Toxicogenomics in regulatory ecotoxicology

Environmental Science and Technology

Volumn 40, Issue 13, 2006, Pages 4055-4065

  Ankley, Gerald T ^a   Daston, George P ^a,j   Degitz, Sigmund J ^a   Denslow, Nancy D ^b   Hoke, Robert A ^c   Kennedy, Sean W ^d   Miracle, Ann L ^e   Perkins, Edward J ^f   Snape, Jason ^g   Tillitt, Donald E ^h   Tyler, Charles R ⁱ   Versteeg, Donald ^j  

^a U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

^c DUPONT COMPANY   (United States)

^d ENVIRONMENT CANADA   (Canada)

^e PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^f U S ARMY ENGINEER RESEARCH AND DEVELOPMENT CENTER   (United States)

^g ASTRAZENECA   (United Kingdom)

^h U S GEOLOGICAL SURVEY   (United States)

ⁱ UNIVERSITY OF EXETER   (United Kingdom)

^j Procter and Gamble ^*

more..

Author keywords

[No Author keywords available]

Indexed keywords

ECOTOXICOLOGY; GENOMICS; TOXICOGENOMICS; TOXICOLOGY;

ECOLOGY; GENES; TOXICITY;

GENETIC ENGINEERING;

ECOLOGY; GENES; GENETIC ENGINEERING; TOXICITY;

ECOTOXICOLOGY; GENOMICS;

BIOINFORMATICS; CONTAMINATION; ECOTOXICOLOGY; GENOMICS; GENOTOXICITY; HUMAN; METABOLOMICS; NONHUMAN; REVIEW; RISK ASSESSMENT; TOXICOGENETICS;

ECOLOGY; GENOMICS; RISK ASSESSMENT; TOXICITY TESTS; TOXICOLOGY;

EID: 33746670071     PISSN: 0013936X     EISSN: None     Source Type: Journal    
DOI: 10.1021/es0630184     Document Type: Review

References (70)

1. Nuwaysir, E. F.; et al. Microarrays and Toxicology: The Advent of Toxicogenomics. Mol. Carcinogen. 1999, 24, 153-159.
2. MacGregor, J. T. The Future of Regulatory Toxicology: Impact of the Biotechnology Revolution. Toxicol. Sci. 2003, 75, 236-248.
3. Waters, M. D.; Fostel, J. M. Toxicogenomics and Systems Toxicology: Aims and Prospects. Nat. Rev. Genet. 2004, 5, 936-948.
4. Bilello, J. A. The Agony and Ecstasy of "OMIC" Technologies in Drug Development. Curr. Mol. Med. 2005, 5, 39-52.
5. Lühe, A.; et al. Toxicogenomics in the Pharmaceutical Industry: Hollow Promises or Real Benefit? Mutat. Res. 2005, 575, 102-115.
6. Boverhof, D. R.; Zacharewski, T. R. Toxicogenomics in Risk Assessment: Applications and Needs. Toxicol. Sci. 2005, 89, 352-360.
7. The Danio rerio Sequencing Project, www.sanger.ac.uk/Projects /D_rerio.
8. The C. elegans Sequencing Consortium. Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology. Science 1998, 282, 2012-2018.
9. Thorgaard, G. H.; et al. Status and Opportunities for Genomics Research with Rainbow Trout. Comp. Biochem. Physiol., B 2002, 133, 609-646.
10. Naruse, K.; et al. Medaka Genomics: A Bridge between Mutant Phenotype and Gene Function. Mech. Dev. 2004, 121, 619-618.
11. Ankley, G. T.; Villeneuve, D. L. The Fathead Minnow in Aquatic Toxicology: Past, Present and Future. Aquat. Toxicol. 2006, 78, 91-102.
12. Xenopus tropicalis Genome Assembly 4.1, http://genome. jsi-psf.org/Xentr4/Xentr4.home.html.
13. Colbourne, J. K.; Singan, V. R.; Gilbert, D. G. wFleaBase: The Daphnia Genome Database. BMC Bioinformatics 2005 7, 45.
14. Merrick, B.A.; Bruno, M. E. Genomic and Proteomic Profiling for Biomarkers and Signature Profiles of Toxicity. Curr. Opin. Mol. Ther. 2004, 6, 600-607.
15. Amin, R. P.; et al. Genomic Interrogation of Mechanism(s) underlying Cellular Responses to Toxicants. Toxicology 2002, 27, 555-563.
16. Hamadeh, H. K.; et al. Prediction of Compound Signature using High Density Gene Expression Profiling. Toxicol. Sci. 2002, 67 232-240.
17. Larkin, P.; et al. Expression Profiling of Estrogenic Compounds using a Sheepshead Minnow cDNA Macroarray. Environ. Health Perspect. 2003, 111, 29-36.
18. Miracle, A. L.; Toth, G.; Lattier, D. L. The Path from Molecular Indicators of Exposure to Describing Dynamic Biological Systems in an Aquatic Organism: Microarrays and the Fathead Minnow. Ecotoxicology 2003, 12, 457-462.
19. Rasooly, R. S.; et al. Genetic and Genomic Tools for Zebrafish Research: The NIH Zebrafish Initiative. Dev. Dy-nam. 2003, 228, 490-496.
20. Williams, T. D.; et al. A DNA Expression Array To Detect Toxic Stress Response in European Flounder (Platichthys flesus). Aquat. Toxicol. 2003, 65, 141-157.
21. Kimura, T.; et al. Large-Scale Isolation of ESTs from Medaka Embryos and Its Application to Medaka Developmental Genetics. Mech. Dev. 2004, 121, 915-932.
22. Snape, J. R.; et al. Ecotoxicogenomics: The Challenge of Integrating Genomics into Aquatic and Terrestrial Ecotoxicology. Aquat. Toxicol. 2004, 67, 143-154.
23. 1-Induced Hepatocellular Carcinoma Compared to Adjacent Liver. Toxicol. Sci. 2005, 88, 319-330.
24. van der Ven, K.; et al. Development and Application of a Brain-Specific cDNA Microarray for Effect Evaluation of Neuro-Active Pharmaceuticals in Zebrafish (Danio rerio). Comp. Biochem. Physiol., B 2005, 141, 408-417.
25. von Schalburg, K. R.; et al. Fish and Chips: Various Methodologies Demonstrate Utility of a 16,006-Gene Salmonid Microarray. BMC Genomics 2005, 6, 126-133.
26. Lettieri, T. Recent Applications of DNA Microarray Technology to Toxicology and Ecotoxicology. Environ. Health Perspect. 2006, 114, 4-9.
27. Pennington, S.; Wilkins, M.; Dunn, M. Proteome Analysis: From Protein Characterization to Biological Function. Trends Cell Biol. 1997, 7, 168-173.
28. Fields, S. Proteomics and the Future. Science 2001, 4, 87-102.
29. Handam, M.; Righetti, P. Elucidating the Cell Proteome. Mass Spectrom. Rev. 2003, 22, 182-194.
30. Shrader, E. A.; et al. Proteomics in Zebrafish Exposed to Endocrine Disrupting Chemicals. Ecotoxicology 2003, 12, 485-488.
31. Stentiford, G. D.; et al. Liver Tumors in Wild Flatfish: A Histopathological, Proteomic and Metabolomic Study. OMICS 2005, 9, 281-299.
32. Aebersold, R.; Mann, M. Mass Spectrometry-Based Proteomics. Nature 2003, 422, 198-207.
33. Fountoulakis, M. Peptide Sequencing by Mass Spectrometry. Mass Spectrom. Rev. 2004, 23, 231-245.
34. Silva, J.; Geromonas, S. Quantitative Proteomic Analysis by Accurate Mass RT-Pairs. Anal. Chem. 2005, 77, 2187-2200.
35. Nicholson, J. K.; et al. Metabolomics: A Platform for Studying Drug Toxicity and Gene Function. Nat. Rev. Drug Discovery 2002, 1, 153-162.
36. Schmidt, C. W. Metabolomics: What's Happening Downstream of DNA. Environ. Health Perspect. 2004, 112, A410-A415.
37. Robertson, D. G. Metabonomics in Toxicology: A Review. Toxicol. Sci. 2005, 85, 809-822.
38. Viant, M. R. Improved Methods for the Acquisition and Interpretation of NMR Metabolomic Data. Biochem. Biophys. Res. Commun. 2003, 310, 943-948.
39. Viant, M. R.; Rosenblum, E. S.; Tieerdema, R. S. NMR-Based Metabolomics: A Powerful Approach for Characterizing the Effects of Environmental Stressors on Organism Health. Environ. Sci. Technol. 2003, 37, 4982-4989.
40. Bundy, J. G.; et al. Environmental Metabonomics: Applying Combination Biomarker Analysis in Earthworms at a Metal Contaminated Site. Ecotoxicology 2004, 13, 797-806.
41. Dunn, W. B.; Bailey, N. J. C.; Johnson, H. E. Measuring the Metabolome: Current Analytical Technologies. Analyst 2005, 130, 606-625.
42. Ideker, T.; et al. Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network. Science 2001, 292, 929-934.
43. Hess, K. R.; et al. Microarrays: Handling the Deluge of Data and Extracting Reliable Information. Trends Biotechnol. 2001, 19, 463-468.
44. Yu, U.; et al. Bioinformatics in the Post-Genome Era. J. Biochem. Mol. Biol. 2004, 37, 75-82.
45. Bushel, P. R.; et al. Computational Selection of Distinct Class- and Subclass-Specific Gene Expression Signatures. J. Biomed. Inform. 2002, 35, 160-170.
46. Naciff, J. M.; et al. Gene Expression Profile Induced by 17α-Ethanol Estradiol, Bisphenol A, and Genistein in the Developing Female Reproductive System of the Rat. Toxicol. Sci. 2002, 68, 184-199.
47. Johnson, C. D.; et al. Genomic Profiles and Predictive Biological Networks in Oxidant-Induced Atherogenesis. Physiol. Genomics 2003, 13, 263-285.
48. Fielden, M. R.; et al. A Gene Expression Signature that Predicts the Future Onset of Drug-Induced Renal Tubular Toxicity. Toxicol. Pathol. 2005, 33, 675-683.
49. U.S. EPA HPV Challenge Program, www.epa.gov/chemrtk/volchall.htm.
50. European Commission. White Paper on the Strategy for a Future Chemicals Policy; Document COM 88; Brussels, 2001.
51. European Commission. Legislative Proposal Concerning the Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH); Vols. 1-6; Document COM 2003 0644 (03); Brussels, Oct 29, 2003; www.europa.eu.int/comm/ environment/chemicals/reach.htm.
52. Ankley, G. T.; et al. A Framework for Assessing the Hazard of Pharmaceutical Materials to Aquatic Species. In Human Pharmaceuticals: Assessing the Impacts on Aquatic Ecosystems; Williams, R. T., Ed.; SETAC Press: Pensacola, FL, 2005; pp 183-238.
53. World Health Organization. ICPS Global Assessment of the State-of-the-Science of Endocrine Disrupters; WHO/PCS/EDC/02.2; International Programme on Chemical Safety: Geneva, 2002.
54. U.S. EPA. Endocrine Disrupter Screening and Testing Advisory Committee (EDSTAC) Report; Office of Science Council and Policy: Washington, DC, 1998; available from EPA.
55. Huet, M.-C. OECD Activity on Endocrine Disrupters Test Guidelines Development. Ecotoxicology 2000, 9, 77-84.
56. Moggs, J. G. Molecular Responses to Xenoestrogens: Mechanistic Insights from Toxicogenomics. Toxicology 2005, 213, 177-193.
57. Benson, W. H.; Di Giulio, R. T. Emerging Molecular and Computational Approaches for Cross-Species Extrapolations: A Workshop Summary. SETAC Globe 2005, 6, 20-21.
58. U.S. EPA. Technical Support Document for Water Quality-Based Toxics Control; EPA/50512-30-001; Washington, DC, 1991.
59. Burkhard, L. P.; Ankley, G. T. Identifying Toxicants: NETAC's Toxicity-Based Approach. Environ. Sci. Technol. 1989, 23, 1438-1443.
60. Bradbury, S. P.; Feijtel, T. C. J.; Van Leeuwen, C. J. Meeting the Scientific Needs of Ecological Risk Assessment in a Regulatory Context. Environ. Sci. Technol. 2004, 38, 463A-470A.
61. Brazma, A.; et al. Minimum Information about a Microarray Experiment (MIAME) - Toward Standards for Microarray Data. Nat. Genet. 2001, 29, 365-371.
62. Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM). Validation and Regulatory Acceptance of Toxicological Test Methods; Publication No. 97-3981; National Institutes of Health: Bethesda, MD, 1997.
63. Corvi, R.; et al. Validation of Toxicogenomics-Based Test Systems: ECVAM-ICCVAM/NICEATM Considerations for Regulatory Use. Environ. Health Perspect. 2006, 114, 420-429.
64. Tennant, R. W. The National Center for Toxicogenomics: Using New Technologies To Inform Mechanistic Toxicology. Environ. Health Perspect. 2002, 110, A8-A10.
65. SETAC. Biomarkers-Biochemical, Physiological and Histological Markers of Anthropogenic Stress; Huggett, R. J., et al., Eds.; Lewis Publishers: Ann Arbor, MI; 1992.
66. Chipman, J. K.; et al. Biomarkers from (Eco) toxicogenomics: The European Flounder as a Non-Model Organism and the Distinction between Compensatory versus Toxic Responses. Abstracts of the 26th Annual Meeting of SETAC, Baltimore, MD, 2005.
67. Balbus, J. M. Ushering in the New Toxicology: Toxicogenomics and the Public Interest. Environ. Health Perspect. 2005, 113, 818-822.
68. OECD. Report of the OECD/IPCS Workshop on Toxicogenomics; OECD Environmental Health and Safety Publications, Series on Testing and Assessment No. 50, April 2005; http://applil.oecd.org/olis/2005doc.nsf/ 43bb6130e5e86e5fc12569fa005d004c/d49a5f7fdfa04f97c1256ff200379c99/$FILE/ JT00183336. DOC.
69. Hutchinson, T. H.; et al. Screening and Testing for Endocrine Disruption in Fish - Biomarkers as Signposts Not Traffic Lights in Risk Assessment. Environ. Health Perspect. 2006, 114 (Suppl. 1), 106-114.
70. Sumpter, J. P.; Jobling, S. Vitellogenesis as a Biomarker for Estrogenic Contamination in the Aquatic Environment. Environ. Health Perspect. 1995, 103, 173-178.