Integrated model of chemical perturbations of a biological pathway using 18 in vitro high-throughput screening assays for the estrogen receptor

Toxicological Sciences

Volumn 148, Issue 1, 2015, Pages 137-154

  Judson, Richard S ^a   Magpantay, Felicia Maria ^b   Chickarmane, Vijay ^c   Haskell, Cymra ^d   Tania, Nessy ^e   Taylor, Jean ^f   Xia, Menghang ^g   Huang, Ruili ^g   Rotroff, Daniel M ^h   Filer, Dayne L ⁱ   Houck, Keith A ^a   Martin, Matthew T ^a   Sipes, Nisha ^j   Richard, Ann M ^a   Mansouri, Kamel ⁱ   Woodrow Setzer, R ^a   Knudsen, Thomas B ^a   Crofton, Kevin M ^a   Thomas, Russell S ^a  

^a U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^b UNIVERSITY OF MANITOBA   (Canada)

^c CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^d UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^e SMITH COLLEGE   (United States)

^f NEW YORK UNIVERSITY   (United States)

^g NATIONAL INSTITUTES OF HEALTH   (United States)

^h NORTH CAROLINA STATE UNIVERSITY   (United States)

ⁱ OAK RIDGE INSTITUTE FOR SCIENCE AND EDUCATION   (United States)

^j NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

more..

Author keywords

Biological modeling; EDSP; Estrogen receptor; High throughput screening; In vitro; Prioritization

Indexed keywords

ENVIRONMENTAL CHEMICAL; ESTROGEN RECEPTOR; ANTIESTROGEN; ESR2 PROTEIN, HUMAN; ESTROGEN; ESTROGEN RECEPTOR ALPHA; ESTROGEN RECEPTOR ALPHA, HUMAN; ESTROGEN RECEPTOR BETA; GREEN FLUORESCENT PROTEIN; HYBRID PROTEIN; MOLECULAR LIBRARY; POLLUTANT;

ARTICLE; CELL GROWTH; CELL PROLIFERATION ASSAY; CHEMICAL STRUCTURE; DIMERIZATION; FALSE NEGATIVE RESULT; HIGH THROUGHPUT SCREENING; IN VITRO STUDY; PROTEIN ANALYSIS; PROTEIN BINDING; TRANSACTIVATION ASSAY; AGONISTS; ANIMAL; ANTAGONISTS AND INHIBITORS; BIOLOGICAL MODEL; BIOLOGY; BOVINE; CELL LINE; CHEMISTRY; DRUG EFFECTS; GENETICS; GOVERNMENT; HUMAN; METABOLISM; MOLECULAR LIBRARY; MOUSE; POLLUTANT; REPORTER GENE; TOXICITY; UNITED STATES;

ANIMALS; CATTLE; CELL LINE; COMPUTATIONAL BIOLOGY; ENVIRONMENTAL POLLUTANTS; ESTROGEN ANTAGONISTS; ESTROGEN RECEPTOR ALPHA; ESTROGEN RECEPTOR BETA; ESTROGENS, NON-STEROIDAL; GENES, REPORTER; GREEN FLUORESCENT PROTEINS; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; MICE; MODELS, BIOLOGICAL; RECEPTORS, ESTROGEN; RECOMBINANT FUSION PROTEINS; SMALL MOLECULE LIBRARIES; UNITED STATES; UNITED STATES ENVIRONMENTAL PROTECTION AGENCY;

EID: 84947781653     PISSN: 10966080     EISSN: 10960929     Source Type: Journal    
DOI: 10.1093/toxsci/kfv168     Document Type: Article

References (47)

1. Akaike, H. (1998). Information Theory and an Extension of the Maximum Liklihood Principle. Springer, New York, NY.
2. Auld, D. S., Thorne, N., Nguyen, D. T., and Inglese, J. (2008). A specific mechanism for nonspecific activation in reporter-gene assays. ACS Chem. Biol. 3, 463-470.
3. Baell, J. B., and Holloway, G. A. (2010). New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J. Med. Chem. 53, 2719-2740.
4. Browne, P., Judson, R. S., Casey, W. M., Kleinstreuer, N. C., and Thomas, R. S. (2015). Screening chemicals for estrogen receptor bioactivity using a computational model. Environ Sci. Technol. 49, 8804-8814.
5. Bruns, R. F., and Watson, I. A. (2012). Rules for identifying potentially reactive or promiscuous compounds. J. Med. Chem., 55, 9763-9772.
6. Chan, W. K., Klock, G., and Bernard, H. U. (1989). Progesterone and glucocorticoid response elements occur in the long control regions of several human papillomaviruses involved in anogenital neoplasia. J. Virol. 63, 3261-3269.
7. Christian, A. E., Haynes, M. P., Phillips, M. C., and Rothblat, G. H. (1997). Use of cyclodextrins for manipulating cellular cholesterol content. J. Lipid Res. 38, 2264-2272.
8. Diel, P., Olff, S., Schmidt, S., and Michna, H. (2001). Molecular identification of potential selective estrogen receptor modulator (SERM) like properties of phytoestrogens in the human breast cancer cell line MCF-7. Planta Med. 67, 510-514.
9. Dix, D. J., Houck, K. A., Martin, M. T., Richard, A. M., Setzer, R. W., and Kavlock, R. J. (2007). The ToxCast program for prioritizing toxicity testing of environmental chemicals. Toxicol. Sci. 95, 5-12.
10. Dutertre, M., and Smith, C. L. (2000). Molecular mechanisms of selective estrogen receptor modulator (SERM) action. J. Pharmacol. Exp. Ther. 295, 431-437.
11. Gronemeyer, H., Gustafsson J. A. and Laudet V. (2004). Principles for modulation of the nuclear receptor superfamily. Nat. Rev. Drug. Discov. 3, 950-964.
12. Higa-Nishiyama, A., Takahashi-Ando, N., Shimizu, T., Kudo, T., Yamaguchi, I., and Kimura, M. (2005). A model transgenic cereal plant with detoxification activity for the estrogenic mycotoxin zearalenone. Transgenic Res. 14, 713-717.
13. Hoerl, A. E., and Kennard, R. W. (1970). Ridge regression: biased estimation for nonorthogonal problems. Technometrics 12, 55-67.
14. Hsieh, J. H., Sedykh, A., Huang, R., Xia, M., and Tice, R. R. (2015). A data analysis pipeline accounting for artifacts in Tox21 quantitative high-throughput screening assays. J. Biomol. Screen 20, 887-897.
15. Huang, R., Sakamuru, S., Martin, M. T., Reif, D. M., Judson, R. S., Houck, K. A., Casey, W., Hsieh, J. H., Shockley, K. R., Ceger, P., et al. (2014). Profiling of the Tox21 10K compound library for agonists and antagonists of the estrogen receptor alpha signaling pathway. Sci. Rep. 4: 5664.
16. Ihaka, R., and Gentleman, R. (1996). R: A language for data analysis and graphics. J.Comput. Graph. Stat. 5, 299-314.
17. Inglese, J., Johnson, R. L., Simeonov, A., Xia, M., Zheng, W., Austin, C. P., and Auld, D. S. (2007). High-throughput screening assays for the identification of chemical probes. Nat. Chem. Biol. 3, 466-479.
18. Judson, R. S., Houck, K. A., Kavlock, R. J., Knudsen, T. B., Martin, M. T., Mortensen, H. M., Reif, D. M., Rotroff, D. M., Shah, I., Richard, A. M., et al. (2010). In vitro screening of environmental chemicals for targeted testing prioritization: the ToxCast project. Environ. Health Perspect. 118, 485-492.
19. Judson, R. S., Kavlock, R. J., Setzer, R. W., Cohen Hubal, E. A., Martin, M. T., Knudsen, T. B., Houck, K. A., Thomas, R. S., Wetmore, B. A., and Dix, D. J. (2011). Estimating toxicityrelated biological pathway altering doses for high-throughput chemical risk assessment. Chem. Res. Toxicol. 24, 451-462.
20. Katzenellenbogen, B. S., Choi, I., Delage-Mourroux, R., Ediger, T. R., Martini, P. G., Montano, M., Sun, J., Weis, K., and Katzenellenbogen, J. A. (2000a). Molecular mechanisms of estrogen action: selective ligands and receptor pharmacology. J. Steroid Biochem. Mol. Biol. 74, 279-285.
21. Katzenellenbogen, B. S., and Katzenellenbogen, J. A. (2000). Estrogen receptor transcription and transactivation: Estrogen receptor alpha and estrogen receptor beta: regulation by selective estrogen receptor modulators and importance in breast cancer. Breast Cancer Res. 2, 335-344.
22. Katzenellenbogen, B. S., Montano, M. M., Ediger, T. R., Sun, J., Ekena, K., Lazennec, G., Martini, P. G., McInerney, E. M., Delage-Mourroux, R., Weis, K., and Katzenellenbogen, J. A. (2000b). Estrogen receptors: selective ligands, partners, and distinctive pharmacology. Recent Prog. Horm. Res. 55, 163-193; discussion 194-165.
23. Kavlock, R., Chandler, K., Houck, K., Hunter, S., Judson, R., Kleinstreuer, N., Knudsen, T., Martin, M., Padilla, S., Reif, D., et al. (2012). Update on EPA's ToxCast program: providing high throughput decision support tools for chemical risk management. Chem Res. Toxicol. 25, 1287-1302.
24. Kleinstreuer, N. C., Ceger, P., Allen, D., Strickland, J., Xiaoqing, C., Hamm, J., and Casey, W. (forthcoming). A Curated Database of Rodent Uterotrophic Bioactivity. Env. Health Perspectives DOI: 10.1289/ehp.1510183.
25. Knudsen, T. B., Houck, K. A., Sipes, N. S., Singh, A. V., Judson, R. S., Martin, M. T., Weissman, A., Kleinstreuer, N. C., Mortensen, H. M., Reif, D. M., et al. (2011). Activity profiles of 309 ToxCast chemicals evaluated across 292 biochemical targets. Toxicology 282, 1-15.
26. Le Guevel, R., and Pakdel, F. (2001). Assessment of oestrogenic potency of chemicals used as growth promoter by in-vitro methods. Hum. Reprod. 16, 1030-1036.
27. Mangelsdorf, D. J., Thummel, C., Beato, M., Herrlich, P., Schutz, G., Umesono, K., Blumberg, B., Kastner, P., Mark, M., Chambon, P., et al. (1995). The nuclear receptor superfamily: the second decade. Cell 83, 835-839.
28. Martin, M. T., Dix, D. J., Judson, R. S., Kavlock, R. J., Reif, D. M., Richard, A. M., Rotroff, D. M., Romanov, S., Medvedev, A., Poltoratskaya, N., et al. (2010). Impact of environmental chemicals on key transcription regulators and correlation to toxicity end points within EPA's ToxCast program. Chem. Res. Toxicol. 23, 578-590.
29. Miller, J. R., Thanabal, V., Melnick, M. M., Lall, M., Donovan, C., Sarver, R. W., Lee, D. Y., Ohren, J., and Emerson, D. (2010). The use of biochemical and biophysical tools for triage of highthroughput screening hits-A case study with Escherichia coli phosphopantetheine adenylyltransferase. Chem. Biol. Drug Des. 75, 444-454.
30. Miller, K. P., Gupta, R. K., and Flaws, J. A. (2006). Methoxychlor metabolites may cause ovarian toxicity through estrogenregulated pathways. Toxicol. Sci. 93, 180-188.
31. Nagel, S. C., Hagelbarger, J. L., and McDonnell, D. P. (2001). Development of an ER action indicator mouse for the study of estrogens, selective ER modulators (SERMs), and xenobiotics. Endocrinology 142, 4721-4728.
32. OECD. (2012). OECD Test No. 457: BG1Luc Estrogen Receptor Transactivation Test Method for Identifying Estrogen Receptor Agonists and Antagonists. 2012.
33. Reif, D. M., Martin, M. T., Tan, S. W., Houck, K. A., Judson, R. S., Richard, A. M., Knudsen, T. B., Dix, D. J., and Kavlock, R. J. (2010). Endocrine profiling and prioritization of environmental chemicals using ToxCast data. Environ. Health Perspect. 118, 1714-1720.
34. Rotroff, D. M., Dix, D. J., Houck, K. A., Kavlock, R. J., Knudsen, T. B., Martin, M. T., Reif, D. M., Richard, A. M., Sipes, N. S., Abassi, Y. A., et al. (2013). Real-time growth kinetics measuring hormone mimicry for toxcast chemicals in T-47D human ductal carcinoma cells. Chem. Res. Toxicol. 26, 1097-1107.
35. Rotroff, D. M., Martin, M. T., Dix, D. J., Filer, D. L., Houck, K. A., Knudsen, T. B., Sipes, N. S., Reif, D. M., Xia, M., Huang, R., et al. (2014). Predictive endocrine testing in the 21st century using in vitro assays of estrogen receptor signaling responses. Environ. Sci. Technol. 48, 8706-8716.
36. Rotroff, D. M., Wetmore, B. A., Dix, D. J., Ferguson, S. S., Clewell, H. J., Houck, K. A., Lecluyse, E. L., Andersen, M. E., Judson, R. S., Smith, C. M., et al. (2010). Incorporating human dosimetry and exposure into high-throughput in vitro toxicity screening. Toxicol. Sci. 117, 348-358.
37. Sipes, N. S., Martin, M. T., Kothiya, P., Reif, D. M., Judson, R. S., Richard, A. M., Houck, K. A., Dix, D. J., Kavlock, R. J., and Knudsen, T. B. (2013). Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays. Chem. Res. Toxicol. 26, 878-895.
38. Stossi, F., Bolt, M. J., Ashcroft, F. J., Lamerdin, J. E., Melnick, J. S., Powell, R. T., Dandekar, R. D., Mancini, M. G., Walker, C. L., Westwick, J. K., et al. (2014). Defining estrogenic mechanisms of bisphenol A analogs through high throughput microscopy-based contextual assays. Chem. Biol. 21, 743-753.
39. Thomas, R. S., Philbert, M. A., Auerbach, S. S., Wetmore, B. A., Devito, M. J., Cote, I., Rowlands, J. C., Whelan, M. P., Hays, S. M., Andersen, M. E., et al. (2013). Incorporating new technologies into toxicity testing and risk assessment: moving from 21st century vision to a data-driven framework. Toxicol. Sci. 136, 4-18.
40. Thorne, N., Auld, D. S., and Inglese, J. (2010). Apparent activity in high-throughput screening: origins of compound-dependent assay interference. Curr. Opin. Chem. Biol. 14, 315-324.
41. Tibshirani, R. (1996). Regression shrinkage and selection via the Lasso. J. Roy. Statis. Soc. Series B Method. 58, 267-288.
42. Wambaugh, J. F., Setzer, R. W., Reif, D. M., Gangwal, S., Mitchell-Blackwood, J., Arnot, J. A., Joliet, O., Frame, A., Rabinowitz, J., Knudsen, T. B., et al. (2013). High-throughput models for exposure-based chemical prioritization in the ExpoCast project. Environ. Sci. Technol. 47, 8479-8488.
43. Wambaugh, J. F., Wang, A., Dionisio, K. L., Frame, A., Egeghy, P., Judson, R., and Setzer, R. W. (2014). High throughput heuristics for prioritizing human exposure to environmental chemicals. Environ. Sci. Technol. 48, 12760-12767.
44. Wambaugh, J. F., Wetmore, B. A., Pearce, R., Strope, C., Goldsmith, R., Sluka, J. P., Sedykh, A., Tropsha, A., Bosgra, S., Shah, I., et al. (2015). Toxicokinetic triage for environmental chemicals. Toxicol. Sci.
45. Wetmore, B. A., Wambaugh, J. F., Ferguson, S. S., Li, L., Clewell, 3rd, H. J., Judson, R. S., Freeman, K., Bao, W., Sochaski, M. A., Chu, T. M., et al. (2013). Relative impact of incorporating pharmacokinetics on predicting in vivo hazard and mode of action from high-throughput in vitro toxicity assays. Toxicol. Sci. 132, 327-346.
46. Wetmore, B. A., Wambaugh, J. F., Ferguson, S. S., Sochaski, M. A., Rotroff, D. M., Freeman, K., Clewell, H. J., 3rd, Dix, D. J., Andersen, M. E., Houck, K. A., et al. (2012). Integration of dosimetry, exposure, and high-throughput screening data in chemical toxicity assessment. Toxicol. Sci. 125, 157-174.
47. Wishart, D. S., Knox, C., Guo, A. C., Cheng, D., Shrivastava, S., Tzur, D., Gautam, B. and Hassanali, M. (2008). "DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 36(Database issue): D901-D906.