Grantee Research Project Results
2016 Progress Report: Cardiotoxicity Adverse Outcome Pathway: Organotypic Culture Model and in vitro-to-in vivo Extrapolation for High-throughput Hazard, Dose-response and Variability Assessments
EPA Grant Number: R835802Center: Organotypic Culture Models For Predictive Toxicology Center
Center Director: Rusyn, Ivan
Title: Cardiotoxicity Adverse Outcome Pathway: Organotypic Culture Model and in vitro-to-in vivo Extrapolation for High-throughput Hazard, Dose-response and Variability Assessments
Investigators: Rusyn, Ivan , Wright, Fred A. , Threadgill, David W.
Current Investigators: Rusyn, Ivan
Institution: Texas A & M University , North Carolina State University
Current Institution: Texas A & M University , North Carolina State University
EPA Project Officer: Callan, Richard
Project Period: June 1, 2015 through May 31, 2019 (Extended to May 31, 2022)
Project Period Covered by this Report: June 1, 2016 through May 31,2017
Project Amount: $6,000,000
RFA: Organotypic Culture Models for Predictive Toxicology Center (2013) RFA Text | Recipients Lists
Research Category: Chemical Safety for Sustainability
Objective:
Important target areas for addressing data gaps through in vitro screening include evaluations of cardiotoxicity. Despite the fact that current conservative estimates relate at least 23% of all cardiovascular disease cases to environmental exposures, the identities of the causative environmental agents remain largely uncharacterized. Moreover, cardiotoxicity remains among the most pronounced reasons, comparable to those associated with hepatotoxicity, for drug attrition during clinical trials and post-marketing. Current pre-clinical approaches for cardiophysiologic evaluations of chemicals rely almost exclusively on large animal models and this approach has significant limitations in terms of cost and complexity of the studies. Hence, there is a pressing demand for the development of comprehensive, multi-parametric screening strategies that provide improved predictability of cardiotoxic effects.
The central hypotheses of this project are that: (1) human induced pluripotent stem cell (iPSC)-derived cardiomyocyte cultures constitute an effective organotypic culture model for predictive toxicity screening of environmental chemicals; (2) a population-based experimental design can assess variation in toxicity to better characterize uncertainties; and (3) integration of pharmacokinetic and high-throughput screening data further improves confidence in NexGen health assessments. The activities in Projects 1 and 2 necessitate targeted, yet comprehensive analytic pipeline for analyzing organotypic culture model data screened for dosimetry, physiological parameters and genetic profiles, culminating in an informed basis for ranking and prioritization. The activity in Project 3 is to collate, analyze and synthesize the results from Projects 1 and 2.
Progress Summary:
Project 1 work was focused on using multi-plexed assays for high-content imaging and high-throughput transcriptomic analyses using iCell cardiomyocyte organotypic culture model and other cell types derived from iPS cells. We conducted a combinatorial in vitro/in silico screening study for functional and mechanistic cardiotoxicity profiling of environmental hazards using a library of 69 representative environmental chemicals and drugs. We used human iPSC-derived cardiomyocytes and examined chemical effects in concentration-response on cardiomyocyte beating and cellular and mitochondrial toxicity. We are analyzing data acquired from screening the first batch of population-wide iCell cardiomyocytes from 30 normal donors (European and African American descent, equal male to female ratio). Transcriptomic analyses were conducted in samples from four representative donors that were selected to reflect the greatest degree of variability in basal cardiac phenotypes and data analyses are underway in collaboration with Project 3. We also have successfully established the experimental protocol for in vitro-to-in vivo extrapolation and the computational pipeline for reverse toxicokinetic analyses. We have collected data on about a dozen chemicals from a list of 140 screened compounds that were without RTK data and also collected information on several drugs. These analyses are being incorporated into concentration-response assessments and additional chemicals are being analyzed.
Project 2 investigators have developed mouse embryonic fibroblast (MEF) cell lines from the entire Collaborative Cross (CC) mouse strain population, and 32 CC lines have been converted into iPS lines. For in vivo experiments in mice, we have acquired an ECGenie for recording electrocardiograms (from institutional resources) that is currently being used to compare cardiomyocyte function in vivo with in vitro activity. Current iPS lines are being used to convert into embryoid bodies for cardiomyocyte generation and screening.
Project 3 investigators have continued their focus on several computational and statistical approaches. The pipeline for handling high-throughput transcriptomic data (e.g., TempO-Seq technology) has been brought to a mature form, with automatic read calling from sequence data, quality controlling the data, filtering of low expressed transcripts, robust testing for differential expression, fitting concentration-response functions and pathway analyses. Informal consultation with EPA personnel has ensured that the work is aligned with relevance in toxicogenomics and to initiatives such as Tox21. In addition, comparison with GTEx data have been used to support the biological relevance of the results. The new options for statistical analyses and grouping/clustering in the ToxPi software have been brought to a new beta version of ToxPi, completely rewritten for ease of use. ToxPi analysis advances have included handling multiple dimensions of prioritization, handling missing data, and quantifying across endpoints with irregular correlation structure. Finally, our new efforts in data integration include leveraging transcriptomic and genetic information using GTEx eQTL data to best prioritize the combination of SNP and tissue-specific expression data. The first step in this process has been the development of improved methods for genetic stratification, which has been accepted for publication. The next steps include further use of a multi-tissue eQTL model that our group has developed, applied to heart and artery tissues from GTEx, to best prioritize polymorphisms to study for cardiomyocyte toxicity susceptibility.
Future Activities:
Project 1 will continue data analyses on the first batch of 30 individuals screened against 140 chemicals and appropriate positive and negative controls. We expect to receive the next batch of cells (15-20 donors) from CDI in October-November 2017 and additional batches of 10-15 donors at quarterly intervals thereafter. These cells will be screened and data analyzed. We also plan to conduct several large batches of targeted transcriptomic analyses using the S1500+ gene list (~3,000 targets) developed by the National Toxicology Program for TempO-seq high-throughput transcriptomics. We will work closely with project 3 staff to analyze data from high-content screening and high-throughput transcriptomics. We will work with project 2 staff to conduct screening of mouse-derived embryoid bodies. We will continue experiments for reverse toxicokinetics based on the data for 140 chemicals that are screened.
Project 2 will complete iPS genetics from the CC MEF resource, and will perform EB exposure on the first 30 CC lines using the selected 140 chemical panel. Baseline in vitro-to-in vivo comparison of cardiomyocyte function using 8 CC lines also will be completed. As the mouse TempO-seq high –throughput transcriptomics panel is developed, these also will be performed.
Although Project 3 has largely finalized the pipeline for dose-response analysis, some stress testing remains to be performed, as well as pushing the limits of inference performed for low-expression genes. We are working on manuscripts for both the TempOSeq pipeline and the new version of ToxPi. Using the new robust methods for population stratification control, we will next develop the list of high-priority variants for testing association and expression in response to toxicity.
Journal Articles: 45 Displayed | Download in RIS Format
Other center views: | All 150 publications | 45 publications in selected types | All 45 journal articles |
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Auerbach S, Filer D, Reif D, Walker V, Holloway AC, Schlezinger J, Srinivasan S, Svoboda D, Judson R, Bucher JR, Thayer KA. Prioritizing environmental chemicals for obesity and diabetes outcomes research: a screening approach using ToxCastTM high-throughput data. Environmental Health Perspectives 2016;124(8):1141-1154. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) R835802C003 (2015) |
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Barton-Maclaren TS, Westphal M, Sarwar E, Mattison D, Chiu WA, Dix D, Kavlock R, Krewski D. Challenges and opportunities in the risk assessment of existing substances in Canada: lessons learned from the international community. International Journal of Risk Assessment and Management 2017;20;(1-3):261-283. |
R835802 (2016) R835802 (2017) R835802 (2018) |
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Blanchette AD, Grimm FA, Dalaijamts C, Hsieh NH, Ferguson K, Luo YS, Anson B, Rusyn I, Chiu WA. Thorough QT/QTc in a dish:An in vitro human model that accurately predicts clinical concentration-QTc relationships. Clinical Pharmacology and Therapeutics 2019;105:1175-1186. |
R835802 (2018) R835802C001 (2018) |
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Blanchette A, Burnett S, Rusyn I, Chiu W. A tiered approach to population-based in vitro testing for cardiotoxicity:Balancing estimates of potency and variability. Journal of Pharmacological and Toxicological Methods 01;119(107154). |
R835802 (2020) |
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Blanchette A, Burnett S, Grimm F, Rusyn I, Chiu W. A Bayesian Method for Population-wide Cardiotoxicity Hazard and Risk Characterization Using an In Vitro Human Model. Toxilogical Sciences 2020;178(2):391-403. |
R835802 (2019) |
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Bokkers BGH, Mengelers MJ, Bakker MI, Chiu WA, Slob W. APROBA-Plus: a probabilistic tool to evaluate and express uncertainty in hazard characterization and exposure assessment of substances. Food and Chemical Toxicology. 2017;110:408-417. |
R835802 (2017) R835802 (2018) |
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Burnett S, Karmakar M, Murphy W, Chiu W, Rusyn I. A new approach method for characterizing inter-species toxicodynamic variability. Journal of Toxicology and Environmental Health, Part A 2021;. |
R835802 (2020) |
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Ceballos D, Luo Y, Chen Z, Blanchette A, Zhou Y, Wright F, Baker E, Chiu W, Rusyn I. Relationships between constituents of energy drinks and beating parameters in human induced pluripotent stem cell (iPSC)-Derived cardiomyocytes. Food and Chemical Toxicology 2021;149:111979. |
R835802 (2019) |
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Chiu WA, Wright FA, Rusyn I. A tiered, Bayesian approach to estimating population variability for regulatory decision-making. ALTEX 2017;34(3):377-388. |
R835802 (2016) R835802 (2017) R835802 (2018) R835166 (2016) R835166 (Final) |
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Chiu WA, Axelrad DA, Dalaijamts C, Dockins C, Shao K, Shapiro AJ, Paoli G. Beyond the RfD:Broad application of a probabilistic approach to improve chemical dose-response assessments for noncancer effects. Environmental Health Perspective 2018;126(6):067009. |
R835802 (2018) R835802C001 (2018) |
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Chiu WA, Guyton KZ, Martin MT, Reif DM, Rusyn I. Use of high-throughput in vitro toxicity screening data in cancer hazard evaluations by IARC Monograph Working Groups. ALTEX 2018;35(1):51-64. |
R835802 (2017) R835802 (2018) R835802C003 (2018) |
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Chiu WA, Rusyn I. Advancing chemical risk assessment decision-making with population variability data: challenges and opportunities. Mammalian Genome 2018;29(1-2):182-189. |
R835802 (2017) R835802 (2018) |
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Cote I, Andersen ME, Ankley GT, Barone S, Birnbaum LS, Boekelheide K, Bois FY, Burgoon LD, Chiu WA, Crawford-Brown D, Crofton KM, DeVito M, Devlin RB, Edwards SW, Guyton KZ, Hattis D, Judson RS, Knight D, Krewski D, Lambert J, Maull EA, Mendrick D, Paoli GM, Patel CJ, Perkins EJ, Poje G, Portier CJ, Rusyn I, Schulte PA, Simeonov A, Smith MT, Thayer KA, Thomas RS, Thomas R, Tice RR, Vandenberg JJ, Villeneuve DL, Wesselkamper S, Whelan M, Whittaker C, White R, Xia M, Yauk C, Zeise L, Zhao J, DeWoskin RS. The next generation of risk assessment multi-year study--highlights of findings, applications to risk assessment, and future directions. Environmental Health Perspectives 2016;124(11):1671-1682. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) R835802C001 (2015) R835166 (Final) |
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Fantke P, Aylward L, Bare J, Chiu WA, Dodson R, Dwyer R, Ernstoff A, Howard B, Jantunen M, Jolliet O, Judson R, Kirchhübel N, Li D, Miller A, Paoli G, Price P, Rhomberg L, Shen B, Shin HM, Teeguarden J, Vallero D, Wambaugh J, Wetmore BA, Zaleski R, McKone TE. Advancements in life cycle human exposure and toxicity characterization. Environmetnal Health Perspective 2018;126:125001. |
R835802 (2018) R835802C001 (2018) |
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Ford L, Lin H, Tsai H, Zhou Y, Wright F, Sedykh A, Shah R, Chiu W, Rusyn I. Hazard and risk characterization of 56 structurally diverse PFAS using a targeted battery of broad coverage assays using six human cell types. TOXICOLOGY 2024;503(153763). |
R835802 (Final) |
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Garbutt TA, Konneker TI, Konganti K, Hillhouse AE, Swift-Haire F, Jones A, Phelps D, Aylor DL, Threadgill D. Permissiveness to form pluripotent stem cells may be an evolutionarily derived characteristic in Mus musculus. Scientific Reports 2018;8:14706. |
R835802 (2018) R835802C002 (2018) |
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Grimm FA, Iwata Y, Sirenko O, Bittner M, Rusyn I. High-content assay multiplexing for toxicity screening in induced pluripotent stem cell-derived cardiomyocytes and hepatocytes. Assay and Drug Development Technologies 2015;13(9):529-546. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) R835802C001 (2015) |
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Grimm FA, Iwata Y, Sirenko O, Chappell GA, Wright FA, Reif DM, Braisted J, Gerhold DL, Yeakley JM, Shepard P, Seligmann B, Roy T, Boogaard PJ, Ketelslegers HB, Rohde AM, Rusyn I. A chemical-biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives. Green Chemistry 2016;18(16):4407-4419. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) R835802C001 (2015) R835166 (Final) |
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Grimm FA, Blanchette A, House JS, Ferguson K, Hsieh NH, Dalaijamts C, Wright AA, Anson B, Wright FA, Chiu WA, Rusyn I. A human population-based organotypic in vitro model for cardiotoxicity screening. ALTEX 2018;35:441-452. |
R835802 (2018) R835802C001 (2018) R835802C003 (2018) |
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Grimm FA, House JS, Wilson MR, Sirenko O, Iwata Y, Wright FA, Ball N, Rusyn I. Multi-Dimensional in Vitro Bioactivity Profiling for Grouping of Glycol Ethers. Regulatory Toxicology and Pharmacology 2019;101:91-102. |
R835802 (2018) R835802C001 (2018) R835166 (Final) |
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Grimm FA, Klaren WD, Li X, Lehmler HJ, Karmakar M, Robertson LW, Chiu WA, Rusyn I. Cardiovascular effects of polychlorinated biphenyls and their major metabolites.Environmental Health Perspectives 2020;128(7):077008. |
R835802 (Final) |
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Grondin CJ, Davis AP, Wiegers TC, King BL, Wiegers JA, Reif DM, Hoppin JA, Mattingly CJ. Advancing exposure science through chemical data curation and integration in the Comparative Toxicogenomics Database. Environmental Health Perspectives 2016;124(10):1592-1599. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) R835802C003 (2015) |
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Guyton KZ, Rusyn I, Chiu WA, Corpet DE, van den Berg M, Ross MK, Christiani DC, Beland FA, Smith MT. Application of the key characteristics of carcinogens in cancer hazard identification. Carcinogenesis 2018;39(4):614-622. |
R835802 (2017) R835802 (2018) |
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House JS, Grimm FA, Jima DD, Zhou Y-H, Rusyn I, Wright FA. A pipeline for high-throughput concentration response modeling of gene expression for toxicogenomics. Frontiers in Genetics 2017;8:168 (11 pp.). |
R835802 (2017) R835802 (2018) |
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Iwata Y, Klaren WD, Lebakken CS, Grimm FA, Rusyn I. High-content assay multiplexing for vascular toxicity screening in induced pluripotent stem cell-derived endothelial cells and human umbilical vein endothelial cells. Assay and Drug Development Technologies 2017;15(6):267-279. |
R835802 (2017) R835802 (2018) R835166 (Final) |
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Judson R, Houck K, Martin M, Richard AM, Knudsen TB, Shah I, Little S, Wambaugh J, Woodrow Setzer R, Kothya P, Phuong J, Filer D, Smith D, Reif D, Rotroff D, Kleinstreuer N, Sipes N, Xia M, Huang R, Crofton K, Thomas RS. Editor's highlight: Analysis of the effects of cell stress and cytotoxicity on in vitro assay activity across a diverse chemical and assay space. Toxicological Sciences 2016;152(2):323-339. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) R835802C003 (2015) |
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Konganti K, Ehrlich A, Rusyn I, Threadgill DW. gQTL:a web application for QTL analysis using the collaborative cross mouse genetic reference population. G3:Genes, Genomes, Genetics 2018;8(8):2559-2562 |
R835802 (2017) R835802 (2018) R835802C001 (2018) R835802C002 (2018) |
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Li G, Shabalin AA, Rusyn I, Wright FA, Nobel AB. An empirical Bayes approach for multiple tissue eQTL analysis. Biostatistics 2018;19(3):391-406. |
R835802 (2017) R835802 (2018) |
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LInd L, Araujo J, Barchosky A, Belcher S, Berridge B, Chiamvimonvat N, Chiu W, Cogliano V, Elmore S, Farraj A. Key Characteristics of Cardiovascular Toxicants. Environmental Health Perspectives 2021;129(9). |
R835802 (2020) |
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Lu E, Grimm F, Rusyn I, De Saeger S, De Bouvre M, Chiu W. Advancing probabilistic risk assessment by integrating human biomonitoring, new approach methods, and Bayesian modeling:A case study with the mycotoxin deoxynivalenol. ENVIRONMENT INTERNATIONAL 2023;182(108326). |
R835802 (Final) R835166 (Final) |
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Marvel SW, To K, Grimm FA, Wright FA, Rusyn I, Reif DM. ToxPi Graphical User Interface 2.0: dynamic exploration, visualization, and sharing of integrated data models. BMC Bioinformatics 2018;19(1):80 (7 pp.). |
R835802 (2017) R835802 (2018) R835802C001 (2018) R835802C003 (2018) |
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Rusyn I, Greene N. The impact of novel assessment methodologies in toxicology on green chemistry and chemical alternatives. Toxicological Sciences 2018;161(2):276-284. |
R835802 (2017) R835802 (2018) |
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Shah I, Setzer RW, Jack J, Houck KA, Judson RS, Knudsen TB, Liu J, Martin MT, Reif DM, Richard AM, Thomas RS, Crofton KM, Dix DJ, Kavlock RJ. Using ToxCast™ data to reconstruct dynamic cell state trajectories and estimate toxicological points of departure. Environmental Health Perspectives 2016;124(7):910-919. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) |
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Sirenko O, Grimm FA, Ryan KR, Iwata Y, Chiu WA, Parham F, Wignall JA, Anson B, Cromwell EF, Behl M, Rusyn I, Tice RR. In vitro cardiotoxicity assessment of environmental chemicals using an organotypic human induced pluripotent stem cell-derived model. Toxicology and Applied Pharmacology 2017;322:60-74. |
R835802 (2016) R835802 (2017) R835802 (2018) R835166 (Final) |
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Tilley SK, Reif DM, Fry RC. Incorporating ToxCast and Tox21 datasets to rank biological activity of chemicals at Superfund sites in North Carolina. Environment International 2017;101:19-26. |
R835802 (2017) R835802 (2018) |
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Wignall JA, Muratov E, Sedykh A, Guyton KZ, Tropsha A, Rusyn I, Chiu WA. Conditional Toxicity Value (CTV) predictor: an in silico approach for generating quantitative risk estimates for chemicals. Environmental Health Perspectives 2018;126(5):057008 (13 pp.). |
R835802 (2017) R835802 (2018) |
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Zhang G, Marvel S, Truong L, Tanguay RL, Reif DM. Aggregate entropy scoring for quantifying activity across endpoints with irregular correlation structure. Reproductive Toxicology 2016;62:92-99. |
R835802 (2015) R835802 (2016) R835802 (2017) R835802 (2018) R835802C003 (2015) R835168 (Final) R835796 (2017) |
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Zhang G, Roell KR, Truong L, Tanguay RL, Reif DM. A data-driven weighting scheme for multivariate phenotypic endpoints recapitulates zebrafish developmental cascades. Toxicology and Applied Pharmacology 2017;314:109-117. |
R835802 (2016) R835802 (2017) R835802 (2018) R835796 (2017) |
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Zhou Y-H, Marron JS, Wright FA. Computation of ancestry scores with mixed families and unrelated individuals. Biometrics 2018;74(1):155-164. |
R835802 (2016) R835802 (2017) R835802 (2018) |
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Kosnik MB, Strickland JD, Marvel SW, Wallis DJ, Wallace K, Richard AM, Reif DM, Shafer TJ. Concentration–response evaluation of ToxCast compounds for multivariate activity patterns of neural network function. ARCHIVES OF TOXICOLOGY 2013;94:469-484. |
R835802 (2019) |
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Li G, Jima D, Wright FA, Nobel AB. HT-eQTL:integrative expression quantitative trait loci analysis in a large number of human tissues. BMC Bioinformatics 2018;19:95. |
R835802 (2018) R835802C003 (2018) |
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Kosnik MB, Reif DM. Determination of chemical-disease risk values to prioritize connections between environmental factors, genetic variants, and human diseases. Toxicology and Applied Pharmacology2019;379:114674. |
R835802C003 (2018) |
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Kosnik MB, Planchart A, Marvel SW, Reif DM, Mattingly CJ. Integration of curated and high-throughput screening data to elucidate environmental influences on disease pathways. Computational Toxicology2019;12:100094. |
R835802C003 (2018) |
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Chen Z, Liu Y, Wright FA, Chiu WA, Rusyn I. Rapid hazard characterization of environmental chemicals using a compendium of human cell lines from different organs. ALTEX-Alternatives to Animal Experimentation 2020; 37(4):623-638 |
R835802 (2019) |
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Hsieh NH, Reisfeld, B, Bois FY, Chiu WA. Applying a global sensitivity analysis workflow to improve the computational efficiencies in physiologically-based pharmacokinetic modeling. Frontiers in Pharmacology 2018 9:588. |
R835802 (2018) R835802C001 (2018) |
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Supplemental Keywords:
Cardiovascular, stem cells, toxicity pathway, tissue mimetics, variability, pharmacokinetic modelProgress and Final Reports:
Original Abstract Subprojects under this Center: (EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
R835802C001 High-throughput Hazard,Dose-responseandPopulationVariabilityAssessmentofCardiotoxicity in aHumanInducedPluripotentStem Cell(iPSC)-derivedinvitro Culture Model
R835802C002 Linking in vitro-to-in vivoToxicity Testing Using
Genetically-matchedOrganoids and Mice from a Novel Genetic Reference Population
R835802C003 A Pipeline for in vitro-to-in vivo Extrapolation, Population Modeling,
& Prioritization
The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.
Project Research Results
- Final Report
- 2020 Progress Report
- 2019 Progress Report
- 2018 Progress Report
- 2017 Progress Report
- 2015 Progress Report
- Original Abstract
45 journal articles for this center