Predictive models and computational toxicology

Methods in Molecular Biology

Volumn 947, Issue , 2013, Pages 343-374

  Knudsen, Thomas ^a   Martin, Matthew ^a   Chandler, Kelly ^a   Kleinstreuer, Nicole ^a   Judson, Richard ^a   Sipes, Nisha ^a  

^a U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

Author keywords

High throughput screening; Predictive models; Predictive toxicology; ToxCast

Indexed keywords

ANIMALIA; DANIO RERIO; MUS; ORYCTOLAGUS CUNICULUS; RATTUS;

EID: 84871881903     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-131-8_26     Document Type: Article

References (81)

1. Gluckman PD, Hanson MA (2004) Living with the past, evolution, development, and patterns of disease. Science 305:1733-1736
2. Kimmel CA, Kimmel GL, Euling SY (2006) Developmental and reproductive toxicity risk assessment for environmental agents. In: Hood RD (ed) Developmental and reproductive toxicology, a practical approach. CRC Press, Boca Raton, FL
3. Stillerman KP, Mattison DR, Guidice LC, Woodruff TJ (2008) Environmental exposures and adverse pregnancy outcomes, a review of the science. Reprod Sci 15:631-650
4. Feil R, Fraga MF (2012) Epigenetics and the environment: emerging patterns and implications. Nat Rev Genet 13:97-109
5. Shepard TH, Lemire RJ (2007) Catalog of teratogenic agents, 12th edn. The Johns Hopkins University Press, Baltimore, 545 pages
6. Judson R, Richard A, Dix DJ, Houck K, Martin M, Kavlock RJ, Dellarco V, Henry HT, Sayre P, Tan S, Carpenter T, Smith E (2009) The toxicity data landscape for environmental chemicals. Environ Health Perspect 117:685-695
7. Woodruff TJ, Zota AR, Schwartz JM (2011) Environmental chemicals in pregnant women in the United States, NHANES 2003-2004. Environ Health Perspect 6:878-885
8. Firestone M, Moya J, Cohen HE, Zartarian V, Xue J (2007) Identifying childhood age groups for exposure assessments and monitoring. Risk Anal 27:701-704
9. Hurtt ME, Cappon GD, Browning A (2003) Proposal for a tiered approach to developmental toxicity testing for veterinary pharmaceutical products for food producing animals. Food Chem Toxicol 41:611-619
10. Carney EW, Tornesi B, Keller C, Findlay HA, Nowland WS, Marshall VA, Ozolins TRS (2007) Refinement of a morphological scoring system for postimplantation rabbit conceptuses. Birth Defects Res B Dev Reprod Toxicol 80:213-222
11. National Research Council (2007) Toxicity testing in the 21st century, a vision and a strategy. The National Academies Press, Washington, DC
12. Collins FS, Gray GM, Bucher JR (2008) Transforming environmental health protection. Science 319:906-907
13. Kavlock RJ, Austin CP, Tice R (2009) Toxicity testing in the 21st century, implications for human health risk assessment. Risk Anal 29:485-487
14. Firestone M, Kavlock R, Zenick H, Kramer M, The US Environmental Protection Agency Working Group on the Future of Toxicity Testing (2010) The U.S. Environmental Protection Agency strategic plan for evaluating the toxicity of chemicals. J Toxicol Environ Health B Crit Rev 13:139-162
15. Dix DJ, Houck KA, Martin MT, Richard AM, Setzer RW, Kavlock RJ (2007) The ToxCast program for prioritizing toxicity testing of environmental chemicals. Toxicol Sci 95:5-12
16. Judson RS, Houck KA, Kavlock RJ, Knudsen TB, Martin MT, Mortensen HM, Reif DM, Rotroff DM, Shah I, Richard AM, Dix DJ (2010) In vitro screening of environmental chemicals for targeted testing prioritization: the ToxCast project. Environ Health Perspect 118: 485-492
17. Martin MT, Judson RS, Reif DM, Kavlock RJ, Dix DJ (2009) Profiling chemicals based on chronic toxicity results from the U.S. EPA ToxRef Database. Environ Health Perspect 117:1-8
18. Martin MT, Mendez E, Corum DG, Judson RS, Kavlock RJ, Rotroff DM, Dix DJ (2009) Profiling the reproductive toxicity of chemicals from multigeneration studies in the Toxicity Reference Database (ToxRefDB). Toxicol Sci 110:181-190
19. Knudsen TB, Martin MT, Kavlock RJ, Judson RS, Dix DJ, Singh AV (2009) Profiling the activity of environmental chemicals in prenatal developmental toxicity studies using the U.S. EPA's ToxRefDB. Reprod Toxicol 28:209-219
20. Brown EC, Classen A, Hathaway CR, Holmstead J, Powell T, Wehrum W, Weinstein K (2000) A practitioner's guide to the Federal Insecticide, Fungicide, and Rodenticide Act. In: Brown EC, Classen A, Hathaway CR, Holmstead J, Powell T, Wehrum W, Weinstein K (eds) Pesticide regulation deskbook. Latham & Watkins Environmental Law Institute, Washington, DC, 164 pages
21. Roberts EM, English PB, Grether JK, Windham GC, Somberg L, Wolff C (2007) Maternal residence near agricultural pesticide applications and autism spectrum disorders among children in the California Central Valley. Environ Health Perspect 115:1482-1489
22. Snijder CA, Roeleveld N, te Velde E, Steegers EAP, Raat H, Hofman A, Jaddoe VWV, Burdorf A (2012) Occupational exposure to chemicals and fetal growth, the Generation R Study. Hum Reprod 27(3):910-920. doi: 10.1093/humrep/der437
23. Knudsen TB, Houck KA, Sipes N, Singh AV, Judson R, Martin MT, Weissman A, Kleinstreuer NC, Mortensen HM, Reif D, Rabinowitz JR, Setzer RW, Richard AM, Dix DJ, Kavlock RJ (2011) Activity profiles of 309 ToxCast™ chemicals evaluated across 292 biochemical targets. Toxicology 282:1-15
24. Morisseau C, Merzlikin O, Lin A, He G, Feng W, Padilla I, Denison MS, Pessah IN, Hammock BD (2009) Toxicology in the fast lane, application of high-throughput bioassays to detect modulation of key enzymes and receptors. Environ Health Perspect 117:1867-1872
25. Judson RS, Kavlock RJ, Setzer RW, Cohen Hubal ES, Martin MT, Knudsen TB, Houck KA, Thomas RS, Wetmore BA, Dix DJ (2011) Estimating toxicity-related biological pathway altering doses for high-throughput chemical risk assessment. Chem Res Toxicol 24:451-462
26. Martin MT, Dix DJ, Judson RS, Kavlock RJ, Reif DM, Richard AM, Rotroff DM, Romanov S, Medvedev M, Poltoratskaya N, Gambarian M, Moeser M, Makarov SS, Houck KA (2010) Impact of environmental chemicals on key transcription regulators and correlation to tox-icity end points within EPA's ToxCast Program. Chem Res Toxicol 23:578-590
27. Huang R, Xia M, Cho MH, Sakamuru S, Shinn P, Houck KA, Dix DJ, Judson RS, Witt KL, Kavlock RJ, Tice RR, Austin CP (2011) Chemical genomics profiling of environmental chemical modulation of human nuclear receptors. Environ Health Perspect 119:1142-1148
28. Rotroff DM, Wetmore BA, Dix DJ, Ferguson SS, Clewell HJ, Houck KA, LeCluyse EL, Andersen ME, Judson R, Smith CM, Sochaski MA, Kavlock RJ, Boellmann F, Martin MT, Reif D, Wambaugh JF, Thomas RS (2010) Incorporating human dosimetry and exposure into high-throughput in vitro toxicity screening. Toxicol Sci 117:348-358
29. Knight AW, Little S, Houck KA, Dix DJ, Judson R, Richard AM, McCarroll N, Akerman G, Yang C, Birrell L, Walmsley RM (2009) Evaluation of high-throughput geno-toxicity assays used in profiling the US EPA ToxCast chemicals. Regul Toxicol Pharmacol 55:188-199
30. Houck KA, Dix DJ, Judson RS, Kavlock RJ, Yang J, Berg EL (2009) Profiling bioactivity of the ToxCast chemical library using BioMAP primary human cell systems. J Biomol Screen 14:1054-1066
31. Barrier M, Jeffay S, Nichols HP, Chandler KJ, Hoopes MR, Slentz-Kesler K, Hunter ES III (2011) Mouse embryonic stem cell adherent cell differentiation and cytotoxicity (ACDC) assay. Reprod Toxicol 31:383-391
32. Chandler KJ, Barrier M, Jeffay S, Nichols HP, Kleinstreuer NC, Singh AV, Reif DM, Sipes NS, Judson RS, Dix DJ, Kavlock RJ, Hunter ES III, Knudsen TB (2011) Evaluation of 309 environmental chemicals using a mouse embryonic stem cell adherent cell differentiation and cytotoxicity assay. PLoS One 6(6):e18540
33. Genschow E, Spielmann H, Scholz G, Pohl I, Seiler A, Clemann N, Bremer S, Becker K (2004) Validation of the embryonic stem cell test in the international ECVAM validation study on three in vitro embryotoxicity tests. Altern Lab Anim 32:209-244
34. Chapin RE, Stedman DB (2009) Endless possibilities: stem cells and the vision for toxicology testing in the 21st century. Toxicol Sci 112:17-22
35. Padilla S, Corum D, Padnos B, Hunter DL, Beam A, Houck KA, Sipes N, Kleinstreuer N, Knudsen T, Dix DJ, Reif DM (2012) Zebrafish developmental screening of the ToxCast phase I chemical library. Reprod Toxicol 33(2):174- 187. doi: 10.1016/j.reprotox.2011.10.18
36. Ankley GT, Bennett RS, Erickson RJ, Hoff DJ, Hornung MW, Johnson RD, Mount DR, Nichols JW, Russom CL, Schmieder PK, Serrrano JA, Tietge JE, Villeneuve DL (2010) Adverse outcome pathways: a conceptual framework to support ecotoxicology research and risk assessment. Environ Toxicol Chem 29:730-741
37. Kleinstreuer NC, Judson RS, Reif DM, Sipes NS, Singh AV, Chandler KJ, DeWoskin R, Dix DJ, Kavlock RJ, Knudsen TB (2011) Environmental impact on vascular development predicted by high throughput screening. Environ Health Perspect 119:1596-1603
38. Knudsen TB, Kleinstreuer NC (2012) Disruption of embryonic vascular development in predictive toxicology. Birth Defects Res C Embryo Today 93:312-323
39. Sipes NS, Martin MT, Reif DM, Kleinstreuer NC, Judson RS, Singh AV, Chandler KJ, Dix DJ, Kavlock RJ, Knudsen TB (2011) Predictive models of prenatal developmental toxicity from ToxCast high-throughput screening data. Toxicol Sci 124:109-127
40. Piersma AH, Rorije E, Beekhuijzen ME, Cooper R, Dix DJ, Heinrich-Hirsch B, Martin MT, Mendez E, Muller A, Paparella M, Ramsingh D, Reaves E, Ridgway P, Schenk E, Stachiw L, Ulbrich B, Hakkert BC (2011) Combined retrospective analysis of 498 rat multi-generation reproductive toxicity studies, on the impact of parameters related to F1 mating and F2 offspring. Reprod Toxicol 31:392-401
41. Martin MT, Knudsen TB, Reif DM, Houck KA, Judson RS, Kavlock RJ, Dix DJ (2011) Predictive model of rat reproductive toxicity from ToxCast high throughput screening. Biol Reprod 85:327-339
42. Schenk B, Weimer M, Bremer S, van der Burg B, Cortvrindt R, Freyberger A, Lazzari G, Pellizzer C, Piersma A, Schafer WR, Seiler A, Witters H, Schwarz M (2010) The ReProTect Feasibility Study, a novel comprehensive in vitro approach to detect reproductive toxicants. Reprod Toxicol 30:200-218
43. Judson R, Martin M, Egeghy P, Gangwal S, Reif D, Kothiya P, Wolf M, Cathey T, Transue T, Smith D, Vail J, Frame A, Mosher S, Cohen HE, Richard A (2012) Aggregating data for computational toxicology applications, the EPA ACToR system. Mol Toxicol 13(2): 1805-1831
44. Judson RS, Mortensen HM, Shah I, Knudsen TB, Elloumi F (2012) Using pathway modules as targets for assay development in xenobiotic screening. Mol Biosyst 8:531-542
45. National Research Council (2000) Scientific frontiers in developmental toxicology and risk assessment. The National Academies Press, Washington, DC
46. Knudsen TB, Kavlock RJ (2008) Comparative bioinformatics and computational toxicology. In: Abbott B, Hansen D (eds) Developmental toxicology, vol 3, Target organ toxicology series. Taylor and Francis, New York, pp 311-360
47. Knudsen TB, Daston GP (2010) Virtual tissues and developmental systems biology. In: McQueen CA (ed) Comprehensive toxicology, vol 12. Academic, Oxford, pp 347-358
48. Reif D, Martin MT, Tan S, Houck KA, Judson R, Richard AM, Knudsen TB, Dix DJ, Kavlock RJ (2010) Endocrine profiling and prioritization of environmental chemicals using ToxCast data. Environ Health Perspect 118:2-8
49. Shah I, Houck KA, Judson R, Kavlock RJ, Martin MT, Reif D, Wambaugh JF, Dix DJ (2011) Using nuclear receptor activity to stratify hepatocarcinogens. PLoS One 6(2):e14584
50. Sipes NS, Padilla S, Knudsen TB (2011) Zebrafish, as an integrative model for twenty-fi rst century toxicity testing. Birth Defects Res C Embryo Today 93:256-267
51. Speilman H (2009) The way forward in reproductive/developmental toxicity testing. Altern Lab Anim 37:641-656
52. Spielmann H, Pohl I, Doering B, Liebsch M, Moldenhauer F (1997) The embryonic stem cell test, an in vitro embryotoxicity test using two permanent mouse cell lines, 3 T3fibroblasts and embryonic stem cells. In Vitro Toxicol 10:119-127
53. West PR, Weir AM, Smith AM, Donley EL, Cezar GG (2010) Predicting human developmental toxicity of pharmaceuticals using human embryonic stem cells and metabolomics. Toxicol Appl Pharmacol 247:18-27
54. van Dartel DA, Pennings JL, Robinson JF, Kleinjans JC, Piersma AH (2011) Discriminating classes of developmental toxicants using gene expression profiling in the embryonic stem cell test. Toxicol Lett 201:143-151
55. Knudsen TB, Kavlock RJ, Daston GP, Stedman DB, Hixon M, Kim J (2011) Developmental toxicity testing for safety assessment, new approaches and technologies. Birth Defects Res B Dev Reprod Toxicol 92:413-420
56. Krishnamurthy P, Schuetz JD (2006) Role of ABCG2/BCRP in biology and medicine. Annu Rev Pharmacol Toxicol 46:381-410
57. Susanto J, Lin Y-H, Chen Y-N, Shen C-R, Yan Y-T, Tsai S-T, Chen C-H, Shen C-N (2008) Porphyrin homeostasis maintained by ABCG2 regulates self-renewal of embryonic stem cells. PLoS One 3(12):e4023. doi: 10.1371/journal. pone.0004023
58. Kleinstreuer NC, Smith AM, West PR, Conard K, Fontaine B, Weir-Hauptman AM, Palmer J, Knudsen TB, Dix DJ, Donley EL, Cezar GG (2011) Identifying developmental toxicity pathways for a subset of ToxCast chemicals using human embryonic stem cells and metab-olomics. Toxicol Appl Pharmacol 257: 111-121
59. Peraza MA, Cromey DW, Carolus B, Carter DE, GandolfiAJ (2006) Morphological and functional alterations in human proximal tubular cell line induced by low level inorganic arsenic, evidence for targeting of mitochondria and initiated apoptosis. J Appl Toxicol 26:356-367
60. Goetz AK, Ren HZ, Schmid JE, Blystone CR, Thillainadarajah I, Best DS, Nichols HP, Strader LF, Wolf DC, Narotsky MG, Rockett JC, Dix DJ (2007) Disruption of testosterone homeostasis as a mode of action for the reproductive toxicity of triazole fungicides in the male rat. Toxicol Sci 95:227-239
61. Tian Y, Ke S, Denison MS, Rabson AB, Gallo MA (1999) Ah receptor and NF-kappa B interactions, a potential mechanism for dioxin toxic-ity. J Biol Chem 274:510-515
62. Abbott BD, Buckalew AR, DeVito MJ, Ross D, Bryant PL, Schmid JE (2003) EGF and TGF-alpha expression in fluence the developmental toxicity of TCDD: dose response and AhR phenotype in EGF, TGF-alpha, and EGF plus TGF-alpha knockout mice. Toxicol Sci 71:84-95
63. Tian YA (2009) Ah receptor and NF-kappa B interplay on the stage of epigenome. Biochem Pharmacol 77:670-680
64. Martin MT, Knudsen TB, Judson RS, Kavlock RJ, Dix DJ (2012) Economic benefits of using adaptive predictive models of reproductive tox-icity in the context of a tiered testing paradigm. Syst Biol Reprod Med 58:3-9
65. Jochum W, Passegue E, Wagner EF (2001) AP-1 in mouse development and tumorigene-sis. Oncogene 20:2401-2412
66. Mark M, Ghyselinck NB, Chambon P (2009) Function of retinoic acid receptors during embryonic development. Nucl Recept Signal 7:e002
67. Wu MY, Hill CS (2009) Tgf-beta superfamily signaling in embryonic development and homeostasis. Dev Cell 16:329-343
68. Yarim GF, Karahan S, Nisbet C (2007) Elevated plasma levels of interleukin 1 beta, tumour necrosis factor alpha and monocyte chemotac-tic protein 1 are associated with pregnancy toxaemia in ewes. Vet Res Commun 31:565-573
69. Wetmore BA, Wambaugh JF, Ferguson SS, Sochaski MA, Rotroff DM, Freeman K, Clewell HJ III, Dix DJ, Andersen ME, Houck KA, Allen B, Judson RS, Singh R, Kavlock RJ, Richard AM, Thomas RS (2012) Integration of dosimetry, exposure and high-throughput screening data in chemical toxicity assessment. Toxicol Sci 125:157-174
70. Selderslaghs IW, Van Rompay AR, De Coen W, Witters HE (2009) Development of a screening assay to identify teratogenic and embryotoxic chemicals using the zebrafish embryo. Reprod Toxicol 28:308-320
71. Brannen KC, Panzica-Kelly JM, Danberry TL, Augustine-Rauch KA (2010) Development of a zebrafish embryo teratogenicity assay and quantitative prediction model. Birth Defects Res B Dev Reprod Toxicol 89:66-77
72. Hermsen SA, van den Brandhof EJ, van der Ven LT, Piersma AH (2011) Relative embryotoxicity of two classes of chemicals in a modified zebrafish embryotoxicity test and comparison with their in vivo potencies. Toxicol In Vitro 25:745-753
73. Hill AJ, Jones M, Dodd A, Diekmann H (2011) A review of developmental toxicity screening using zebrafish larvae. Int J Toxicol 30:105
74. McCollum CW, Ducharme NA, Bondesson M, Gustafsson J-A (2011) Developmental toxicity screening in zebrafish. Birth Defects Res C Embryo Today 93:67-114
75. Sordino P, Duboule D (1996) A molecular approach to the evolution of vertebrate paired appendages. Trends Ecol Evol 11:114-119
76. Buckles GR, Thorpe CJ, Ramel MC, Lekven AC (2004) Combinatorial Wnt control of zebrafish midbrain-hindbrain boundary formation. Mech Dev 121:437-447
77. Ahn D, Ho RK (2008) Tri-phasic expression of posterior Hox genes during development of pectoralfins in zebrafish: implications for the evolution of vertebrate paired appendages. Dev Biol 322:220-233
78. Serbedzija GN, Flynn E, Willett CE (1999) Zebrafish angiogenesis, a new model for drug screening. Angiogenesis 3:353-359
79. Parng C, Seng WL, Semino C, McGrath P (2002) Zebrafish, a preclinical model for drug screening. Assay Drug Dev Technol 1(1 Pt 1):41-48
80. Knudsen TB, DeWoskin R (2011) Systems modeling in developmental toxicity, Chapter 37. In: Casciano DA, Sahu SC (eds) Handbook of systems toxicology. Wiley, Chichester, UK, pp 599-617
81. Hester SD, Belmonte JM, Gens JS, Clendenon SG, Glazier JA (2011) A multi-cell, multi-scale model of vertebrate segmentation and somite formation. PLoS Comput Biol 7(10):e1002155. doi: 10.1371/journal.pcbi.1002155