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Advancing the Adverse Outcome Pathway Concept – An International ‘Horizon Scanning’ Approach
Our ability to conduct whole organism toxicity tests to understand chemical safety has been outpaced by our ability to synthesize new chemicals for a wide variety of commercial applications. Therefore, to increase efficiencies in chemical risk assessment, scientists and risk assessors are turning to mechanistic-based studies, making greater use of in vitro and in silico methods, to evaluate potential environmental and human health hazards. A framework that has gained traction for capturing available knowledge describing the linkage between mechanistic data and the apical toxicity endpoints, required for regulatory assessments, is the adverse outcome pathway (AOP). A number of international activities have focused on AOP development and plausible applications to regulatory decision-making. These interactions have prompted dialog between research scientists and regulatory communities to consider how best to use the AOP framework in risk assessment. While expert-facilitated discussions have been instrumental in moving the science of AOPs forward, it was recognized that a survey of the broader scientific community would aid in identifying current limitations while guiding future initiatives for the AOP framework. To that end, a global ‘Horizon Scanning’ exercise was conducted to solicit questions concerning the challenges or limitations that must be addressed to realize the full potential of the AOP framework in research and regulatory decision making. The majority of questions received fell into several broad topical areas including the concepts of AOP networks and quantitative AOPs, collaboration on and communication of AOP knowledge, AOP discovery and development, chemical and cross-species extrapolation, exposure considerations, and AOP applications. An expert ranking exercise was then conducted to identify the most important questions for each category. These questions were used to develop four broad themes to inform and guide future AOP research and regulatory initiatives. In addition, frequently asked questions (FAQs) were identified and addressed by experts in the field. Answers to FAQs will aid in framing further discussions about common misperceptions about AOPs and allow for clarification of AOP topics. The need for clarification occurred with surprising frequency, indicating that improvements are needed in communicating the AOP framework among the scientific and regulatory communities. Overall, the ‘Horizon Scanning’ effort brought together the global scientific community to guide the direction of future initiatives and identify key questions surrounding the AOP framework. The views expressed in this manuscript are those of the authors and may not reflect U.S. EPA policy. This dataset is not publicly accessible because: It is available online and was collected through the Society of Environmental Toxicology and Chemistry in support of a Pellston Workshop. It can be accessed through the following means: All materials associated with this paper are found at the provided URL as the main document or as the supplemental files. Format: http://onlinelibrary.wiley.com/doi/10.1002/etc.3805/full. This dataset is associated with the following publication: LaLone, C., G. Ankley, S. Belanger, M. Embry, G. Hodges, D. Knapen, S. Munn, E. Perkins, M. Rudd, D. Villeneuve, M. Whelan, C. Willett, X. Zhang, and M. Hecker. Advancing the adverse outcome pathway framework - An international horizon scanning approach. SOCIETY OF ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY JOURNAL. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 36(6): 1411-1421, (2017).
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Defining the Biologically Plausible Taxonomic Domain of Applicability of an Adverse Outcome Pathway: A Case Study Linking Nicotinic Acetylcholine Receptor Activation to Colony Death
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Supporting Information for "Jensen, M.A., Blatz, D.J. and LaLone, C.A. (2023), Defining the Biologically Plausible Taxonomic Domain of Applicability of an Adverse Outcome Pathway: A Case Study Linking Nicotinic Acetylcholine Receptor Activation to Colony Death. Environ Toxicol Chem, 42: 71-87. https://doi.org/10.1002/etc.5501". This dataset is associated with the following publication: Jensen, M., D. Blatz, and C. Lalone. Defining the Biologically Plausible Taxonomic Domain of Applicability of an Adverse Outcome Pathway: A Case Study Linking Nicotinic Acetylcholine Receptor Activation to Colony Death. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 42(1): 71-87, (2023).
Extracting and benchmarking emerging adverse outcome pathway knowledge
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A collection of R scripts useful for extracting and analyzing adverse outcome pathway network data from the adverse outcome pathway wiki (aopwiki.org). This dataset is associated with the following publication: Pollesch, N., D. Villeneuve, and J. O'Brien. Extracting and benchmarking emerging adverse outcome pathway knowledge. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 168(2): 349-364, (2019).
Differentiating Pathway-Specific From Nonspecific Effects in High-Throughput Toxicity Data: A Foundation for Prioritizing Adverse Outcome Pathway Development
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Previous work identified a ‘cytotoxic burst’ (CTB) phenomenon wherein large numbers of the ToxCast assays begin to respond at or near test chemical concentrations that elicit cytotoxicity, and a statistical approach to defining the bounds of the CTB was developed. To focus AOP development on the molecular targets corresponding to ToxCast assays indicating pathway-specific effects, we conducted a meta-analysis to identify which assays most frequently respond at concentrations below the CTB. A preliminary list of potentially important, target-specific assays was determined by ranking assays by the fraction of chemical hits below the CTB compared to the number of chemicals tested. Additional priority assays were identified using a diagnostic-odds-ratio approach which gives greater ranking to assays with high specificity but low responsivity. Combined, the two prioritization methods identified several novel targets (e.g., peripheral benzodiazepine and progesterone receptors) to prioritize for AOP development, and affirmed the importance of a number of existing AOPs aligned with ToxCast targets (e.g., thyroperoxidase, estrogen receptor, aromatase). This dataset is associated with the following publication: Fay, K., J. Swintek, D. Villeneuve, S. Edwards, M. Nelms, B. Blackwell, and G. Ankley. Differentiating pathway-specific from non-specific effects in high-throughput toxicity data: A foundation for prioritizing adverse outcome pathway development. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 163(2): 500-515, (2018).
Adverse Outcome Pathway Networks II: Network Analytics
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The data set provides a set of txt files and cytoscape files that were used to construct the example AOP networks included in the paper. Additionally, a supplementary table file provides all the network statistics discussed in the manuscript (e.g., node degree calculations, betweenness centrality, eccentricity, etc.). This dataset is associated with the following publication: Villeneuve, D., M. Angrish, M. Fortin, I. Katsiadaki, M. Leonard, L. Margiotta-Casaluci, S. Munn, J. O'Brien, N. Pollesch, C. Smith, X. Zhang, and D. Knapen. Adverse outcome pathway networks II: Network analytics. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 37(6): 1734-1748, (2018).
Use of Threshold of Toxicological Concern (TTC) with High Throughput Exposure Predictions (HTE) as a Risk-Based Screening Approach to Prioritize More Than Seven Thousand Chemicals
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The dataset that was evaluated in this approach was taken from Wambaugh et al [29] who filtered the Tox21 library to reflect substances with similar uses to those in NHANES. The zip file contains the supplementary information being provided for the re-analysis performed in this dataset. There was no specific code as such developed for the analysis aside from using KNIME to help combine different outputs from different tools including Leadscope in order to arrive at the counts reflected in Table 2 of the manuscript. Instead of this very laborious approach, we re-did the analysis using Toxtree alone and streamlined the processing of the outcomes with R. This is documented in the supplementary information file. List of files: SMARTS Toxtree schemes use to identify carbamates, OPs and steroids Carbamates.tml OPs.tml Steroids.tml R code used to manipulate the various outputs derived from processing the associated sdf through the Kroes, specific Toxtree schemes and Cramer scheme within Toxtree TTC_HTTK.R R data file HTTK_TTC_070218.RData sdf file used in the analysis HTTK_7K_mod_kekule.sdf. This dataset is associated with the following publication: Patlewicz, G., J. Wambaugh, S. Felter, T. Simon, and R. Becker. Utilizing Threshold of Toxicological Concern (TTC) with High Throughput Exposure Predictions (HTE) as a Risk-Based Prioritization Approach for thousands of chemicals. Computational Toxicology. Elsevier B.V., Amsterdam, NETHERLANDS, 7: 58-67, (2018).
Adverse outcome pathway (AOP) development and weight of evidence evaluation as illustrated by ecological case studies using online tools such as ECOTOX and SeqAPASS
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The majority of this dataset includes the query output from online databases ECOTOX and SeqAPASS used to support the ecological AOP case studies described within the manuscript. The final worksheet includes the raw data used to generate concentration vs response curves for four putative chemical initiators (Supplemental Figure S4). This dataset is associated with the following publication: Fay, K., D. Villeneuve, C. LaLone, Y. Song, K.E. Tollefsen, and G. Ankley. Practical approaches to adverse outcome pathway (AOP) development as illustrated by ecological case studies. SOCIETY OF ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY JOURNAL. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 36(6): 1429–1449, (2017).
Interactive Chemical Safety for Sustainablity Toxicity Forecaster Dashboard
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EPA researchers have been using advances in computational toxicology to address lack of data on the thousands of chemicals. EPA released chemical data on 1,800 chemicals. The 1,800 chemicals were screened in more than 800 rapid, automated tests (called high-throughput screening assays) to determine potential human health effects. The data is available through the interactive Chemical Safety for Sustainability Dashboards (iCSS dashboard) and the complete data sets are also available for download.
환경부 화학물질안전원 화학물질안전관리정보
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유해화학물질 사용량의 지속적인 증가로 인해 일반국민 및 화학사고 대응기관을 위한 인체 노출 위험성, 화학물질 사고시 초동대응정보, 2차 피해확산 장비를 위한 방제 정보등