The following paper represents a mini-review of an intensive ten year progression of genome-to-phenome discovery guided by the adverse outcome pathway (AOP) concept. This example is presented as a means to stimulate crossover of this toxicological concept to enhance genome-to-phenome discovery within the broader biological sciences community. The case study demonstrates the benefits of the AOP approach for establishing causal linkages across multiple levels of biological organization ultimately linking molecular initiation (often at the genomic scale) to organism-level phenotypes of interest. The case study summarizes a US military effort to identify the mechanism(s) underlying toxicological phenotypes of lethargy and weight loss in response to nitroaromatic munitions exposures, such as 2,4,6-trinitrotolune (TNT). Initial key discoveries are described including the toxicogenomic results that nitrotoluene exposures inhibited expression within the peroxisome proliferator activated receptor α (PPARα) pathway. We channeled the AOP concept to test the hypothesis that inhibition of PPARα signaling in nitrotoluene exposures impacted lipid metabolic processes, thus affecting systemic energy budgets, ultimately resulting in body weight loss. Results from a series of transcriptomic, proteomic, lipidomic, in vitro PPARα nuclear signaling, and PPARα knock-out investigations ultimately supported various facets of this hypothesis. Given these results, we next proceeded to develop a formalized AOP description of PPARα antagonism leading to body weight loss. This AOP was refined through intensive literature review and polished through multiple rounds of peer-review leading to final international acceptance as an Organisation for Economic Cooperation and Development (OECD)-approved AOP. Briefly, that AOP identifies PPARα antagonist binding as the molecular initiating event (MIE) leading to a series of key events (KEs) including inhibition of nuclear transactivation for genes controlling lipid metabolism and ketogenesis, inhibition of fatty acid beta-oxidation and ketogenesis dynamics, negative energy budget, and ultimately the adverse outcome (AO) of body-weight loss. Given that the PPARα antagonism MIE represented a reliable indicator of AO progression within the pathway, a phylogenetic analysis was conducted which indicated that PPARα amino acid relatedness generally tracked species relatedness. Additionally, PPARα amino acid relatedness analysis using SeqAPASS predicted susceptibility to the MIE across vertebrates providing context for AOP extrapolation across species. Overall, we hope this illustrative example of how the AOP concept has benefited toxicology sows a seed within the broader biological sciences community to repurpose the concept to facilitate enhanced genome-to-phenome discovery in biology.

中文翻译：

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在毒理学中启用基因组到表型组发现的不良结果通路概念示例

以下论文是对不利结果通路 (AOP) 概念指导下的基因组到现象组发现的十年密集进展的小型回顾。这个例子是作为一种手段来刺激这个毒理学概念的交叉，以在更广泛的生物科学界内加强基因组到现象的发现。案例研究证明了 AOP 方法在建立跨多个生物组织水平的因果联系方面的好处，最终将分子起始（通常在基因组规模）与感兴趣的生物体水平表型联系起来。该案例研究总结了美国军方为确定暴露于硝基芳烃弹药（如 2,4,6-三硝基甲苯 (TNT)）而导致嗜睡和体重减轻的潜在毒理学表型的机制。描述了最初的关键发现，包括硝基甲苯暴露抑制过氧化物酶体增殖物激活受体 α (PPARα) 通路中的表达的毒理学结果。我们引导 AOP 概念来测试假设，即在硝基甲苯暴露中抑制 PPARα 信号会影响脂质代谢过程，从而影响全身能量预算，最终导致体重减轻。一系列转录组学、蛋白质组学、脂质组学、体外 PPARα 核信号传导和 PPARα 敲除研究的结果最终支持了这一假设的各个方面。鉴于这些结果，我们接下来继续对导致体重减轻的 PPARα 拮抗作用进行正式的 AOP 描述。该 AOP 通过密集的文献审查得到完善，并通过多轮同行审查完善，最终被国际认可为经济合作与发展组织 (OECD) 批准的 AOP。简而言之，AOP 将 PPARα 拮抗剂结合识别为导致一系列关键事件 (KE) 的分子起始事件 (MIE)，包括抑制控制脂质代谢和生酮的基因的核反式激活、抑制脂肪酸 β-氧化和生酮动力学，负能量预算，最终导致体重减轻的不良结果 (AO)。鉴于 PPARα 拮抗作用 MIE 代表了该途径内 AO 进展的可靠指标，因此进行了系统发育分析，表明 PPARα 氨基酸相关性通常跟踪物种相关性。此外，使用 SeqAPASS 的 PPARα 氨基酸相关性分析预测了脊椎动物对 MIE 的易感性，为跨物种的 AOP 外推提供了背景。总的来说，我们希望这个关于 AOP 概念如何有益于毒理学的说明性例子在更广泛的生物科学界播下种子，重新利用这一概念以促进生物学中增强的基因组到现象组的发现。