood hypercoagulability<span> and thrombosis have been observed in patients during clinical trials<span> of candidate drugs, yet these safety risks are seldom identified during preclinical testing, leading to increased mortality and morbidity, and increased attrition rates in the clinic. Current preclinical models — standard cell cultures, flow chambers, and animal models — are often ill-equipped to predict thrombosis in the clinic. </span></span></span><em>In vitro</em><span> models are typically assembled without critical biomechanical forces, such as shear stress and mechanical strain, or relevant cytoarchitecture, such as interactions between different tissue types, which are essential to physiological function. In addition, animal models not only are expensive and costly but also possess inherent cross-species biological differences that are difficult, if not impossible, to reconcile for accurate human predictions. As a preclinical platform with a potentially higher predictive value, organs-on-chips are fluidic systems that reproduce organ-level function via cellular components of human origin, tissue–tissue interfaces, and dynamic mechanical forces. Compared with other current preclinical models, organs-on-chips combine the advantages of tunability and ease of biochemical, histological, and image analysis, while bypassing difficulties in cross-species translation. In this review, we delineate the limitations of current preclinical models, which are often unable to predict drug-induced thrombosis, and report some recent advancements in Organs-on-Chips technology that represent a promising alternative for modeling tissue-specific thrombotic events and derisking next-generation drug discovery.</span></p></div>","PeriodicalId":93968,"journal":{"name":"Current opinion in toxicology","volume":null,"pages":null},"PeriodicalIF":4.6,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.cotox.2019.08.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46129810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
A proposal for creating a taxonomy of chemical interactions using concepts from the aggregate exposure and adverse outcome pathways 提出一项利用总暴露和不良后果途径的概念建立化学相互作用分类的建议
IF 4.6 Pub Date : 2019-08-01 DOI: 10.1016/j.cotox.2019.05.007
Paul Price , Jeremy Leonard

Currently, there is no single taxonomy for organizing data on the various types of chemical interactions that may affect risks from combined exposures. A taxonomy of chemical interactions is proposed that is based on a combination of the aggregate exposure pathways (AEPs) and adverse outcome pathways (AOPs) (AEP–AOP framework). The AEP–AOP framework organizes data on the causal events that ocur over the entire source–exposure–response continuum of a chemical's release. The proposed taxonomy uses this framework in two ways. First, four top-level categories are established based on the location in the continuum where a chemical interaction occurs. Second, each top-level category has two or more subcategories that are based on concepts taken from AEPs and AOPs. The categories and subcategories are potentially useful in developing standardized definitions for interaction terms and improving our understanding of the impacts of chemical interactions on risk to human health and the environment.

目前,还没有一个单一的分类法来组织可能影响综合暴露风险的各种化学相互作用的数据。提出了一种化学相互作用的分类法,该分类法基于总暴露途径(AEPs)和不良后果途径(AOPs) (AEP-AOP框架)的组合。AEP-AOP框架组织了在化学物质释放的整个源-暴露-反应连续体中发生的因果事件的数据。建议的分类法以两种方式使用这个框架。首先,根据化学相互作用在连续体中的位置,建立了四个顶级类别。其次,每个顶级类别都有两个或多个子类别,这些子类别基于取自aep和AOPs的概念。这些类别和子类别可能有助于为相互作用术语制定标准化定义,并增进我们对化学相互作用对人类健康和环境风险的影响的理解。
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引用次数: 3
Mechanistic integration of exposure and effects: advances to apply systems toxicology in support of regulatory decision-making 暴露和影响的机制整合:应用系统毒理学支持监管决策的进展
IF 4.6 Pub Date : 2019-08-01 DOI: 10.1016/j.cotox.2019.09.001
Annie M. Jarabek , David E. Hines

Modernizing risk assessment methods that underlie risk management decisions developed to protect public and environmental health will require interdisciplinary dialog and communication. Alignment of exposures across traditional data streams such as data from in vivo laboratory animal and epidemiological or clinical studies, as well as integration of novel data types from emerging testing technologies and new methods of analysis, will improve causal inference. We propose a mechanistic scaffold that supports a source-to-outcome structure and an associated workflow pipeline which facilitates needed data curation and transparency regarding operational assumptions. The scaffold and workflow components enhance the utility and repurposing of data with the flexibility to support regulatory decision-making in a fit-for-purpose fashion. Efficient use of data based on this scaffold across various modeling approaches will promote “one health” characterization to improve, promote, and protect the health of all species and the environment. Associated data standards to facilitate leveraging and sharing of data will increase communication and collaboration across different disciplines to enable that end.

为保护公众和环境健康而制定的风险管理决策所依据的风险评估方法的现代化将需要跨学科的对话和沟通。跨传统数据流(如来自活体实验动物和流行病学或临床研究的数据)的暴露校准,以及来自新兴测试技术和新分析方法的新数据类型的整合,将改善因果推理。我们提出了一个支持源到结果结构的机制框架和一个相关的工作流管道,它促进了所需的数据管理和关于操作假设的透明度。脚手架和工作流组件增强了数据的实用性和重用性,并具有灵活性,可以以适合目的的方式支持监管决策。在各种建模方法中有效利用基于该支架的数据将促进“同一健康”特征,以改善、促进和保护所有物种和环境的健康。促进数据利用和共享的相关数据标准将增加不同学科之间的沟通和协作,从而实现这一目标。
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引用次数: 9
An assessment of environmental health measures in the Deepwater Horizon Research Consortia 深水地平线研究联盟环境健康措施评估
IF 4.6 Pub Date : 2019-08-01 DOI: 10.1016/j.cotox.2019.07.003
Huaqin Pan , Stephen W. Edwards , Cataia Ives , Hannah Covert , Emily W. Harville , Maureen Y. Lichtveld , Jeffrey K. Wickliffe , Carol M. Hamilton

Research consortia play a key role in our understanding of how environmental exposures influence health and wellbeing, especially in the case of catastrophic events such as the Deepwater Horizon oil spill. A common challenge that prevents the optimal use of these data is the difficulty of harmonizing data regarding the environmental exposures and health effects across the studies within and among consortia. A review of the measures used by members of the Deepwater Horizon Research Consortia highlights the challenges associated with balancing timely implementation of a study to support disaster relief with optimizing the long-term value of the data. The inclusion of common, standard measures at the study design phase and a priori discussions regarding harmonization of study-specific measures among consortia members are key to overcoming this challenge. As more resources become available to support the use of standard measures, researchers now have the tools needed to rapidly coordinate their studies without compromising research focus or timely completion of the original study goals.

研究联盟在我们理解环境暴露如何影响健康和福祉方面发挥了关键作用,特别是在深水地平线石油泄漏等灾难性事件的情况下。阻碍这些数据得到最佳利用的一个共同挑战是,难以协调各财团内部和各财团之间关于环境暴露和健康影响的研究数据。对深水地平线研究联盟成员使用的措施进行了回顾,强调了在及时实施研究以支持救灾与优化数据的长期价值之间取得平衡所面临的挑战。在研究设计阶段纳入共同的标准措施,并在财团成员之间先验地讨论如何协调研究特定措施,是克服这一挑战的关键。随着越来越多的资源可用于支持使用标准措施,研究人员现在拥有了快速协调研究所需的工具,而不会影响研究重点或及时完成最初的研究目标。
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引用次数: 3
期刊
Current opinion in toxicology
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