Corrigendum: Analysis of the effects of cell stress and cytotoxicity on in vitro assay activity across a diverse chemical and assay space [Toxicological Sciences, 152, (2016) (323-339)] doi: 10.1093/toxsci/kfw092;Analysis of the effects of cell stress and cytotoxicity on in vitro assay activity across a diverse chemical and assay space

Toxicological Sciences

Volumn 152, Issue 2, 2016, Pages 323-339

  Judson, Richard ^a   Houck, Keith ^a   Martin, Matt ^a   Richard, Ann M ^a   Knudsen, Thomas B ^a   Shah, Imran ^a   Little, Stephen ^a   Wambaugh, John ^a   Setzer, R Woodrow ^a   Kothya, Parth ^a   Phuong, Jimmy ^a   Filer, Dayne ^a   Smith, Doris ^a   Reif, David ^b   Rotroff, Daniel ^b   Kleinstreuer, Nicole ^c   Sipes, Nisha ^d   Xia, Menghang ^e   Huang, Ruili ^e   Crofton, Kevin ^a   Thomas, Russell S ^a   more..

^a U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

^c ILS NICEATM Research Triangle Park   (United States)

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

^e NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Cell stress; Cytotoxicity; High throughput screening; In vitro; Oxidative stress

Indexed keywords

CONSUMER; CYTOTOXICITY ASSAY; DISEASE MODEL; ENZYMATIC DEGRADATION; GENE DISRUPTION; HAZARD ASSESSMENT; HIGH THROUGHPUT SCREENING; HUMAN; IN VITRO STUDY; MEMBRANE; OXIDATIVE STRESS; BIOASSAY; PHYSIOLOGICAL STRESS; PROCEDURES; TOXICITY TESTING;

BIOLOGICAL ASSAY; HUMANS; IN VITRO TECHNIQUES; STRESS, PHYSIOLOGICAL; TOXICITY TESTS;

EID: 84992690576     PISSN: 10966080     EISSN: 10960929     Source Type: Journal    
DOI: 10.1093/toxsci/kfw148     Document Type: Erratum

References (55)

1. Abassi, Y. A., Xi, B., Zhang, W., Ye, P., Kirstein, S. L., Gaylord, M. R., Feinstein, S. C., Wang, X., and Xu, X. (2009). Kinetic cell-based morphological screening: prediction of mechanism of compound action and off-target effects. Chem. Biol. 16, 712-723.
2. Akaike, H. (1998). Information Theory and an Extension of the Maximum Likelihood Principle. Springer, New York.
3. Ankley, G. T., Bennett, R. S., Erickson, R. J., Hoff, D. J., Hornung, M. W., Johnson, R. D., Mount, D. R., Nichols, J. W., Russom, C. L., Schmieder, P. K., et al. (2010). Adverse outcome pathways: a conceptual framework to support ecotoxicology research and risk assessment. Environ. Toxicol. Chem. 29, 730-741.
4. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000). Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29.
5. Attene-Ramos, M. S., Huang, R., Michael, S., Witt, K. L., Richard, A., Tice, R. R., Simeonov, A., Austin, C. P., andXia,M. (2015). Profiling of the Tox21 chemical collection for mitochondrial function to identify compounds that acutely decrease mitochondrial membrane potential. Environ. Health Perspect. 123, 49-56.
6. Attene-Ramos, M. S., Miller, N., Huang, R., Michael, S., Itkin, M., Kavlock, R. J., Austin, C. P., Shinn, P., Simeonov, A., Tice, R. R., and., et al. (2013). The Tox21 robotic platform for the assessment of environmental chemicals-From vision to reality. Drug Discov. Today 18, 716-723.
7. 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.
8. Berg, E. L., Kunkel, E. J., and Hytopoulos, E. (2005). Biological complexity and drug discovery: A practical systems biology approach. Syst. Biol. (Stevenage) 152, 201-206.
9. Berg, E. L., Kunkel, E. J., Hytopoulos, E., and Plavec, I. (2006). Characterization of compound mechanisms and secondary activities by BioMAP analysis. J. Pharmacol. Toxicol. Methods 53, 67-74.
10. Berg, E. L., Yang, J., Melrose, J., Nguyen, D., Privat, S., Rosler, E., Kunkel, E. J., and Ekins, S. (2010). Chemical target and pathway toxicity mechanisms defined in primary human cell systems. J. Pharmacol. Toxicol. Methods 61, 3-15.
11. Bolt, M. J., Stossi, F., Callison, A. M., Mancini, M. G., Dandekar, R., and Mancini, M. A. (2015). Systems level-based RNAi screening by high content analysis identifies UBR5 as a regulator of estrogen receptor-alpha protein levels and activity. Oncogene 34, 154-164.
12. Boobis, A. R., Doe, J. E., Heinrich-Hirsch, B., Meek, M. E., Munn, S., Ruchirawat, M., Schlatter, J., Seed, J., and Vickers, C. (2008). IPCS framework for analyzing the relevance of a noncancer mode of action for humans. Crit. Rev. Toxicol. 38, 87-96.
13. Bruns, R. F., and Watson, I. A. (2012). Rules for identifying potentially reactive or promiscuous compounds. J. Med. Chem. 55, 9763-9772.
14. Collins, F. S., Gray, G. M., and Bucher, J. R. (2008). Toxicology. Transforming environmental health protection. Science 319, 906-907.
15. Dionisio, K. L., Frame, A., Goldsmith, M. R., Wambaugh, J., Liddell, A., Cathey, T., Smith, D., Vail, J., Ernstoff, A. S., et al. (2013). Exploring consumer exposure pathways and patterns of use for chemicals in the environment. Toxicol. Rep. 2, 228-237.
16. 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.
17. Giuliano, K. A., Cheung, W. S., Curran, D. P., Day, B. W., Kassick, A. J., Lazo, J. S., Nelson, S. G., Shin, Y., and Taylor, D. L. (2005). Systems cell biology knowledge created from high content screening. Assay Drug Dev. Technol. 3, 501-514.
18. Giuliano, K. A., Gough, A. H., Taylor, D. L., Vernetti, L. A., and Johnston, P. A. (2010). Early safety assessment using cellular systems biology yields insights into mechanisms of action. J. Biomol. Screen. 15, 783-797.
19. Giuliano, K. A., Johnston, P. A., Gough, A., and Taylor, D. L. (2006). Systems cell biology based on high-content screening. Methods Enzymol. 414, 601-619.
20. Harding, H. P., Zhang, Y., Zeng, H., Novoa, I., Lu, P. D., Calfon, M., Sadri, N., Yun, C., Popko, B., Paules, R., et al. (2003). An integrated stress response regulates amino acid metabolism and resistance to oxidative stress. Mol. Cell 11, 619-633.
21. Houck, K. A., Dix, D. J., Judson, R. S., Kavlock, R. J., Yang, J., and Berg, E. L. (2009). Profiling bioactivity of the ToxCast chemical library using BioMAP primary human cell systems. J. Biomol. Screen. 14, 1054-1066.
22. Hsu, C. W., Zhao, J., Huang, R., Hsieh, J. H., Hamm, J., Chang, X., Houck, K., and Xia, M. (2014). Quantitative high-throughput profiling of environmental chemicals and drugs that modulate farnesoid X receptor. Sci. Rep. 4, 6437.
23. 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.
24. Huang, R., Xia, M., Cho, M. H., Sakamuru, S., Shinn, P., Houck, K. A., Dix, D. J., Judson, R. S., Witt, K. L., Kavlock, R. J., et al. (2011). Chemical genomics profiling of environmental chemical modulation of human nuclear receptors. Environ. Health Perspect. 119, 1142-1148.
25. Imran, Shah, Woodrow, Setzer, John, Jack, Keith, Houck, Thomas, Knudsen, Matt, Martin, David, Reif, Ann, M. Richard, David, J. Dix, and Robert, J. Kavlock. Elucidating dynamic modulation of cellular state function during chemical perturbation. Environ. Health Perspect. Forthcoming.
26. 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.
27. 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 highthroughput chemical risk assessment. Chem. Res. Toxicol. 24, 451-462.
28. 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.
29. Kitamura, S., Suzuki, T., Sanoh, S., Kohta, R., Jinno, N., Sugihara, K., Yoshihara, S., Fujimoto, N., Watanabe, H., and Ohta, S. (2005). Comparative study of the endocrine-disrupting activity of bisphenol A and 19 related compounds. Toxicol. Sci. 84, 249-259.
30. Kleinstreuer, N. C., Yang, J., Berg, E. L., Knudsen, T. B., Richard, A. M., Martin, M. T., Reif, D. M., Judson, R. S., Polokoff, M., Dix, D. J., et al. (2014). Phenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanisms. Nat. Biotechnol. 32, 583-591.
31. Knight, A. W., Little, S., Houck, K., Dix, D., Judson, R., Richard, A., McCarroll, N., Akerman, G., Yang, C., Birrell, L., et al. (2009). Evaluation of high-throughput genotoxicity assays used in profiling the US EPA ToxCast chemicals. Regul. Toxicol. Pharmacol. 55, 188-199.
32. 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., J. R., et al. (2011). Activity profiles of 309 ToxCast chemicals evaluated across 292 biochemical targets. Toxicology 282, 1-15.
33. 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.
34. Meek, M. E., Bucher, J. R., Cohen, S. M., Dellarco, V., Hill, R. N., Lehman-McKeeman, L. D., Longfellow, D. G., Pastoor, T., Seed, J., and Patton, D. E. (2003). A framework for human relevance analysis of information on carcinogenic modes of action. Crit. Rev. Toxicol. 33, 591-653.
35. Muller, P. Y., and Milton, M. N. (2012). The determination and interpretation of the therapeutic index in drug development. Nat. Rev. Drug Discov. 11, 751-761.
36. NCBI. (2008). PubChem. Available at http://pubchem.ncbi.nlm. nih.gov/. Accessed August 8, 2008.
37. NRC. (2007). Toxicity Testing in the 21st Century: A Vision and a Strategy. National Academies Press, Washington, DC.
38. O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., and Hutchison, G. R. (2011)."Open Babel: An open chemical toolbox. J. Cheminform. 3, 33.
39. Romanov, S., Medvedev, A., Gambarian, M., Poltoratskaya, N., Moeser, M., Medvedeva, L., Diatchenko, L., and Makarov, S. (2008). Homogeneous reporter system enables quantitative functional assessment of multiple transcription factors. Nat. Methods 5, 253-260.
40. Rotroff, D. M., Beam, A. L., Dix, D. J., Farmer, A., Freeman, K. M., Houck, K. A., Judson, R. S., LeCluyse, E. L., Martin, M. T., Reif, D. M., et al. (2010). Xenobiotic-metabolizing enzyme and transporter gene expression in primary cultures of human hepatocytes modulated by ToxCast chemicals. J. Toxicol. Environ. Health B Crit. Rev. 13, 329-346.
41. 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.
42. Seed, J., Carney, E. W., Corley, R. A., Crofton, K. M., DeSesso, J. M., Foster, P. M., Kavlock, R., Kimmel, G., Klaunig, J., Meek, M. E., et al. (2005). Overview: Using mode of action and life stage information to evaluate the human relevance of animal toxicity data. Crit. Rev. Toxicol. 35, 664-672.
43. Shen, J., Xu, L., Fang, H., Richard, A. M., Bray, J. D., Judson, R. S., Zhou, G., Colatsky, T. J., Aungst, J. L., Teng, C., et al. (2013). EADB: An estrogenic activity database for assessing potential endocrine activity. Toxicol. Sci. 135, 277-291.
44. Shukla, S. J., Huang, R., Austin, C. P., and Xia, M. (2010). The future of toxicity testing: A focus on in vitro methods using a quantitative high-throughput screening platform. Drug Discov. Today 15, 997-1007.
45. 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.
46. 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 microscopybased contextual assays. Chem. Biol. 21, 743-753.
47. Sturla, S. J., Boobis, A. R., FitzGerald, R. E., Hoeng, J., Kavlock, R. J., Schirmer, K., Whelan, M., Wilks, M. F., and Peitsch, M. C. (2014). Systems toxicology: from basic research to risk assessment. Chem. Res. Toxicol. 27, 314-329.
48. Taylor, D. L., and Giuliano, K. A. (2005). Multiplexed high content screening assays create a systems cell biology approach to drug discovery. Drug Discov. Today Suppl, 13-18.
49. 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., 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.
50. 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.
51. Tice, R. R., Austin, C. P., Kavlock, R. J., and Bucher, J. R. (2013). Improving the human hazard characterization of chemicals: A tox21 update. Environ. Health Perspect. 121, 756-765.
52. Vichai, V., and Kirtikara, K. (2006). Sulforhodamine B colorimetric assay for cytotoxicity screening. Nat. Protoc. 1, 1112-1116.
53. 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.
54. Xia, M., Huang, R., Witt, K. L., Southall, N., Fostel, J., Cho, M. H., Jadhav, A., Smith, C. S., Inglese, J., Portier, C. J., et al. (2008). Compound cytotoxicity profiling using quantitative highthroughput screening. Environ. Health Perspect. 116, 284-291.
55. Yap, C. W. (2011). PaDEL-descriptor: An open source software to calculate molecular descriptors and fingerprints. J. Comput. Chem. 32, 1466-1474.