The potential of embryonic stem cells combined with -omics technologies as model systems for toxicology

Current Medicinal Chemistry

Volumn 16, Issue 36, 2009, Pages 4814-4827

  Winkler, J ^a   Sotiriadou, I ^a   Chen, S ^a   Hescheler, J ^a   Sachinidis, A ^a  

^a UNIVERSITY OF COLOGNE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

8 HYDROXYDEOXYGUANOSINE; AROCLOR 1254; PARACETAMOL; RO 65 7199C; RO 66 0074; SEROTONIN 6 ANTAGONIST; UNCLASSIFIED DRUG;

DISEASE MODEL; DRUG SCREENING; EMBRYONIC STEM CELL; GENE EXPRESSION; GENOTOXICITY; HUMAN; IN VITRO STUDY; LIVER TOXICITY; MICROARRAY ANALYSIS; NEPHROTOXICITY; NONHUMAN; PLURIPOTENT STEM CELL; PROTEOMICS; REVIEW; TOXICITY TESTING; TOXICOGENETICS; TOXICOLOGY; TRANSCRIPTOMICS;

ANIMALS; DRUG DISCOVERY; EMBRYONIC STEM CELLS; HUMANS; MICROARRAY ANALYSIS; MODELS, BIOLOGICAL; PLURIPOTENT STEM CELLS; PROTEOMICS; TOXICITY TESTS; TOXICOGENETICS;

EID: 71949126099     PISSN: 09298673     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986709789909657     Document Type: Review

References (171)

1. Michelson, S.; Joho, K. Drug discovery, drug development and the emerging world of pharmacogenomics: prospecting for information in a data-rich landscape. Curr. Opin. Mol. Ther., 2000, 2, 651-654 (Pubitemid 32057561)
2. Johnson, D.E.; Wolfgang, G.H. Predicting human safety: screening and computational approaches. Drug Discov. Today, 2000, 5, 445-454 (Pubitemid 30700432)
3. Kraljevic, S.; Stambrook, P.J.; Pavelic, K. Accelerating drug discovery. EMBO Rep., 2004, 5, 837-842
4. Ames, B.N.; McCann, J.; Yamasaki, E. Methods for detecting carcinogens and mutagens with the Salmonella/mammalian-microsome mutagenicity test. Mutat. Res., 1975, 31, 347-364
5. Galloway, S.M.; Aardema, M.J.; Ishidate, M., Jr.; Ivett, J.L.; Kirkland, D.J.; Morita, T.; Mosesso, P.; Sofuni, T. Report from working group on in vitro tests for chromosomal aberrations. Mutat. Res., 1994, 312, 241-261 (Pubitemid 24187387)
6. Chaudhary, K.W.; O'Neal, J.M.; Mo, Z.L.; Fermini, B.; Gallavan, R.H.; Bahinski, A. Evaluation of the rubidium efflux assay for preclinical identification of HERG blockade. Assay Drug Dev. Technol., 2006, 4, 73-82.
7. Murphy, S.M.; Palmer, M.; Poole, M.F.; Padegimas, L.; Hunady, K.; Danzig, J.; Gill, S.; Gill, R.; Ting, A.; Sherf, B.; Brunden, K.; Stricker-Krongrad, A. Evaluation of functional and binding assays in cells expressing either recombinant or endogenous hERG channel. J. Pharmacol. Toxicol. Methods, 2006, 54, 42-55. (Pubitemid 43975015)
8. Wienkers, L.C.; Heath, T.G. Predicting in vivo drug interactions from in vitro drug discovery data. Nat. Rev. Drug Discov., 2005, 4, 825-833 (Pubitemid 41553963)
9. Vignati, L.; Turlizzi, E.; Monaci, S.; Grossi, P.; Kanter, R.; Monshouwer, M. An in vitro approach to detect metabolite toxicity due to CYP3A4-dependent bioactivation of xenobiotics. Toxicology, 2005, 216, 154-167
10. Kramer, J.A.; Sagartz, J.E.; Morris, D.L. The application of discovery toxicology and pathology towards the design of safer pharmaceutical lead candidates. Nat. Rev. Drug Discov., 2007, 6, 636-649
11. van, O.B.; Stierum, R. Nutrigenomics: exploiting systems biology in the nutrition and health arena. Curr. Opin. Biotechnol., 2002, 13, 517-521
12. Tong, W.; Cao, X.; Harris, S.; Sun, H.; Fang, H.; Fuscoe, J.; Harris, A.; Hong, H.; Xie, Q.; Perkins, R.; Shi, L.; Casciano, D. Array-Track - supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. Environ. Health Perspect., 2003, 111, 1819-1826 (Pubitemid 37526962)
13. Gomase, V.S.; Tagore, S. Toxicogenomics. Curr. Drug Metab., 2008, 9, 250-254
14. Waters, M.D.; Fostel, J.M. Toxicogenomics and systems toxicology: aims and prospects. Nat. Rev. Genet., 2004, 5, 936-948
15. Velculescu, V.E.; Zhang, L.; Vogelstein, B.; Kinzler, K.W. Serial analysis of gene expression. Science, 1995, 270, 484-487
16. Brenner, S.; Johnson, M.; Bridgham, J.; Golda, G.; Lloyd, D.H.; Johnson, D.; Luo, S.; McCurdy, S.; Foy, M.; Ewan, M.; Roth, R.; George, D.; Eletr, S.; Albrecht, G.; Vermaas, E.; Williams, S.R.; Moon, K.; Burcham, T.; Pallas, M.; DuBridge, R.B.; Kirchner, J.; Fearon, K.; Mao, J.; Corcoran, K. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol., 2000, 18, 630-634 (Pubitemid 30415296)
17. Brenner, S.; Williams, S.R.; Vermaas, E.H.; Storck, T.; Moon, K.; McCollum, C.; Mao, J.I.; Luo, S.; Kirchner, J.J.; Eletr, S.; Du-Bridge, R.B.; Burcham, T.; Albrecht, G. In vitro cloning of complex mixtures of DNA on microbeads: Physical separation of differentially expressed cDNAs. Proc. Natl. Acad. Sci. USA, 2000, 97, 1665-1670 (Pubitemid 30118500)
18. Lettieri, T. Recent applications of DNA microarray technology to toxicology and ecotoxicology. Environ. Health Perspect., 2006, 114, 4-9. (Pubitemid 43056861)
19. Guerreiro, N.; Staedtler, F.; Grenet, O.; Kehren, J.; Chibout, S.D. Toxicogenomics in drug development. Toxicol. Pathol., 2003, 31, 471-479
20. Nuwaysir, E.F.; Bittner, M.; Trent, J.; Barrett, J.C.; Afshari, C.A. Microarrays and toxicology: the advent of toxicogenomics. Mol. Carcinog., 1999, 24, 153-159
21. Lovett, R.A. Toxicogenomics. Toxicologists brace for genomics revolution. Science, 2000, 289, 536-537
22. Harries, H.M.; Fletcher, S.T.; Duggan, C.M.; Baker, V.A. The use of genomics technology to investigate gene expression changes in cultured human liver cells. Toxicol. In Vitro, 2001, 15, 399-405. (Pubitemid 32889665)
23. Burczynski, M.E.; McMillian, M.; Ciervo, J.; Li, L.; Parker, J.B.; Dunn, R.T.; Hicken, S.; Farr, S.; Johnson, M.D. Toxicogenomics-based discrimination of toxic mechanism in HepG2 human hepatoma cells. Toxicol. Sci., 2000, 58, 399-415. (Pubitemid 32042437)
24. Boorman, G.A.; Anderson, S.P.; Casey, W.M.; Brown, R.H.; Crosby, L.M.; Gottschalk, K.; Easton, M.; Ni, H.; Morgan, K.T. Toxicogenomics, drug discovery, and the pathologist. Toxicol. Pathol., 2002, 30, 15-27.
25. Castle, A.L.; Carver, M.P.; Mendrick, D.L. Toxicogenomics: a new revolution in drug safety. Drug Discov. Today, 2002, 7, 728-736
26. Fredrickson, H.L.; Perkins, E.J.; Bridges, T.S.; Tonucci, R.J.; Fleming, J.K.; Nagel, A.; Diedrich, K.; Mendez-Tenorio, A.; Doktycz, M.J.; Beattie, K.L. Towards environmental toxicogenomics - development of a flow-through, high-density DNA hybridization array and its application to ecotoxicity assessment. Sci. Total Environ., 2001, 274, 137-149
27. Hamadeh, H.K.; Bushel, P.R.; Jayadev, S.; Martin, K.; DiSorbo, O.; Sieber, S.; Bennett, L.; Tennant, R.; Stoll, R.; Barrett, J.C.; Blanchard, K.; Paules, R.S.; Afshari, C.A. Gene expression analysis reveals chemical-specific profiles. Toxicol. Sci., 2002, 67, 219-231 (Pubitemid 34746475)
28. Olden, K.; Guthrie, J.; Newton, S. A bold new direction for environmental health research. Am. J. Public Health, 2001, 91, 1964-1967 (Pubitemid 33111640)
29. Simmons, P.T.; Portier, C.J. Toxicogenomics: the new frontier in risk analysis. Carcinogenesis, 2002, 23, 903-905
30. Storck, T.; von Brevern, M.C.; Behrens, C.K.; Scheel, J.; Bach, A. Transcriptomics in predictive toxicology. Curr. Opin. Drug Discov. Dev., 2002, 5, 90-97
31. Horii, I. [Clinical toxicology and toxicogenomics]. Chudoku. Kenkyu., 2002, 15, 263-269
32. Lakkis, M.M.; Decristofaro, M.F.; Ahr, H.J.; Mansfield, T.A. Application of toxicogenomics to drug development. Expert Rev. Mol. Diagn., 2002, 2, 337-345
33. Quinn-Senger, K.E.; Ramachandran, R.; Rininger, J.A.; Kelly, K.M.; Lewin, D.A. Staking out novelty on the genomic frontier. Curr. Opin. Chem. Biol., 2002, 6, 418-426
34. Ulrich, R.; Friend, S.H. Toxicogenomics and drug discovery: will new technologies help us produce better drugs? Nat. Rev. Drug Discov., 2002, 1, 84-88
35. Waring, J.F.; Halbert, D.N. The promise of toxicogenomics. Curr. Opin. Mol. Ther., 2002, 4, 229-235
36. Kramer, J.A.; Kolaja, K.L. Toxicogenomics: an opportunity to optimise drug development and safety evaluation. Expert Opin. Drug Saf., 2002, 1, 275-286
37. Goodsaid, F.M.; Smith, R.J.; Rosenblum, I.Y. Quantitative PCR deconstruction of discrepancies between results reported by different hybridization platforms. Environ Health Perspect., 2004, 112, 456-460
38. Tugendreich, S.; Pearson, C.I.; Sagartz, J.; Jarnagin, K.; Kolaja, K. NSAID-induced acute phase response is due to increased intestinal permeability and characterized by early and consistent alterations in hepatic gene expression. Toxicol. Pathol., 2006, 34, 168-179
39. Hamadeh, H.K.; Amin, R.P.; Paules, R.S.; Afshari, C.A. An overview of toxicogenomics. Curr. Issues Mol. Biol., 2002, 4, 45-56.
40. Li, H.H.; Aubrecht, J.; Fornace, A.J., Jr. Toxicogenomics: overview and potential applications for the study of non-covalent DNA interacting chemicals. Mutat. Res., 2007, 623, 98-108.
41. Sawada, H.; Takami, K.; Asahi, S. A toxicogenomic approach to drug-induced phospholipidosis: analysis of its induction mechanism and establishment of a novel in vitro screening system. Toxicol. Sci., 2005, 83, 282-292 (Pubitemid 40227898)
42. Goldstone, H.M.; Stegeman, J.J. Molecular mechanisms of 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin cardiovascular embryotoxicity. Drug Metab. Rev., 2006, 38, 261-289 (Pubitemid 43739011)
43. Silkworth, J.B.; Carlson, E.A.; McCulloch, C.; Illouz, K.; Goodwin, S.; Sutter, T.R. Toxicogenomic analysis of gender, chemical, and dose effects in livers of TCDD- or aroclor 1254-exposed rats using a multifactor linear model. Toxicol. Sci., 2008, 102, 291-309.
44. Boverhof, D.R.; Burgoon, L.D.; Tashiro, C.; Sharratt, B.; Chittim, B.; Harkema, J.R.; Mendrick, D.L.; Zacharewski, T.R. Comparative toxicogenomic analysis of the hepatotoxic effects of TCDD in Sprague Dawley rats and C57BL/6 mice. Toxicol. Sci., 2006, 94, 398-416.
45. Moller, A.; Soldan, M.; Volker, U.; Maser, E. Two-dimensional gel electrophoresis: a powerful method to elucidate cellular responses to toxic compounds. Toxicology, 2001, 160, 129-138 (Pubitemid 32200473)
46. Wetmore, B.A.; Merrick, B.A. Toxicoproteomics: proteomics applied to toxicology and pathology. Toxicol. Pathol., 2004, 32, 619-642
47. Bandara, L.R.; Kennedy, S. Toxicoproteomics - a new preclinical tool. Drug Discov. Today, 2002, 7, 411-418
48. Snodin, D.J. An EU perspective on the use of in vitro methods in regulatory pharmaceutical toxicology. Toxicol. Lett., 2002, 127, 161-168 (Pubitemid 34615506)
49. Kikkawa, R.; Fujikawa, M.; Yamamoto, T.; Hamada, Y.; Yamada, H.; Horii, I. In vivo hepatotoxicity study of rats in comparison with in vitro hepatotoxicity screening system. J. Toxicol. Sci., 2006, 31, 23-34. (Pubitemid 43375666)
50. Ross, P.L.; Huang, Y.N.; Marchese, J.N.; Williamson, B.; Parker, K.; Hattan, S.; Khainovski, N.; Pillai, S.; Dey, S.; Daniels, S.; Purkayastha, S.; Juhasz, P.; Martin, S.; Bartlet-Jones, M.; He, F.; Jacobson, A.; Pappin, D.J. Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents. Mol. Cell Proteom., 2004, 3, 1154-1169
51. Gluckmann, M.; Fella, K.; Waidelich, D.; Merkel, D.; Kruft, V.; Kramer, P.J.; Walter, Y.; Hellmann, J.; Karas, M.; Kroger, M. Prevalidation of potential protein biomarkers in toxicology using iTRAQ reagent technology. Proteomics, 2007, 7, 1564-1574 (Pubitemid 46841819)
52. Merrick, B.A. The plasma proteome, adductome and idiosyncratic toxicity in toxicoproteomics research. Brief Funct. Genom. Proteom., 2008, 7, 35-49.
53. Kumagai, K.; Ando, Y.; Kiyosawa, N.; Ito, K.; Kawai, R.; Yamoto, T.; Manabe, S.; Teranishi, M. Toxicoproteomic investigation of the molecular mechanisms of cycloheximide-induced hepatocellular apoptosis in rat liver. Toxicology, 2006, 228, 299-309. (Pubitemid 44708456)
54. Petricoin, E.F.; Rajapaske, V.; Herman, E.H.; Arekani, A.M.; Ross, S.; Johann, D.; Knapton, A.; Zhang, J.; Hitt, B.A.; Conrads, T.P.; Veenstra, T.D.; Liotta, L.A.; Sistare, F.D. Toxicoproteomics: serum proteomic pattern diagnostics for early detection of drug induced cardiac toxicities and cardioprotection. Toxicol. Pathol., 2004, 32 Suppl 1:122-30., 122-130
55. Mortuza, G.B.; Neville, W.A.; Delaney, J.; Waterfield, C.J.; Camilleri, P. Characterisation of a potential biomarker of phospholipidosis from amiodarone-treated rats. Biochim. Biophys. Acta, 2003, 1631, 136-146 (Pubitemid 36287509)
56. Sarwal, M.M.; Li, L. Designer genes: Filling the gap in transplantation. Transplantation, 2006, 82, 1261-1272 (Pubitemid 44832907)
57. Pennie, W.D.; Kimber, I. Toxicogenomics; transcript profiling and potential application to chemical allergy. Toxicol. In Vitro, 2002, 16, 319-326 (Pubitemid 34521705)
58. Zidek, N.; Hellmann, J.; Kramer, P.J.; Hewitt, P.G. Acute hepatotoxicity: a predictive model based on focused illumina microarrays. Toxicol. Sci., 2007, 99, 289-302.
59. Buck, W.R.; Waring, J.F.; Blomme, E.A. Use of traditional end points and gene dysregulation to understand mechanisms of toxicity: toxicogenomics in mechanistic toxicology. Methods Mol. Biol., 2008, 460, 23-44.
60. Decristofaro, M.F.; Daniels, K.K. Toxicogenomics in Biomarker Discovery. Methods Mol. Biol., 2008, 460, 185-194.
61. Suter, L.; Haiker, M.; de Vera, M.C.; Albertini, S. Effect of two 5-HT6 receptor antagonists on the rat liver: a molecular approach. Pharmacogenom. J., 2003, 3, 320-334 (Pubitemid 38072170)
62. McMillian, M.; Nie, A.; Parker, J.B.; Leone, A.; Kemmerer, M.; Bryant, S.; Herlich, J.; Yieh, L.; Bittner, A.; Liu, X.; Wan, J.; Johnson, M.D.; Lord, P. Drug-induced oxidative stress in rat liver from a toxicogenomics perspective. Toxicol. Appl. Pharmacol., 2005, 207, 171-178 (Pubitemid 41265511)
63. Minami, K.; Saito, T.; Narahara, M.; Tomita, H.; Kato, H.; Sugiyama, H.; Katoh, M.; Nakajima, M.; Yokoi, T. Relationship between hepatic gene expression profiles and hepatotoxicity in five typical hepatotoxicant-administered rats. Toxicol. Sci., 2005, 87, 296-305. (Pubitemid 41222682)
64. Nakayama, K.; Kawano, Y.; Kawakami, Y.; Moriwaki, N.; Sekijima, M.; Otsuka, M.; Yakabe, Y.; Miyaura, H.; Saito, K.; Sumida, K.; Shirai, T. Differences in gene expression profiles in the liver between carcinogenic and non-carcinogenic isomers of compounds given to rats in a 28-day repeat-dose toxicity study. Toxicol. Appl. Pharmacol., 2006, 217, 299-307. (Pubitemid 44855817)
65. Powell, C.L.; Kosyk, O.; Ross, P.K.; Schoonhoven, R.; Boysen, G.; Swenberg, J.A.; Heinloth, A.N.; Boorman, G.A.; Cunningham, M.L.; Paules, R.S.; Rusyn, I. Phenotypic anchoring of acetaminophen-induced oxidative stress with gene expression profiles in rat liver. Toxicol. Sci., 2006, 93, 213-222 (Pubitemid 44288265)
66. Hendriksen, P.J.; Freidig, A.P.; Jonker, D.; Thissen, U.; Bogaards, J.J.; Mumtaz, M.M.; Groten, J.P.; Stierum, R.H. Transcriptomics analysis of interactive effects of benzene, trichloroethylene and methyl mercury within binary and ternary mixtures on the liver and kidney following subchronic exposure in the rat. Toxicol. Appl. Pharmacol., 2007, 225, 171-188
67. Kiyosawa, N.; Uehara, T.; Gao, W.; Omura, K.; Hirode, M.; Shimizu, T.; Mizukawa, Y.; Ono, A.; Miyagishima, T.; Nagao, T.; Urushidani, T. Identification of glutathione depletion-responsive genes using phorone-treated rat liver. J. Toxicol. Sci., 2007, 32, 469-486
68. Hirode, M.; Ono, A.; Miyagishima, T.; Nagao, T.; Ohno, Y.; Urushidani, T. Gene expression profiling in rat liver treated with compounds inducing phospholipidosis. Toxicol. Appl. Pharmacol., 2008.
69. Uehara, T.; Kiyosawa, N.; Hirode, M.; Omura, K.; Shimizu, T.; Ono, A.; Mizukawa, Y.; Miyagishima, T.; Nagao, T.; Urushidani, T. Gene expression profiling of methapyrilene-induced hepatotoxicity in rat. J. Toxicol. Sci., 2008, 33, 37-50. (Pubitemid 351340762)
70. Dai, X.; He, Y.D.; Dai, H.; Lum, P.Y.; Roberts, C.J.; Waring, J.F.; Ulrich, R.G. Development of an approach for ab initio estimation of compound-induced liver injury based on global gene transcriptional profiles. Genome Inform., 2006, 17, 77-88.
71. Auman, J.T.; Chou, J.; Gerrish, K.; Huang, Q.; Jayadev, S.; Blanchard, K.; Paules, R.S. Identification of genes implicated in methapyrilene-induced hepatotoxicity by comparing differential gene expression in target and nontarget tissue. Environ. Health Perspect., 2007, 115, 572-578
72. Ellinger-Ziegelbauer, H.; Stuart, B.; Wahle, B.; Bomann, W.; Ahr, H.J. Characteristic expression profiles induced by genotoxic carcinogens in rat liver. Toxicol. Sci., 2004, 77, 19-34. (Pubitemid 38128642)
73. Ellinger-Ziegelbauer, H.; Stuart, B.; Wahle, B.; Bomann, W.; Ahr, H.J. Comparison of the expression profiles induced by genotoxic and nongenotoxic carcinogens in rat liver. Mutat. Res., 2005, 575, 61-84.
74. Nie, A.Y.; McMillian, M.; Parker, J.B.; Leone, A.; Bryant, S.; Yieh, L.; Bittner, A.; Nelson, J.; Carmen, A.; Wan, J.; Lord, P.G. Predictive toxicogenomics approaches reveal underlying molecular mechanisms of nongenotoxic carcinogenicity. Mol. Carcinog., 2006, 45, 914-933
75. Wang, E.J.; Snyder, R.D.; Fielden, M.R.; Smith, R.J.; Gu, Y.Z. Validation of putative genomic biomarkers of nephrotoxicity in rats. Toxicology, 2008, 246, 91-100.
76. Thukral, S.K.; Nordone, P.J.; Hu, R.; Sullivan, L.; Galambos, E.; Fitzpatrick, V.D.; Healy, L.; Bass, M.B.; Cosenza, M.E.; Afshari, C.A. Prediction of nephrotoxicant action and identification of candidate toxicity-related biomarkers. Toxicol. Pathol., 2005, 33, 343-355
77. Marin-Kuan, M.; Nestler, S.; Verguet, C.; Bezencon, C.; Piguet, D.; Mansourian, R.; Holzwarth, J.; Grigorov, M.; Delatour, T.; Mantle, P.; Cavin, C.; Schilter, B. A toxicogenomics approach to identify new plausible epigenetic mechanisms of ochratoxin A carcinogenicity in rat. Toxicol. Sci., 2006, 89, 120-134 (Pubitemid 43013761)
78. Mantovani, A.; Maranghi, F. Risk assessment of chemicals potentially affecting male fertility. Contraception, 2005, 72, 308-313 (Pubitemid 41338114)
79. Dam, K.; Seidler, F.J.; Slotkin, T.A. Transcriptional biomarkers distinguish between vulnerable periods for developmental neurotoxicity of chlorpyrifos: Implications for toxicogenomics. Brain Res. Bull., 2003, 59, 261-265
80. Baken, K.A.; Vandebriel, R.J.; Pennings, J.L.; Kleinjans, J.C.; van Loveren, H. Toxicogenomics in the assessment of immunotoxicity. Methods, 2007, 41, 132-141
81. Rokushima, M.; Omi, K.; Imura, K.; Araki, A.; Furukawa, N.; Itoh, F.; Miyazaki, M.; Yamamoto, J.; Rokushima, M.; Okada, M.; Torii, M.; Kato, I.; Ishizaki, J. Toxicogenomics of drug-induced hemolytic anemia by analyzing gene expression profiles in the spleen. Toxicol. Sci., 2007, 100, 290-302. (Pubitemid 47617825)
82. Wei, Y.; Liu, Y.; Wang, J.; Tao, Y.; Dai, J. Toxicogenomic analysis of the hepatic effects of perfluorooctanoic acid on rare minnows (Gobiocypris rarus). Toxicol. Appl. Pharmacol., 2008, 226, 285-297 (Pubitemid 351172417)
83. Yang, L.; Kemadjou, J.R.; Zinsmeister, C.; Bauer, M.; Legradi, J.; Muller, F.; Pankratz, M.; Jakel, J.; Strahle, U. Transcriptional profiling reveals barcode-like toxicogenomic responses in the zebrafish embryo. Genome Biol., 2007, 8, R227. (Pubitemid 351917450)
84. Finne, E.F.; Cooper, G.A.; Koop, B.F.; Hylland, K.; Tollefsen, K.E. Toxicogenomic responses in rainbow trout (Oncorhynchus mykiss) hepatocytes exposed to model chemicals and a synthetic mixture. Aquat. Toxicol., 2007, 81, 293-303.
85. Tilton, S.C.; Givan, S.A.; Pereira, C.B.; Bailey, G.S.; Williams, D.E. Toxicogenomic profiling of the hepatic tumor promoters indole-3-carbinol, 17beta-estradiol and beta-naphthoflavone in rainbow trout. Toxicol. Sci., 2006, 90, 61-72.
86. Wintz, H.; Yoo, L.J.; Loguinov, A.; Wu, Y.Y.; Steevens, J.A.; Holland, R.D.; Beger, R.D.; Perkins, E.J.; Hughes, O.; Vulpe, C.D. Gene expression profiles in fathead minnow exposed to 2, 4-DNT: correlation with toxicity in mammals. Toxicol. Sci., 2006, 94, 71-82.
87. Jelinek, R. Use of chick embryo in screening for embryotoxicity. Teratog. Carcinog. Mutagen., 1982, 2, 255-261 (Pubitemid 13169088)
88. Kucera, P.; Burnand, M.B. Routine teratogenicity test that uses chick embryos in vitro. Teratog. Carcinog. Mutagen., 1987, 7, 427-447
89. Villalobos, S.A.; Papoulias, D.M.; Pastva, S.D.; Blankenship, A.L.; Meadows, J.; Tillitt, D.E.; Giesy, J.P. Toxicity of o, p′-DDE to medaka d-rR strain after a one-time embryonic exposure by in ovo nanoinjection: an early through juvenile life cycle assessment. Chemosphere, 2003, 53, 819-826
90. Papoulias, D.M.; Villalobos, S.A.; Meadows, J.; Noltie, D.B.; Giesy, J.P.; Tillitt, D.E. In ovo exposure to o, p -DDE affects sexual development but not sexual differentiation in Japanese medaka (Oryzias latipes). Environ. Health Perspect., 2003, 111, 29-32.
91. Dipaolo, J.A.; Elis, J.; Erwin, H. Teratogenic Response by Hamsters, Rats and Mice to Aflatoxin B1. Nature, 1967, 215, 638-639
92. Geissler, F.; Faustman, E.M. Developmental toxicity of aflatoxin B1 in the rodent embryo in vitro: contribution of exogenous biotransformation systems to toxicity. Teratology, 1988, 37, 101-111
93. Danielsson, B.R.; Danielson, M.; Khayat, A.; Wide, M. Comparative embryotoxicity of selenite and selenate: uptake in murine embryonal and fetal tissues and effects on blastocysts and embryonic cells in vitro. Toxicology, 1990, 63, 123-136 (Pubitemid 20278677)
94. Beekhuijzen, M.E.; Verhoef, A.; Klaassen, R.; Rompelberg, C.J.; Piersma, A.H. Comparison of in vitro and in vivo developmental toxicity and pharmacokinetics of phenytoin in the rat. Pharmacol. Toxicol., 2000, 87, 96-102. (Pubitemid 30643440)
95. Boess, F.; Kamber, M.; Romer, S.; Gasser, R.; Muller, D.; Albertini, S.; Suter, L. Gene expression in two hepatic cell lines, cultured primary hepatocytes, and liver slices compared to the in vivo liver gene expression in rats: possible implications for toxicogenomics use of in vitro systems. Toxicol. Sci., 2003, 73, 386-402. (Pubitemid 36701742)
96. Kienhuis, A.S.; Wortelboer, H.M.; Hoflack, J.C.; Moonen, E.J.; Kleinjans, J.C.; van Ommen, B.; van Delft, J.H.; Stierum, R.H. Comparison of coumarin-induced toxicity between sandwich-cultured primary rat hepatocytes and rats in vivo: a toxicogenomics approach. Drug Metab. Dispos., 2006, 34, 2083-2090
97. Barros, S.A.; Martin, R.B. Predictive Toxicogenomics in Preclinical Discovery. Methods Mol. Biol., 2008, 460, 89-112, 89-112.
98. Bharadwaj, L.; Dhami, K.; Schneberger, D.; Stevens, M.; Renaud, C.; Ali, A. Altered gene expression in human hepatoma HepG2 cells exposed to low-level 2, 4-dichlorophenoxyacetic acid and potassium nitrate. Toxicol. In Vitro, 2005, 19, 603-619 (Pubitemid 40723600)
99. Harris, A.J.; Dial, S.L.; Casciano, D.A. Comparison of basal gene expression profiles and effects of hepatocarcinogens on gene expression in cultured primary human hepatocytes and HepG2 cells. Mutat. Res., 2004, 549, 79-99.
100. Thum, T.; Borlak, J. Detection of early signals of hepatotoxicity by gene expression profiling studies with cultures of metabolically competent human hepatocytes. Arch. Toxicol., 2008, 82, 89-101. (Pubitemid 351187672)
101. Cotovio, J.; Grandidier, M.H.; Portes, P.; Roguet, R.; Rubinstenn, G. The in vitro skin irritation of chemicals: optimisation of the EPISKIN prediction model within the framework of the ECVAM validation process. Altern. Lab. Anim., 2005, 33, 329-349
102. Borlon, C.; Godard, P.; Eskes, C.; Hartung, T.; Zuang, V.; Toussaint, O. The usefulness of toxicogenomics for predicting acute skin irritation on in vitro reconstructed human epidermis. Toxicology, 2007, 241, 157-166 (Pubitemid 47600468)
103. Martin, G.R. Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc. Natl. Acad. Sci. USA, 1981, 78, 7634-7638
104. Evans, M.J.; Kaufman, M.H. Establishment in culture of pluripotential cells from mouse embryos. Nature, 1981, 292, 154-156 (Pubitemid 11050741)
105. Thomson, J.A.; Itskovitz-Eldor, J.; Shapiro, S.S.; Waknitz, M.A.; Swiergiel, J.J.; Marshall, V.S.; Jones, J.M. Embryonic Stem Cell Lines Derived from Human Blastocysts. Science, 1998, 282, 1145-1147
106. Bhatia, M. Hematopoietic development from human embryonic stem cells. Hematology. Am. Soc. Hematol. Educ. Program, 2007, 2007, 11-16
107. Seissler, J.; Schott, M. Generation of insulin-producing beta cells from stem cells- perspectives for cell therapy in type 1 diabetes. Horm. Metab. Res., 2008, 40, 155-161
108. Watt, A.J.; Forrester, L.M. Deriving and identifying hepatocytes from embryonic stem cells. Stem Cell Rev., 2006, 2, 19-22. (Pubitemid 44195974)
109. Winkler, J.; Hescheler, J.; Sachinidis, A. Embryonic stem cells for basic research and potential clinical applications in cardiology. Biochim. Biophys. Acta, 2005, 1740, 240-248 (Pubitemid 40798234)
110. Yu, D.; Silva, G.A. Stem cell sources and therapeutic approaches for central nervous system and neural retinal disorders. Neurosurg. Focus., 2008, 24, E11.
111. Reppel, M.; Boettinger, C.; Hescheler, J. Beta-adrenergic and muscarinic modulation of human embryonic stem cell-derived cardiomyocytes. Cell Physiol. Biochem., 2004, 14, 187-196 (Pubitemid 39179186)
112. Mummery, C.; Ward-van Oostwaard, D.; Doevendans, P.; Spijker, R.; van den Brink, S.; Hassink, R.; van der Heyden, M.; Opthof, T.; Pera, M.; de la Riviere, A.B.; Passier, R.; Tertoolen, L. Differentiation of human embryonic stem cells to cardiomyocytes: Role of coculture with visceral endoderm-like cells. Circulation, 2003, 107, 2733-2740 (Pubitemid 36667249)
113. Doetschman, T.C.; Eistetter, H.; Katz, M.; Schmidt, W.; Kemler, R. The in vitro development of blastocyst-derived embryonic stem cell lines: formation of visceral yolk sac, blood islands and myocardium. J. Embryol. Exp. Morphol., 1985, 87, 27-45.
114. Mariappan, D.; Winkler, J.; Chen, S.; Schulz, H.; Hescheler, J.; Sachinidis, A. Transcriptional profiling of CD31(+) cells isolated from murine embryonic stem cells. Genes Cells, 2009, 14, 243-260
115. Rust, W.; Balakrishnan, T.; Zweigerdt, R. Cardiomyocyte enrichment from human embryonic stem cell cultures by selection of ALCAM surface expression. Regenerat. Med., 2009, 4, 225-237
116. Li, M.; Pevny, L.; Lovell-Badge, R.; Smith, A. Generation of purified neural precursors from embryonic stem cells by lineage selection. Curr. Biol., 1998, 8, 971-974 (Pubitemid 28447948)
117. Muller, M.; Fleischmann, B.K.; Selbert, S.; Ji, G.J.; Endl, E.; Middeler, G.; Muller, O.J.; Schlenke, P.; Frese, S.; Wobus, A.M.; Hescheler, J.; Katus, H.A.; Franz, W.M. Selection of ventricular-like cardiomyocytes from ES cells in vitro. FASEB J., 2000, 14, 2540-2548
118. Doss, M.; Winkler, J.; Chen, S.; Hippler-Altenburg, R.; Sotiriadou, I.; Halbach, M.; Pfannkuche, K.; Liang, H.; Schulz, H.; Hummel, O.; Hubner, N.; Rottscheidt, R.; Hescheler, J.; Sachinidis, A. Global transcriptome analysis of murine embryonic stem cell-derived cardiomyocytes. Genome Biol., 2007, 8, R56. (Pubitemid 351859206)
119. Anderson, D.; Self, T.; Mellor, I.R.; Goh, G.; Hill, S.J.; Denning, C. Transgenic enrichment of cardiomyocytes from human embryonic stem cells. Mol. Ther., 2007, 15, 2027-2036 (Pubitemid 350011743)
120. Huber, I.; Itzhaki, I.; Caspi, O.; Arbel, G.; Tzukerman, M.; Gepstein, A.; Habib, M.; Yankelson, L.; Kehat, I.; Gepstein, L. Identification and selection of cardiomyocytes during human embryonic stem cell differentiation. FASEB J., 2007, 21, 2551-2563 (Pubitemid 47230684)
121. Kita-Matsuo, H.; Barcova, M.; Prigozhina, N.; Salomonis, N.; Wei, K.; Jacot, J.G.; Nelson, B.; Spiering, S.; Haverslag, R.; Kim, C.; Talantova, M.; Bajpai, R.; Calzolari, D.; Terskikh, A.; McCulloch, A.D.; Price, J.H.; Conklin, B.R.; Chen, H.S.; Mercola, M. Lentiviral vectors and protocols for creation of stable hESC lines for fluorescent tracking and drug resistance selection of cardiomyocytes. PLoS One, 2009, 4, e5046.
122. Willems, E.; Bushway, P.; Mercola, M. Natural and synthetic regulators of embryonic stem cell cardiogenesis. Pediatr. Cardiol., 2009, 30, 635-642
123. Wicell Research Institute. WiCell's Proven Protocols. Online 2008.
124. ES Cell International Pte L. Methodology manual human embryonic stem cell culture. Online 2005.
125. Harvard Medical School. Human Embryonic Stem (HUES) Cell Collection. Online 2009.
126. Hasegawa, K.; Fujioka, T.; Nakamura, Y.; Nakatsuji, N.; Suemori, H. A method for the selection of human embryonic stem cell sublines with high replating efficiency after single-cell dissociation. Stem Cells, 2006, 24, 2649-2660 (Pubitemid 46053003)
127. Ellerstrom, C.; Strehl, R.; Noaksson, K.; Hyllner, J.; Semb, H. Facilitated expansion of human embryonic stem cells by single-cell enzymatic dissociation. Stem Cells, 2007, 25, 1690-1696 (Pubitemid 47121846)
128. Watanabe, K.; Ueno, M.; Kamiya, D.; Nishiyama, A.; Matsumura, M.; Wataya, T.; Takahashi, J.B.; Nishikawa, S.; Nishikawa, S.I.; Muguruma, K.; Sasai, Y. A ROCK inhibitor permits survival of dissociated human embryonic stem cells. Nat. Biotech., 2007, 25, 681-686 (Pubitemid 46897207)
129. Thomas, R.J.; Anderson, D.; Chandra, A.; Smith, N.M.; Young, L.E.; Williams, D.; Denning, C. Automated, scalable culture of human embryonic stem cells in feeder-free conditions. Biotechnol. Bioeng., 2009, 102, 1636-1644
130. Doss, M.X.; Koehler, C.I.; Gissel, C.; Hescheler, J.; Sachinidis, A. Embryonic stem cells: a promising tool for cell replacement therapy. J. Cell Mol. Med., 2004, 8, 465-473 (Pubitemid 44145479)
131. Wobus, A.M.; Hescheler, J. [Development of an in vitro cardiomyocytes cell model for embryotoxicological and pharmacological studies]. ALTEX, 1992, 9, 29-42.
132. Spielmann, H.; Pohl, I.; Döring, B.; Liebsch, M.; Moldenhauer, F. The embryonic stem cell test (EST), an in vitro embryotoxicity test using two permanent mouse cell lines; 3T3 fibroblasts and embryonic stem cells. Toxicol. In Vitro, 1997, 10, 119-127 (Pubitemid 27234596)
133. Genschow, E.; Spielmann, H.; Scholz, G.; Pohl, I.; Seiler, A.; Clemann, N.; Bremer, S.; Becker, K. Validation of the embryonic stem cell test in the international ECVAM validation study on three in vitro embryotoxicity tests. Altern. Lab. Anim., 2004, 32, 209-244 (Pubitemid 39517737)
134. Scholz, G.; Pohl, I.; Genschow, E.; Klemm, M.; Spielmann, H. Embryotoxicity screening using embryonic stem cells in vitro: correlation to in vivo teratogenicity. Cells Tissues Org., 1999, 165, 203-211
135. Cao, T.; Lu, K.; Fu, X.; Heng, B.C. Differentiated fibroblastic progenies of human embryonic stem cells for toxicology screening. Cloning Stem Cells, 2008, 10, 1-10.
136. zur Nieden, N.I.; Ruf, L.J.; Kempka, G.; Hildebrand, H.; Ahr, H.J. Molecular markers in embryonic stem cells. Toxicol. In Vitro, 2001, 15, 455-461
137. Seiler, A.; Visan, A.; Buesen, R.; Genschow, E.; Spielmann, H. Improvement of an in vitro stem cell assay for developmental toxicity: the use of molecular endpoints in the embryonic stem cell test. Reprod. Toxicol., 2004, 18, 231-240 (Pubitemid 38333047)
138. zur Nieden, N.I.; Kempka, G.; Ahr, H.J. Molecular multiple endpoint embryonic stem cell test - a possible approach to test for the teratogenic potential of compounds. Toxicol. Appl. Pharmacol., 2004, 194, 257-269
139. Festag, M.; Sehner, C.; Steinberg, P.; Viertel, B. An in vitro embryotoxicity assay based on the disturbance of the differentiation of murine embryonic stem cells into endothelial cells. I: Establishment of the differentiation protocol. Toxicol. In Vitro, 2007, 21, 1619-1630 (Pubitemid 350086873)
140. Peters, A.K.; Steemans, M.; Hansen, E.; Mesens, N.; Verheyen, G.R.; Vanparys, P. Evaluation of the embryotoxic potency of compounds in a newly revised high throughput embryonic stem cell test. Toxicol. Sci., 2008, 105(2), 342-350
141. Peters, A.K.; Wouwer, G.V.; Weyn, B.; Verheyen, G.R.; Vanparys, P.; Gompel, J.V. Automated analysis of contractility in the embryonic stem cell test, a novel approach to assess embryotoxicity. Toxicol. In Vitro, 2008, 22(8), 1948-1956
142. Calabro, A.R.; Konsoula, R.; Barile, F.A. Evaluation of in vitro cytotoxicity and paracellular permeability of intact monolayers with mouse embryonic stem cells. Toxicol. In Vitro, 2008, 22, 1273-1284
143. Cezar, G.G. Can human embryonic stem cells contribute to the discovery of safer and more effective drugs? Curr. Opin. Chem. Biol., 2007, 11, 405-409
144. Zeng, X.; Chen, J.; Deng, X.; Liu, Y.; Rao, M.S.; Cadet, J.L.; Freed, W.J. An in vitro model of human dopaminergic neurons derived from embryonic stem cells: MPP+ toxicity and GDNF neuroprotection. Neuropsychopharmacology, 2006, 31, 2708-2715 (Pubitemid 44764167)
145. Takahashi, K.; Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell, 2006, 126, 663-676 (Pubitemid 44233629)
146. Wernig, M.; Meissner, A.; Foreman, R.; Brambrink, T.; Ku, M.; Hochedlinger, K.; Bernstein, B.E.; Jaenisch, R. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature, 2007, 448, 318-324 (Pubitemid 47080337)
147. Takahashi, K.; Tanabe, K.; Ohnuki, M.; Narita, M.; Ichisaka, T.; Tomoda, K.; Yamanaka, S. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell, 2007, 131, 861-872 (Pubitemid 350138099)
148. Park, I.H.; Zhao, R.; West, J.A.; Yabuuchi, A.; Huo, H.; Ince, T.A.; Lerou, P.H.; Lensch, M.W.; Daley, G.Q. Reprogramming of human somatic cells to pluripotency with defined factors. Nature, 2008, 451, 141-146
149. Kim, D.; Kim, C.H.; Moon, J.I.; Chung, Y.G.; Chang, M.Y.; Han, B.S.; Ko, S.; Yang, E.; Cha, K.Y.; Lanza, R.; Kim, K.S. Generation of human induced pluripotent stem cells by direct delivery of reprogramming proteins. Cell Stem Cell, 2009, 4, 472-476
150. Ebert, A.D.; Yu, J.; Rose, F.F.; Mattis, V.B.; Lorson, C.L.; Thomson, J.A.; Svendsen, C.N. Induced pluripotent stem cells from a spinal muscular atrophy patient. Nature, 2008, 457, 277-280
151. Dimos, J.T.; Rodolfa, K.T.; Niakan, K.K.; Weisenthal, L.M.; Mitsumoto, H.; Chung, W.; Croft, G.F.; Saphier, G.; Leibel, R.; Goland, R.; Wichterle, H.; Henderson, C.E.; Eggan, K. Induced pluripotent stem cells generated from patients with ALS can be differentiated into motor neurons. Science, 2008, 321, 1218-1221
152. Park, I.H.; Arora, N.; Huo, H.; Maherali, N.; Ahfeldt, T.; Shimamura, A.; Lensch, M.W.; Cowan, C.; Hochedlinger, K.; Daley, G.Q. Disease-specific induced pluripotent stem cells. Cell, 2008, 134, 877-886
153. Hochedlinger, K.; Jaenisch, R. Nuclear reprogramming and pluripotency. Nature, 2006, 441, 1061-1067
154. Collas, P.; Taranger, C.K. Toward reprogramming cells to pluripotency. Ernst. Schering. Res Found Workshop, 2006, 47-67.
155. Lensch, M.W. Cellular reprogramming and pluripotency induction. Br. Med. Bull., 2009, 90, 19-35.
156. Yauk, C.L.; Berndt, M.L. Review of the literature examining the correlation among DNA microarray technologies. Environ. Mol. Mutagen, 2007, 48, 380-394
157. Mattes, W.B. Public Consortium Efforts in Toxicogenomics. Methods Mol. Biol., 2008, 460, 221-238.
158. ILSI. Application of Genomics to Mechanism-based Risk Assessment. Internet Communication 2008.
159. Goodsaid, F.M. Identification and measurement of genomic biomarkers of nephrotoxicity. J. Pharmacol. Toxicol. Methods, 2004, 49, 183-186
160. Mattes, W.B. Annotation and cross-indexing of array elements on multiple platforms. Environ. Health Perspect., 2004, 112, 506-510
161. Thompson, K.L.; Afshari, C.A.; Amin, R.P.; Bertram, T.A.; Car, B.; Cunningham, M.; Kind, C.; Kramer, J.A.; Lawton, M.; Mirsky, M.; Naciff, J.M.; Oreffo, V.; Pine, P.S.; Sistare, F.D. Identification of platform-independent gene expression markers of cisplatin nephrotoxicity. Environ. Health Perspect., 2004, 112, 488-494 (Pubitemid 38404560)
162. Waters, M.; Boorman, G.; Bushel, P.; Cunningham, M.; Irwin, R.; Merrick, A.; Olden, K.; Paules, R.; Selkirk, J.; Stasiewicz, S.; Weis, B.; Van Houten, B.; Walker, N.; Tennant, R. Systems toxicology and the chemical effects in biological systems (CEBS) knowledge base. EHP Toxicogenom., 2003, 111, 15-28. (Pubitemid 36157427)
163. Waters, M.; Stasiewicz, S.; Merrick, B.A.; Tomer, K.; Bushel, P.; Paules, R.; Stegman, N.; Nehls, G.; Yost, K.J.; Johnson, C.H.; Gustafson, S.F.; Xirasagar, S.; Xiao, N.; Huang, C.C.; Boyer, P.; Chan, D.D.; Pan, Q.; Gong, H.; Taylor, J.; Choi, D.; Rashid, A.; Ahmed, A.; Howle, R.; Selkirk, J.; Tennant, R.; Fostel, J. CEBS - Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. Nucleic Acids Res., 2008, 36, D892-D900. (Pubitemid 351149841)
164. Medlin, J. Toxicogenomics research consortium sails into uncharted waters. Environ. Health Perspect., 2002, 110, A744-A746. (Pubitemid 36024290)
165. NIEHS. Introduction to the Toxicogenomics Research Consortium (TRC) Internet Communication 2001.
166. InnoMed. InnoMed PredTox Internet Communication 2008.
167. FDA. FDA and the Critical Path Institute Announce Predictive Safety Testing Consortium Internet Communication 2006.
168. Waters, M.; Yauk, C. Consensus recommendations to promote and advance predictive systems toxicology and toxicogenomics. Environ. Mol. Mutagen., 2007, 48, 400-403 (Pubitemid 47011769)
169. Fostel, J.M. Future of toxicogenomics and safety signatures: balancing public access to data with proprietary drug discovery. Pharmacogenomics, 2007, 8, 425-430
170. Boulton, M.; Wride, M. Can Toxicogenomics be Used to Identify Chemicals that Cause Ocular Injury? ALTEX, 2006, 23(Suppl), 318-20, 318-320
171. Shah, R.R. Can pharmacogenetics help rescue drugs withdrawn from the market? Pharmacogenomics, 2006, 7, 889-908.