Analysis of the ToxCast Chemical-Assay Space Using the Comparative Toxicogenomics Database

Chemical Research in Toxicology

Volumn 28, Issue 11, 2015, Pages 2210-2223

  Hu, Bingjie ^a   Gifford, Eric ^a   Wang, Huijun ^a   Bailey, Wendy ^a   Johnson, Timothy ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPARATIVE TOXICOLOGY; DATA BASE; HUMAN; HUMAN CELL; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; SAFETY; TOXICITY TESTING; ADVERSE DRUG REACTION; ANIMAL; BIOASSAY; FACTUAL DATABASE; PRECLINICAL STUDY; PROCEDURES; TOXICOGENETICS;

DRUG; ENDOCRINE DISRUPTOR; PESTICIDE;

ANIMALS; BIOLOGICAL ASSAY; DATABASES, FACTUAL; DRUG EVALUATION, PRECLINICAL; DRUG-RELATED SIDE EFFECTS AND ADVERSE REACTIONS; ENDOCRINE DISRUPTORS; HUMANS; PESTICIDES; PHARMACEUTICAL PREPARATIONS; TOXICITY TESTS; TOXICOGENETICS;

EID: 84947079827     PISSN: 0893228X     EISSN: 15205010     Source Type: Journal    
DOI: 10.1021/acs.chemrestox.5b00369     Document Type: Article

References (56)

1. Olson, H., Betton, G., Robinson, D., Thomas, K., Monro, A., Kolaja, G., Lilly, P., Sanders, J., Sipes, G., and Bracken, W. (2000) Concordance of the toxicity of pharmaceuticals in humans and in animals Regul. Toxicol. Pharmacol. 32, 56-67 10.1006/rtph.2000.1399
2. Huang, R., Southall, N., Cho, M.-H., Xia, M., Inglese, J., and Austin, C. P. (2008) Characterization of diversity in toxicity mechanism using in vitro cytotoxicity assays in quantitative high throughput screening Chem. Res. Toxicol. 21, 659-667 10.1021/tx700365e
3. Schmidt, C. W. (2009) TOX 21: new dimensions of toxicity testing Environ. Health Perspect. 117, A348-A353 10.1289/ehp.117-a348
4. Dambach, D. M., Andrews, B. A., and Moulin, F. (2005) New technologies and screening strategies for hepatotoxicity: use of in vitro models Toxicol. Pathol. 33, 17-26 10.1080/01926230590522284
5. 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 Discovery Today 15, 997-1007 10.1016/j.drudis.2010.07.007
6. 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 10.1093/toxsci/kfl103
7. Kavlock, R., Chandler, K., Houck, K., Hunter, S., Judson, R., Kleinstreuer, N., Knudsen, T., Martin, M., Padilla, S., and Reif, D. (2012) Update on EPA's ToxCast program: providing high throughput decision support tools for chemical risk management Chem. Res. Toxicol. 25, 1287-1302 10.1021/tx3000939
8. 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., and Dix, D. J. (2010) In vitro screening of environmental chemicals for targeted testing prioritization: the ToxCast project Environ. Health Perspect. 118, 485-492 10.1289/ehp.0901392
9. Martin, M. T., Judson, R. S., Reif, D. M., Kavlock, R. J., and Dix, D. J. (2009) Profiling chemicals based on chronic toxicity results from the US EPA ToxRef Database Environ. Health Perspect. 117, 392-399 10.1289/ehp.0800074
10. Shah, I., Houck, K., Judson, R. S., Kavlock, R. J., Martin, M. T., Reif, D. M., Wambaugh, J., and Dix, D. J. (2011) Using nuclear receptor activity to stratify hepatocarcinogens PLoS One 6, e14584 10.1371/journal.pone.0014584
11. Martin, M. T., Knudsen, T. B., Reif, D. M., Houck, K. A., Judson, R. S., Kavlock, R. J., and Dix, D. J. (2011) Predictive model of rat reproductive toxicity from ToxCast high throughput screening Biol. Reprod. 85, 327-339 10.1095/biolreprod.111.090977
12. Sipes, N. S., Martin, M. T., Reif, D. M., Kleinstreuer, N. C., Judson, R. S., Singh, A. V., Chandler, K. J., Dix, D. J., Kavlock, R. J., and Knudsen, T. B. (2011) Predictive models of prenatal developmental toxicity from ToxCast high-throughput screening data Toxicol. Sci. 124, 109-127 10.1093/toxsci/kfr220
13. 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 10.1021/tx400021f
14. Davis, A. P., Murphy, C. G., Rosenstein, M. C., Wiegers, T. C., and Mattingly, C. J. (2008) The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study BMC Med. Genomics 1, 48 10.1186/1755-8794-1-48
15. Davis, A. P., Murphy, C. G., Johnson, R., Lay, J. M., Lennon-Hopkins, K., Saraceni-Richards, C., Sciaky, D., King, B. L., Rosenstein, M. C., and Wiegers, T. C. (2013) The comparative toxicogenomics database: update 2013 Nucleic Acids Res. 41, D1104-D1114 10.1093/nar/gks994
16. Davis, A. P., Wiegers, T. C., Roberts, P. M., King, B. L., Lay, J. M., Lennon-Hopkins, K., Sciaky, D., Johnson, R., Keating, H., and Greene, N. (2013) A CTD-Pfizer collaboration: manual curation of 88 000 scientific articles text mined for drug-disease and drug-phenotype interactions Database 2013, bat080 10.1093/database/bat080
17. Davis, A. P., Wiegers, T. C., Rosenstein, M. C., and Mattingly, C. J. (2012) MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database Database 2012, bar065 10.1093/database/bar065
18. Bolton, E. E., Wang, Y., Thiessen, P. A., and Bryant, S. H. (2008) PubChem: integrated platform of small molecules and biological activities Annu. Rep. Comput. Chem. 4, 217-241 10.1016/S1574-1400(08)00012-1
19. R Development Core Team. ((2014) R: A language and environment for statistical computing, R Foundation for Statistical Computing.
20. Evans, S., Waller, P. C., and Davis, S. (2001) Use of proportional reporting ratios (PRRs) for signal generation from spontaneous adverse drug reaction reports. Pharmacoepidemiol Pharmacoepidemiol. Drug Saf. 10, 483-486 10.1002/pds.677
21. Ng, H. W., Perkins, R., Tong, W., and Hong, H. (2014) Versatility or Promiscuity: The Estrogen Receptors, Control of Ligand Selectivity and an Update on Subtype Selective Ligands Int. J. Environ. Res. Public Health 11, 8709-8742 10.3390/ijerph110908709
22. Krasowski, M. D., Ni, A., Hagey, L. R., and Ekins, S. (2011) Evolution of promiscuous nuclear hormone receptors: LXR, FXR, VDR, PXR, and CAR Mol. Cell. Endocrinol. 334, 39-48 10.1016/j.mce.2010.06.016
23. Gonzalez, F. J. (1990) Molecular genetics of the P-450 superfamily Pharmacol. Ther. 45, 1-38 10.1016/0163-7258(90)90006-N
24. Pichard, L., Fabre, I., Fabre, G., Domergue, J., Saint Aubert, B., Mourad, G., and Maurel, P. (1990) Cyclosporin A drug interactions. Screening for inducers and inhibitors of cytochrome P-450 (cyclosporin A oxidase) in primary cultures of human hepatocytes and in liver microsomes Drug Metab. Dispos. 18, 595-606
25. TM chemicals evaluated across 292 biochemical targets Toxicology 282, 1-15 10.1016/j.tox.2010.12.010
26. Huang, Q., Jin, X., Gaillard, E. T., Knight, B. L., Pack, F. D., Stoltz, J. H., Jayadev, S., and Blanchard, K. T. (2004) Gene expression profiling reveals multiple toxicity endpoints induced by hepatotoxicants Mutat. Res., Fundam. Mol. Mech. Mutagen. 549, 147-167 10.1016/j.mrfmmm.2003.12.020
27. Cho, K.-h., Kim, H.-j., Rodriguez-Iturbe, B., and Vaziri, N. D. (2009) Niacin ameliorates oxidative stress, inflammation, proteinuria, and hypertension in rats with chronic renal failure Am. J. Physiol. 297, F106-F113 10.1152/ajprenal.00126.2009
28. Sam, F., Kerstetter, D. L., Pimental, D. R., Mulukutla, S., Tabaee, A., Bristow, M. R., Colucci, W. S., and Sawyer, D. B. (2005) Increased reactive oxygen species production and functional alterations in antioxidant enzymes in human failing myocardium J. Card. Failure 11, 473-480 10.1016/j.cardfail.2005.01.007
29. Thomas, R. S., Black, M., Li, L., Healy, E., Chu, T.-M., Bao, W., Andersen, M., and Wolfinger, R. (2012) A comprehensive statistical analysis of predicting in vivo hazard using high-throughput in vitro screening Toxicol. Sci. 128, 398-417 10.1093/toxsci/kfs159
30. Martin, M. T., Mendez, E., Corum, D. G., Judson, R. S., Kavlock, R. J., Rotroff, D. M., and Dix, D. J. (2009) Profiling the reproductive toxicity of chemicals from multigeneration studies in the toxicity reference database Toxicol. Sci. 110, 181-190 10.1093/toxsci/kfp080
31. Knudsen, T. B., Martin, M. T., Kavlock, R. J., Judson, R. S., Dix, D. J., and Singh, A. V. (2009) Profiling the activity of environmental chemicals in prenatal developmental toxicity studies using the US EPA's ToxRefDB Reprod. Toxicol. 28, 209-219 10.1016/j.reprotox.2009.03.016
32. Bowes, J., Brown, A. J., Hamon, J., Jarolimek, W., Sridhar, A., Waldron, G., and Whitebread, S. (2012) Reducing safety-related drug attrition: the use of in vitro pharmacological profiling Nat. Rev. Drug Discovery 11, 909-922 10.1038/nrd3845
33. 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. Screening 14, 1054-1066 10.1177/1087057109345525
34. Rockman, H. A., Koch, W. J., and Lefkowitz, R. J. (2002) Seven-transmembrane-spanning receptors and heart function Nature 415, 206-212 10.1038/415206a
35. Tang, C.-M. and Insel, P. A. (2004) GPCR expression in the heart:"new" receptors in myocytes and fibroblasts Trends Cardiovasc. Med. 14, 94-99 10.1016/j.tcm.2003.12.007
36. Zuscik, M. J., Chalothorn, D., Hellard, D., Deighan, C., McGee, A., Daly, C. J., Waugh, D. J., Ross, S. A., Gaivin, R. J., and Morehead, A. J. (2001) Hypotension, autonomic failure, and cardiac hypertrophy in transgenic mice overexpressing the α1B-adrenergic receptor J. Biol. Chem. 276, 13738-13743
37. Vecchione, C., Fratta, L., Rizzoni, D., Notte, A., Poulet, R., Porteri, E., Frati, G., Guelfi, D., Trimarco, V., and Mulvany, M. J. (2002) Cardiovascular influences of α1b-adrenergic receptor defect in mice Circulation 105, 1700-1707 10.1161/01.CIR.0000012750.08480.55
38. Heng, B. C., Aubel, D., and Fussenegger, M. (2013) An overview of the diverse roles of G-protein coupled receptors (GPCRs) in the pathophysiology of various human diseases Biotechnol. Adv. 31, 1676-1694 10.1016/j.biotechadv.2013.08.017
39. Curran, M. E., Splawski, I., Timothy, K. W., Vincen, G. M., Green, E. D., and Keating, M. T. (1995) A molecular basis for cardiac arrhythmia: HERG mutations cause long QT syndrome Cell 80, 795-803 10.1016/0092-8674(95)90358-5
40. Splawski, I., Timothy, K. W., Sharpe, L. M., Decher, N., Kumar, P., Bloise, R., Napolitano, C., Schwartz, P. J., Joseph, R. M., and Condouris, K. (2004) Ca v 1.2 calcium channel dysfunction causes a multisystem disorder including arrhythmia and autism Cell 119, 19-31 10.1016/j.cell.2004.09.011
41. Belpoggi, F., Soffritti, M., Guarino, M., Lambertini, L., Cevolani, D., and Maltoni, C. (2002) Results of Long-Term Experimental Studies on the Carcinogenicity of Ethylene-bis-Dithiocarbamate (Mancozeb) in Rats Ann. N. Y. Acad. Sci. 982, 123-136 10.1111/j.1749-6632.2002.tb04928.x
42. LIVERTOX Database, http://livertox.nih.gov/TetracyclineAndOxytetracyline.htm. National Library of Medicine.
43. Kuroda, H., Ohtsuru, A., Futakuchi, M., Kawashita, Y., Nagayama, Y., Fukuda, E., Namba, H., Shirai, T., Kanematsu, T., and Yamashita, S. (2002) Distinctive gene expression of receptor-type tyrosine kinase families during rat hepatocarcinogenesis Int. J. Mol. Med. 9, 473-480 10.3892/ijmm.9.5.473
44. Gaughran, F., Payne, J., Sedgwick, P. M., Cotter, D., and Berry, M. (2006) Hippocampal FGF-2 and FGFR1 mRNA expression in major depression, schizophrenia and bipolar disorder Brain Res. Bull. 70, 221-227 10.1016/j.brainresbull.2006.04.008
45. Cohen, P. (2000) The regulation of protein function by multisite phosphorylation-a 25 year update Trends Biochem. Sci. 25, 596-601 10.1016/S0968-0004(00)01712-6
46. Shah, R. R., Morganroth, J., and Shah, D. R. (2013) Hepatotoxicity of tyrosine kinase inhibitors: clinical and regulatory perspectives Drug Saf. 36, 491-503 10.1007/s40264-013-0048-4
47. Force, T. and Kolaja, K. L. (2011) Cardiotoxicity of kinase inhibitors: the prediction and translation of preclinical models to clinical outcomes Nat. Rev. Drug Discovery 10, 111-126 10.1038/nrd3252
48. Villeneuve, J.-P. and Pichette, V. (2004) Cytochrome P450 and liver diseases Curr. Drug Metab. 5, 273-282 10.2174/1389200043335531
49. Wienkers, L. C. and Heath, T. G. (2005) Predicting in vivo drug interactions from in vitro drug discovery data Nat. Rev. Drug Discovery 4, 825-833 10.1038/nrd1851
50. Shah, F. and Greene, N. (2014) Analysis of Pfizer Compounds in EPA's ToxCast Chemicals-Assay Space Chem. Res. Toxicol. 27, 86-98 10.1021/tx400343t
51. Denu, J. M. and Dixon, J. E. (1998) Protein tyrosine phosphatases: mechanisms of catalysis and regulation Curr. Opin. Chem. Biol. 2, 633-641 10.1016/S1367-5931(98)80095-1
52. Paul, S. and Lombroso, P. (2003) Receptor and nonreceptor protein tyrosine phosphatases in the nervous system Cell. Mol. Life Sci. 60, 2465-2482 10.1007/s00018-003-3123-7
53. Wagner, K. R., Mei, L., and Huganir, R. L. (1991) Protein tyrosine kinases and phosphatases in the nervous system Curr. Opin. Neurobiol. 1, 65-73 10.1016/0959-4388(91)90011-U
54. Mestres, J., Gregori-Puigjané, E., Valverde, S., and Sole, R. V. (2008) Data completeness-the Achilles heel of drug-target networks Nat. Biotechnol. 26, 983-984 10.1038/nbt0908-983
55. Chen, B., Dong, X., Jiao, D., Wang, H., Zhu, Q., Ding, Y., and Wild, D. J. (2010) Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data BMC Bioinf. 11, 255 10.1186/1471-2105-11-255
56. Bento, A. P., Gaulton, A., Hersey, A., Bellis, L. J., Chambers, J., Davies, M., Krüger, F. A., Light, Y., Mak, L., and McGlinchey, S. (2014) The ChEMBL bioactivity database: an update Nucleic Acids Res. 42, D1083-D1090 10.1093/nar/gkt1031