Recent applications of DNA microarray technology to toxicology and ecotoxicology

Environmental Health Perspectives

Volumn 114, Issue 1, 2006, Pages 4-9

  Lettieri, Teresa ^a  

^a JOINT RESEARCH CENTRE   (Italy)

Author keywords

Ecotoxicology; Gene expression profile; Genetic signature; Microarray; Toxicogenomics; Toxicology

Indexed keywords

CHEMICAL COMPOUND; DNA;

COMMERCIAL PHENOMENA; DNA MICROARRAY; ECOTOXICOLOGY; ENVIRONMENTAL CHANGE; ENVIRONMENTAL EXPOSURE; EXPERIMENTAL DESIGN; GENE EXPRESSION PROFILING; GENE TECHNOLOGY; GENETIC DATABASE; GENETIC IDENTIFICATION; GENETIC TOXICOLOGY; HUMAN; MEDICAL INFORMATION; MICROORGANISM; NATURAL POPULATION; NONHUMAN; PREDICTION; PRIORITY JOURNAL; QUALITY CONTROL; REVIEW; STANDARDIZATION; STRESS; TOXICITY TESTING;

ANIMALS; DATABASES, GENETIC; ECOLOGY; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TOXICOGENETICS; TOXICOLOGY;

EID: 30344484578     PISSN: 00916765     EISSN: 15529924     Source Type: Journal    
DOI: 10.1289/ehp.8194     Document Type: Review

References (87)

1. Afshari CA, Nuwaysir EF, Barrett JC. 1999. Application of complementary DNA microarray technology to carcinogen identification, toxicology, and drug safety evaluation. Cancer Res 59:4759-4760.
2. Amin RP, Vickers AE, Sistare F, Thompson KL, Roman RJ, Lawton M, et al. 2004. Identification of putative gene-based markers of renal toxicity. Environ Health Perspect 112:465-479.
3. Andrew AS, Warren AJ, Barchowsky A, Temple KA, Klei L, Soucy NV, et al. 2003. Genomic and proteomic profiling of responses to toxic metals in human lung cells. Environ Health Perspect 111:825-835.
4. Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, et al. 2004. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306:79-86.
5. Baker VA, Harries HM, Waring JF, Duggan CM, Ni HA, Jolly RA, et al. 2004. Clofibrate-induced gene expression changes in rat liver: a cross-laboratory analysis using membrane cDNA arrays. Environ Health Perspect 112:428-438.
6. Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, et al. 2004. Submission of microarray data to public repositories. PLoS Biol 2:1276-1277.
7. Bartosiewicz MJ, Jenkins D, Renn S, Emery J, Buckpitt A. 2001. Unique gene expression patterns in liver and kidney associated with exposure to chemical toxicants. J Pharmacol Exp Ther 297:895-905.
8. Blum JL, Knoebl I, Larkin P, Kroll KJ, Denslow ND. 2004. Use of suppressive subtractive hybridization and cDNA arrays to discover patterns of altered gene expression in the liver of dihydrotestosterone and 11-ketotestosterone exposed adult male largemouth bass (Micropterus salmoides). Mar Environ Res 58:565-569.
9. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, et al. 2001. Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nat Genet 29:365-371.
10. Brazma A, Parkinson HS, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, et al. 2003. ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 31:68-71.
11. Bulera SJ, Eddy SM, Ferguson E, Jatkoe TA, Reindel JF, Bleavins MR, et al. 2001. RNA expression in the early characterization of hepatotoxicants in Wistar rats by high-density DNA microarrays. Hepatology 33:1239-1258.
12. Burchiel SW, Knall CM, Davis JW II, Paules RS, Boggs SE, Afshari CA. 2001. Analysis of genetic and epigenetic mechanisms of toxicity: potential roles of toxicogenomics and proteomics in toxicology. Toxicol Sci 59:193-195.
13. Burczynski ME, McMillian M, Ciervo J, Li L, Parker JB, Dunn RT II, et al. 2000. Toxicogenomics-based discrimination of toxic mechanism in HepG2 human hepatoma cells. Toxicol Sci 58:399-415.
14. Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, et al. 2001. Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell 12:323-337.
15. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, et al. 1996. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 14:457-460.
16. Diener LC, Schulte PM, Dixon DG, Greenberg BM. 2004. Optimization of differential display polymerase chain reaction as a bioindicator for the cladoceran Daphnia magna. Environ Toxicol 19:179-190.
17. EBI (European Bioinformatics Institute). 2005a. ArrayExpress. Available: http://www.ebi.ac.uk/arrayexpress [accessed 23 July 2005].
18. EBI (European Bioinformatics Institute). 2005b. Tox-MIAMExpress. Available: http://www.ebi.ac.uk/tox-miamexpress [accessed 23 July 2005].
19. Edgar R, Domrachev M, Lash AE. 2002. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207-210.
20. Environmental Health Perspectives. 2004. Application of Genomics to Mechanism-Based Risk Assessment [Minimonograph]. Environ Health Perspect 112:417-506.
21. Ezendam J, Staedtler F, Pennings J, Vandebriel RJ, Pieters R, Boffetta P, et al. 2004. Toxicogenomics of subchronic hexachlorobenzene exposure in Brown Norway rats. Environ Health Perspect 112:782-791.
22. Fay JC, McCullough HL, Sniegowski PD, Eisen MB. 2004. Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. Genome Biol 5(4):R26.
23. Fielden MR, Zacharewski TR. 2001. Challenges and limitations of gene expression profiling in mechanistic and predictive toxicology. Toxicol Sci 60:6-10.
24. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, et al. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11:4241-4257.
25. Gracey AY, Troll JV, Somero GN. 2001. Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Proc Natl Acad Sci USA 98:1993-1998.
26. Grunstein M, Hogness DS. 1975. Colony hybridization: a method for the isolation of cloned DNAs that contain a specific gene. Proc Natl Acad Sci USA 72:3961-3965.
27. Hamadeh HK, Bushel PR, Jayadev S, Martin K, DiSorbo O, Sieber S, et al. 2002. Gene expression analysis reveals chemical-specific profiles. Toxicol Sci 67:219-231.
28. Hittel D, Storey KB. 2001. Differential expression of adipose- and heart-type fatty acid binding proteins in hibernating ground squirrels. Biochim Biophys Acta 1522:238-243.
29. Hoyt PR, Doktycz MJ, Beattie KL, Greeley MS Jr. 2003. DNA microarrays detect 4-nonylphenol-induced alterations in gene expression during zebrafish early development. Ecotoxicology 12:469-474.
30. Hughes TR, Roberts CJ, Dai H, Jones AR, Meyer MR, Slade D, et al. 2000. Widespread aneuploidy revealed by DNA microarray expression profiling. Nat Genet 25:333-337.
31. Ikeo K, Ishi-i J, Tamura T, Gojobori T, Tateno Y. 2003. CIBEX: Center for Information Biology Gene Expression database. C R Biol 326:1079-1082.
32. Irwin R, Parker J, Lobenhofer E, Burka L, Blackshear P, Vallant M, et al. 2005. Transcriptional profiling of the left and median liver lobes of male F344/n rats following exposure to acetaminophen. Toxicol Pathol 33:111-117.
33. Jin W, Riley RM, Wolfinger RD, White KP, Passador-Gurgel G, Gibson G. 2001. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat Genet 29:389-395.
34. Kane MD, Jatkoe TA, Stumpf CR, Lu J, Thomas JD, Madore SJ. 2000. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res 28:4552-4557.
35. Kitagawa E, Takahashi J, Momose Y, Iwahashi H. 2002. Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environ Sci Technol 36: 3908-3915.
36. Knudsen S. 2004. Guide to Analysis of DNA Microarray Data. Hoboken, NJ:Wiley-Liss.
37. Kramer JA, Pettit SD, Amin RP, Bertram TA, Car B, Cunningham M, et al. 2004. Overview on the application of transcription profiling using selected nephrotoxicants for toxicology assessment. Environ Health Perspect 112:460-464.
38. Larkin P, Folmar LC, Hemmer MJ, Poston AJ, Denslow ND. 2003. Expression profiling of estrogenic compounds using a sheepshead minnow cDNA macroarray. Environ Health Perspect 111:839-846.
39. Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, et al. 1997. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci USA 94:13057-13062.
40. Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ. 1999. High density synthetic oligonucleotide arrays. Nat Genet 21:20-24.
41. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, et al. 1996. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14:1675-1680.
42. Lovett RA. 2000. Toxicogenomics. Toxicologists brace for genomics revolution. Science 289:536-537.
43. Ludwikow A, Gallois P, Sadowski J. 2004. Ozone-induced oxidative stress response in Arabidopsis: transcription profiling by microarray approach. Cell Mol Biol Lett 9:829-842.
44. Mattes WB, Pettit SD, Sansone SA, Bushel PR, Waters MD. 2004. Database development in toxicogenomics: issues and efforts. Environ Health Perspect 112:495-505.
45. Momose Y, Iwahashi H. 2001. Bioassay of cadmium using a DNA microarray: genome-wide expression patterns of Saccharomyces cerevisiae response to cadmium. Environ Toxicol Chem 20:2353-2360.
46. National Institute of Genetics. 2005. CIBEX. Center for Information Biology Gene Expression Database. Available: http://cibex.nig.ac.jp [accessed 23 July 2005].
47. NCBI (National Center for Biotechnology Information). 2005a. GEO. Gene Expression Omnibus. Available: http://www.ncbi.nlm.nih.gov/geo [accessed 23 July 2005].
48. NCBI (National Center for Biotechnology Information). 2005b. List of Finished and Ongoing Genomics Projects. Available: http://www.ncbi.nlm.nih.gov/Genomes/index.html [accessed 23 July 2005].
49. NCTR (National Center for Toxicoinformatics Research). 2005. ArrayTrack. Available: http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack [accessed 23 July 2005].
50. Neumann NF, Galvez F. 2002. DNA microarrays and toxicogenomics: applications for ecotoxicology? Biotechnol Adv 20:391-419.
51. Newton RK, Aardema M, Aubrecht J. 2004. The utility of DNA microarrays for characterizing genotoxicity. Environ Health Perspect 112:420-422.
52. NIEHS (National Institute of Environmental Health Sciences). 2005. CEBS. Chemical Effects in Biological Systems. Available: http://cebs.niehs.nih.gov [accessed 23 July 2005].
53. Nuwaysir EF, Bittner M, Trent J, Barrett JC, Afshari CA. 1999. Microarrays and toxicology: the advent of toxicogenomics. Mol Carcinog 24:153-159.
54. Olden K, Guthrie J. 2001. Genomics: implications for toxicology. Mutat Res 473:3-10.
55. Oleksiak MF, Churchill GA, Crawford DL. 2002. Variation in gene expression within and among natural populations. Nat Genet 32:261-266.
56. Panicker G, Call DR, Krug MJ, Bej AK. 2004. Detection of pathogenic Vibrio spp. in shellfish by using multiplex PCR and DNA microarrays. Appl Environ Microbiol 70:7436-7444.
57. Pennie W, Pettit SD, Lord PG. 2004. Toxicogenomics in risk assessment: an overview of an HESI collaborative research program. Environ Health Perspect 112:417-419.
58. Perkins EJ, Lotufo GR. 2003. Playing in the mud-using gene expression to assess contaminant effects on sediment dwelling invertebrates. Ecotoxicology 12:453-456.
59. Ranz JM, Castillo-Davis CI, Meiklejohn CD, Hartl DL. 2003. Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300:1742-1745.
60. Renn SC, Aubin-Horth N, Hofmann HA. 2004. Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray. BMC Genomics 5(4):42.
61. Rise ML, Jones SR, Brown GD, Von Schalburg KR, Davidson WS, Koop BF. 2004a. Microarray analyses identify molecular biomarkers of Atlantic salmon macrophage and hematopoietic kidney response to Piscirickettsia salmonis infection. Physiol Genomics 20:21-35.
62. Rise ML, von Schalburg KR, Brown GD, Mawer MA, Devlin RH, Kuipers N, et al. 2004b. Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res 14:478-490.
63. Schena M. 1999. DNA Microarrays: A Practical Approach. New York:Oxford University Press.
64. Schena M. 2003. Microarray Analysis. Hoboken, NJ:Wiley-Liss.
65. Schena M, Heller RA, Theriault TP, Konrad K, Lachenmeier E, Davis RW. 1998. Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol 16:301-306.
66. Schena M, Shalon D, Davis RW, Brown PO. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470.
67. Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW. 1996. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA 93:10614-10619.
68. Schulze A, Downward J. 2001. Navigating gene expression using microarrays - a technology review. Nat Cell Biol 3:E190-E195.
69. Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, et al. 2002. Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 31:279-292.
70. Seki M, Satou M, Sakurai T, Akiyama K, Iida K, Ishida J, et al. 2004. RIKEN Arabidopsis full-length (RAFL) cDNA and its applications for expression profiling under abiotic stress conditions. J Exp Bot 55:213-223.
71. Simmons PT, Portier CJ. 2002. Toxicogenomics: the new frontier in risk analysis. Carcinogenesis 23:903-905.
72. Smith LL. 2001. Key challenges for toxicologists in the 21st century. Trends Pharmacol Sci 22:281-285.
73. Snape JR, Maund SJ, Pickford DB, Hutchinson TH. 2004. Ecotoxicogenomics: the challenge of integrating genomics into aquatic and terrestrial ecotoxicology. Aquatic Toxic 67:143-154.
74. Snell TW, Brogdon SE, Morgan MB. 2003. Gene expression profiling in ecotoxicology. Ecotoxicology 12:475-483.
75. Southern EM. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503-517.
76. Southern EM. 2000. Blotting at 25. Trends Biochem Sci 25:585-588.
77. Tennant RW. 2002. The National Center for Toxicogenomics: using new technologies to inform mechanistic toxicology. Environ Health Perspect 110:A8-A10.
78. Thompson KL, Afshari CA, Amin RP, Bertram TA, Car B, Cunningham M, et al. 2004. Identification of platform-independent gene expression markers of cisplatin nephro-toxicity. Environ Health Perspect 112:488-494.
79. Tong W, Harris S, Cao X, Fang H, Shi L, Sun H, et al. 2004. Development of public toxicogenomics software for microarray data management and analysis. Mutat Res 549:241-253.
80. Townsend JP, Cavalieri D, Hartl DL. 2003. Population genetic variation in genome-wide gene expression. Mol Biol Evol 20:955-963.
81. Troester MA, Hoadley KA, Parker JS, Perou CM. 2004. Prediction of toxicant-specific gene expression signatures after chemotherapeutic treatment of breast cell lines. Environ Health Perspect 112:1607-1613.
82. Ulrich R, Friend SH. 2002. Toxicogenomics and drug discovery: will new technologies help us produce better drugs? Nat Rev Drug Discov 1:84-88.
83. Ulrich RG, Rockett JC, Gibson GG, Pettit SD. 2004. Overview of an interlaboratory collaboration on evaluating the effects of model hepatotoxicants on hepatic gene expression. Environ Health Perspect 112:423-427.
84. Waring JF, Ciurlionis R, Jolly RA, Heindel M, Ulrich RG. 2001. Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity. Toxicol Lett 120:359-368.
85. Waring JF, Ulrich RG, Flint N, Morfitt D, Kalkuhl A, Staedtler F, et al. 2004. Interlaboratory evaluation of rat hepatic gene expression changes induced by methapyrilene. Environ Health Perspect 112:439-448.
86. Waters M, Boorman G, Bushel P, Cunningham M, Irwin R, Merrick A, et al. 2003. Systems toxicology and the Chemical Effects in Biological Systems (CEBS) knowledge base. Environ Health Perspect 111:811-824.
87. Williams TD, Gensberg K, Minchin SD, Chipman JK. 2003. A DNA expression array to detect toxic stress response in European flounder (Platichthys flesus). Aquat Toxicol 65:141-157.