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Simmons DeGroot Metabolism mRNA transfection ApplInVitroTox Data
The US EPA’s ToxCast program is designed to assess chemical perturbations of molecular and cellular endpoints using a variety of high-throughput screening (HTS) assays. However, existing HTS assays have limited or no xenobiotic metabolism which could lead to false positive (chemical is detoxified in vivo) as well as false negative results (chemical is bioactivated in vivo) and thus potential mischaracterization of chemical hazard. We have addressed this challenge by introducing the ten most prevalent human liver cytochrome P450 (CYP) enzymes into a human cell line (HEK293T) with low endogenous metabolic capacity. The CYP enzymes were introduced via transfection of modified mRNAs as singlets or as a mixture in relative proportions expressed in the liver. Initial experiments using luminogenic CYP450 substrates demonstrate that cell models express metabolic enzymes from the transfected mRNAs and activities are significantly increased when co-transfected with a CYP accessory protein, P450 oxidoreductase (POR). Transfected HEK293T cells demonstrate the ability to produce predicted metabolites following treatment with well-studied CYP substrates, with metabolite formation occurring through 18 hours post-treatment. As a demonstration of how this method can be used to retrofit existing HTS assays, a proof-of-concept screen for cytotoxicity in HEK293T cells was conducted using 56 test compounds. The results demonstrate that the xenobiotic metabolism conferred by transfection of CYP-encoding mRNAs shifts the dose-response relationship for certain test chemicals such as aflatoxin B1 (bioactivation) and fenazaquin (detoxification). Overall, transfection of CYP-encoding mRNAs is an effective and portable solution for retrofitting metabolic competence to existing cell-based HTS assays. This dataset is associated with the following publication: DeGroot, D., A. Swank, R. Thomas, M. Strynar, M. Lee, P. Carmichael, and S. Simmons. mRNA transfection retrofits cell-based assays with xenobiotic metabolism. JOURNAL OF PHARMACOLOGICAL & TOXICOLOGICAL METHODS. Elsevier Science Ltd, New York, NY, USA, 92: 77-94, (2018).
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ToxCast bioactivity data for p,p'-DDD and analogues
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Bioactivity data for p,p'-DDD and analogues from ToxCast assays conducted in liver cells were sourced from the EPA’s CompTox Chemistry Dashboard. The links also provide access to the ToxCast assay information and annotation data user guide. This dataset is associated with the following publication: Lizarraga, L., J. Dean, J. Kaiser, S. Wesselkamper, J. Lambert, and J. Zhao. A Case Study on the Application of An Expert-driven Read-Across Approach in Support of Quantitative Risk Assessment of p,p’-Dichlorodiphenyldichloroethane. REGULATORY TOXICOLOGY AND PHARMACOLOGY. Elsevier Science Ltd, New York, NY, USA, 103: 301-313, (2019).
ToxCast bioactivity data for p,p'-DDD and analogues
공공데이터포털
Bioactivity data for p,p'-DDD and analogues from ToxCast assays conducted in liver cells were sourced from the EPA’s CompTox Chemistry Dashboard. The links also provide access to the ToxCast assay information and annotation data user guide. This dataset is associated with the following publication: Lizarraga, L., J. Dean, J. Kaiser, S. Wesselkamper, J. Lambert, and J. Zhao. A Case Study on the Application of An Expert-driven Read-Across Approach in Support of Quantitative Risk Assessment of p,p’-Dichlorodiphenyldichloroethane. REGULATORY TOXICOLOGY AND PHARMACOLOGY. Elsevier Science Ltd, New York, NY, USA, 103: 301-313, (2019).
ToxCast Phase I
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Background: Chemical toxicity testing is being transformed by advances in biology and computer modeling, concerns over animal use and the thousands of environmental chemicals lacking toxicity data. EPA's ToxCast program aims to address these concerns by screening and prioritizing chemicals for potential human toxicity using in vitro assays and in silico approaches. Objectives: This project aims to evaluate the use of in vitro assays for understanding the types of molecular and pathway perturbations caused by environmental chemicals and to build initial prioritization models of in vivo toxicity. Methods: We tested 309 mostly pesticide active chemicals in 467 assays across 9 technologies, including high-throughput cell-free assays and cell-based assays in multiple human primary cells and cell lines, plus rat primary hepatocytes. Both individual and composite scores for effects on genes and pathways were analyzed. Results: Chemicals display a broad spectrum of activity at the molecular and pathway levels. Many expected interactions are seen, including endocrine and xenobiotic metabolism enzyme activity. Chemicals range in promiscuity across pathways, from no activity to affecting dozens of pathways. We find a statistically significant inverse association between the number of pathways perturbed by a chemical at low in vitro concentrations and the lowest in vivo dose at which a chemical causes toxicity. We also find associations between a small set in vitro assays and rodent liver lesion formation. Conclusions: This approach promises to provide meaningful data on the thousands of untested environmental chemicals, and to guide targeted testing of environmental contaminants.
ToxCast Phase I
공공데이터포털
Background: Chemical toxicity testing is being transformed by advances in biology and computer modeling, concerns over animal use and the thousands of environmental chemicals lacking toxicity data. EPA's ToxCast program aims to address these concerns by screening and prioritizing chemicals for potential human toxicity using in vitro assays and in silico approaches. Objectives: This project aims to evaluate the use of in vitro assays for understanding the types of molecular and pathway perturbations caused by environmental chemicals and to build initial prioritization models of in vivo toxicity. Methods: We tested 309 mostly pesticide active chemicals in 467 assays across 9 technologies, including high-throughput cell-free assays and cell-based assays in multiple human primary cells and cell lines, plus rat primary hepatocytes. Both individual and composite scores for effects on genes and pathways were analyzed. Results: Chemicals display a broad spectrum of activity at the molecular and pathway levels. Many expected interactions are seen, including endocrine and xenobiotic metabolism enzyme activity. Chemicals range in promiscuity across pathways, from no activity to affecting dozens of pathways. We find a statistically significant inverse association between the number of pathways perturbed by a chemical at low in vitro concentrations and the lowest in vivo dose at which a chemical causes toxicity. We also find associations between a small set in vitro assays and rodent liver lesion formation. Conclusions: This approach promises to provide meaningful data on the thousands of untested environmental chemicals, and to guide targeted testing of environmental contaminants.
MMartin DFiler tcpl: the ToxCast pipeline for high-throughput screening data
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The tcpl package provides a set of tools for processing and modeling high-throughput and high-content chemical screening data. This dataset is associated with the following publication: Filer, D.L., P. Kothiya, R.W. Setzer, R.S. Judson, and M.T. Martin. (BIOINFORMATICS) tcpl: The ToxCast Pipeline for High-Throughput Screening Data. BIOINFORMATICS. Oxford University Press, Cary, NC, USA, 1-3, (2016).
MMartin DFiler tcpl: the ToxCast pipeline for high-throughput screening data
공공데이터포털
The tcpl package provides a set of tools for processing and modeling high-throughput and high-content chemical screening data. This dataset is associated with the following publication: Filer, D.L., P. Kothiya, R.W. Setzer, R.S. Judson, and M.T. Martin. (BIOINFORMATICS) tcpl: The ToxCast Pipeline for High-Throughput Screening Data. BIOINFORMATICS. Oxford University Press, Cary, NC, USA, 1-3, (2016).
High-throughput screening tools facilitate calculation of a combined exposure-bioactivity index for chemicals with endocrine activity
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Dataset consists of high throughput in vitro bioactivity data and exposure predictions from the U.S. EPA’s Toxicity and Exposure Forecaster (ToxCast and ExpoCast) project. This dataset is associated with the following publication: Wegner, S., C. Pinto, C. Ring, and J. Wambaugh. High-throughput screening tools facilitate calculation of a combined exposure-bioactivity index for chemicals with endocrine activity. ENVIRONMENT INTERNATIONAL. Elsevier B.V., Amsterdam, NETHERLANDS, 137: 105470, (2020).
High-throughput screening tools facilitate calculation of a combined exposure-bioactivity index for chemicals with endocrine activity
공공데이터포털
Dataset consists of high throughput in vitro bioactivity data and exposure predictions from the U.S. EPA’s Toxicity and Exposure Forecaster (ToxCast and ExpoCast) project. This dataset is associated with the following publication: Wegner, S., C. Pinto, C. Ring, and J. Wambaugh. High-throughput screening tools facilitate calculation of a combined exposure-bioactivity index for chemicals with endocrine activity. ENVIRONMENT INTERNATIONAL. Elsevier B.V., Amsterdam, NETHERLANDS, 137: 105470, (2020).
Respirometric Screening and Characterization of Mitochondrial Toxicants Within the ToxCast Phase I and II Chemical Libraries
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These are the raw data files for TOXSCI manuscript 19-0578 entitled, “Respirometric Screening and Characterization of Mitochondrial Toxicants Within the ToxCast Phase I and II Chemical Libraries”: Description from readme.txt file: 1) sc_seahorse.lvl0.merged.data.csv- contains all mapped raw OCR data from tier 1 single-concentration RSA screening of 1,042 Toxcast Phase I and II chemicals 2) mc_seahorse.lvl0.merged.data.csv- contains all mapped raw OCR data from tier 2 multi-concentration RSA screening of 249 actives from tier 1 3) EFA.lvl0.merged.data.csv- contains all mapped raw OCR data from tier 3 EFA screening of 149 putative electron transport chain inhibitors 4) mc5_mc6_ncct_mito_nov2019.csv- level 5 and 6 outputs from ToxCast pipeline (tcpl) analysis 5) RawMC3_ToxCast_by_aeid.csv- level 3 tcpl outputs for all mitochondrial ToxCast assays 6) RawMC5_ToxCast_by_aeid.csv- level 5 tcpl outputs for all mitochondrial ToxCast assays 7) ref.set.chems.csv- sixty reference chemicals used to compared assay performance 8) study_code.R- R script used to analyze data and generate figures and tables. This dataset is associated with the following publication: Hallinger, D., H. Lindsay, K. Friedman, D. Suarez, and S. Simmons. Respirometric Screening and Characterization of Mitochondrial Toxicants Within the ToxCast Phase I and II Chemical Libraries. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 176(1): 175-192, (2020).
Respirometric Screening and Characterization of Mitochondrial Toxicants Within the ToxCast Phase I and II Chemical Libraries
공공데이터포털
These are the raw data files for TOXSCI manuscript 19-0578 entitled, “Respirometric Screening and Characterization of Mitochondrial Toxicants Within the ToxCast Phase I and II Chemical Libraries”: Description from readme.txt file: 1) sc_seahorse.lvl0.merged.data.csv- contains all mapped raw OCR data from tier 1 single-concentration RSA screening of 1,042 Toxcast Phase I and II chemicals 2) mc_seahorse.lvl0.merged.data.csv- contains all mapped raw OCR data from tier 2 multi-concentration RSA screening of 249 actives from tier 1 3) EFA.lvl0.merged.data.csv- contains all mapped raw OCR data from tier 3 EFA screening of 149 putative electron transport chain inhibitors 4) mc5_mc6_ncct_mito_nov2019.csv- level 5 and 6 outputs from ToxCast pipeline (tcpl) analysis 5) RawMC3_ToxCast_by_aeid.csv- level 3 tcpl outputs for all mitochondrial ToxCast assays 6) RawMC5_ToxCast_by_aeid.csv- level 5 tcpl outputs for all mitochondrial ToxCast assays 7) ref.set.chems.csv- sixty reference chemicals used to compared assay performance 8) study_code.R- R script used to analyze data and generate figures and tables. This dataset is associated with the following publication: Hallinger, D., H. Lindsay, K. Friedman, D. Suarez, and S. Simmons. Respirometric Screening and Characterization of Mitochondrial Toxicants Within the ToxCast Phase I and II Chemical Libraries. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 176(1): 175-192, (2020).