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FAIR-ifying the Exposome Journal: Templates for Chemical Structures and Transformations 公平的暴露期刊:化学结构和转化的模板

Exposome

Pub Date : 2021-12-24 DOI: 10.1093/exposome/osab006

Emma L. Schymanski, Evan E. Bolton

The exposome, the totality of lifetime exposures, is a new and highly complex paradigm for health and disease. Tackling this challenge requires an effort well beyond single individuals or laboratories, where every piece of the puzzle will be vital. The launch of this new Exposome journal coincides with the evolution of the exposome through its teenage years and into a growing maturity in an increasingly open and FAIR (findable, accessible, interoperable, reusable) world. This letter discusses how both authors and the Exposome journal alike can help increase the FAIRness of the chemical structural information and the associated metadata in the journal, aiming to capture more details about the chemistry of exposomics. The proposed chemical structure template can serve as an interoperable supplementary format that is made accessible through the website and more findable by linking the DOI of this data file to the article DOI metadata, supporting further reuse. An additional Transformations template provides authors with a means to connect predecessor (parent, substrate) molecules to successor (transformation product, metabolite) molecules and thus provide FAIR connections between observed (i.e., experimental) chemical exposures and biological responses, to help improve the public knowledgebase on exposome-related transformations. These connections are vital to extend current biochemical knowledge and to fulfil the current Exposome definition of “the cumulative measure of environmental influences and associated biological responses throughout the lifespan including exposures from the environment, diet, behaviour, and endogenous processes”.

接触量，即终生接触的总量，是一种新的、高度复杂的健康和疾病范例。应对这一挑战需要的努力远远超出个人或实验室的范畴，因为每一块拼图都至关重要。这本新的《暴露》杂志的发行恰逢《暴露》杂志在一个日益开放和公平(可查找、可访问、可互操作、可重复使用)的世界中从青少年时期发展到日益成熟。这封信讨论了作者和《Exposome》杂志如何帮助提高期刊中化学结构信息和相关元数据的公平性，旨在获取更多关于暴露组学化学的细节。提出的化学结构模板可以作为一种可互操作的补充格式，可以通过网站访问，并且通过将该数据文件的DOI链接到文章DOI元数据更容易找到，从而支持进一步重用。一个额外的转化模板为作者提供了一种将前驱(母体、底物)分子连接到后继(转化产物、代谢物)分子的方法，从而在观察到的(即实验的)化学暴露和生物反应之间提供公平的联系，以帮助改善与暴露相关的转化的公共知识库。这些联系对于扩展当前的生化知识和实现当前的暴露学定义至关重要，即“在整个生命周期中对环境影响和相关生物反应的累积测量，包括来自环境、饮食、行为和内源性过程的暴露”。

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引用次数: 9

Plasma metabolomics of autism spectrum disorder and influence of shared components in proband families. 自闭症谱系障碍的血浆代谢组学及原发性家族中共同成分的影响。

Exposome

Pub Date : 2021-10-07 eCollection Date: 2021-01-01 DOI: 10.1093/exposome/osab004

Ming Kei Chung, Matthew Ryan Smith, Yufei Lin, Douglas I Walker, Dean Jones, Chirag J Patel, Sek Won Kong

Prevalence of autism spectrum disorder (ASD) has been increasing in the United States in the past decades. The exact mechanisms remain enigmatic, and diagnosis of the disease still relies primarily on assessment of behavior. We first used a case-control design (75 idiopathic cases and 29 controls, enrolled at Boston Children's Hospital from 2007-2012) to identify plasma biomarkers of ASD through a metabolome-wide association study approach. Then we leveraged a family-based design (31 families) to investigate the influence of shared genetic and environmental components on the autism-associated features. Using untargeted high-resolution mass spectrometry metabolomics platforms, we detected 19 184 features. Of these, 191 were associated with ASD (false discovery rate < 0.05). We putatively annotated 30 features that had an odds ratio (OR) between <0.01 and 5.84. An identified endogenous metabolite, O-phosphotyrosine, was associated with an extremely low autism odds (OR 0.17; 95% confidence interval 0.06-0.39). We also found that glutathione metabolism was associated with ASD (P = 0.048). Correlations of the significant features between proband and parents were low (median = 0.09). Of the 30 annotated features, the median correlations within families (proband-parents) were -0.15 and 0.24 for the endogenous and exogenous metabolites, respectively. We hypothesize that, without feature identification, family-based correlation analysis of autism-associated features can be an alternative way to assist the prioritization of potentially diagnostic features. A panel of ASD diagnostic metabolic markers with high specificity could be derived upon further studies.

过去几十年来，自闭症谱系障碍（ASD）的发病率在美国不断上升。自闭症的确切机制仍是个谜，诊断该疾病仍主要依靠行为评估。我们首先采用病例对照设计（75 例特发性病例和 29 例对照，2007-2012 年期间在波士顿儿童医院登记），通过全代谢组关联研究方法确定 ASD 的血浆生物标志物。然后，我们利用基于家庭的设计（31 个家庭）来研究共同的遗传和环境因素对自闭症相关特征的影响。利用非靶向高分辨率质谱代谢组学平台，我们发现了 19 184 个特征。其中，191 个特征与 ASD 相关（误发现率小于 0.05）。我们推测注释了 30 个特征，其几率比（OR）在 P = 0.048 之间。）原告和父母之间的重要特征相关性较低（中位数 = 0.09）。在 30 个已注释的特征中，内源性代谢物和外源性代谢物在家系（原告-父母）内的相关性中位数分别为-0.15 和 0.24。我们假设，在不进行特征鉴定的情况下，对自闭症相关特征进行基于家系的相关性分析可以作为一种替代方法，帮助确定潜在诊断特征的优先次序。经过进一步研究，可以得出一组具有高度特异性的 ASD 诊断代谢标记物。

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引用次数: 0

Analytical strategies for chemical exposomics: exploring limits and feasibility 化学暴露的分析策略：探索局限性和可行性

Exposome

Pub Date : 2021-09-20 DOI: 10.1093/exposome/osab003

C. M. Vitale, E. Price, G. Miller, A. David, J. Antignac, R. Barouki, J. Klánová

Tackling the challenges of chemical exposomics will require the implementation of diverse analytical strategies and technological advancements. Herein, high-resolution mass spectrometry-based methods applied in current chemical exposome studies have been surveyed and are shown to be limited. Notably, liquid chromatography separations almost exclusively employ reversed-phase C18 columns using water-methanol gradients with formic acid additive, whilst gas chromatography is underexploited in the field at this stage. A systematic evaluation of strategies applied in related disciplines (i.e. metabolomics, proteomics, multi-residue trace analysis) was undertaken to provide practical guidance for the development of chemical exposomics. The approaches were assessed on the basis of their costs (i.e. capital expenditure, overhead and maintenance fees, expertise required, consumables) and potential benefits (i.e. improvements to sensitivity, coverage, reproducibility, throughput, ease of use) to prioritize those with promise for chemical exposomics application. Alongside a need for technological investments (e.g. advanced hardware updates), numerous low cost strategies showed high potential benefits (e.g. different column phases, enhanced sample fractionation) and are feasible for rapid adoption.

应对化学暴露的挑战需要实施多样化的分析策略和技术进步。在此，已经对当前化学暴露研究中应用的基于高分辨率质谱的方法进行了调查，并表明这些方法是有限的。值得注意的是，液相色谱分离几乎完全使用反相C18柱，使用含有甲酸添加剂的水-甲醇梯度，而气相色谱在该领域现阶段的开发不足。对相关学科（即代谢组学、蛋白质组学、多残基痕量分析）中应用的策略进行了系统评估，为化学暴露组学的发展提供了实际指导。这些方法是根据其成本（即资本支出、管理费和维护费、所需专业知识、耗材）和潜在效益（即灵敏度、覆盖率、再现性、产量、易用性的改进）进行评估的，以优先考虑那些有希望应用化学暴露组学的方法。除了需要技术投资（如先进的硬件更新）外，许多低成本策略显示出很高的潜在效益（如不同的柱相、增强的样品分馏），并且可以快速采用。

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引用次数: 7

Integrating the exposome into a multi-omic research framework. 将暴露体整合到多组学研究框架中。

Exposome

Pub Date : 2021-01-01 Epub Date: 2021-11-30 DOI: 10.1093/exposome/osab002

Gary W Miller

引用次数: 4

Exposome: a new field, a new journal. 一个新的领域，一个新的期刊。

Exposome

Pub Date : 2021-01-01 Epub Date: 2021-03-16 DOI: 10.1093/exposome/osab001

Gary W Miller

引用次数: 5

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Exposome

Pub Date : 2020-12-31 DOI: 10.1016/b978-0-12-814079-6.00019-5

引用次数: 0

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