Recent Applications of DNA Microarray Technology to Toxicology and Ecotoxicology

Gene expression is a unique way of characterizing how cells and organisms adapt to changes in the external environment. The measurements of gene expression levels upon exposure to a chemical can be used both to provide information about the mechanism of action of the toxicant and to form a sort of “genetic signature” for the identification of toxic products. The development of high-quality, commercially available gene arrays has allowed this technology to become a standard tool in molecular toxicology. Several national and international initiatives have provided the proof-of-principle tests for the application of gene expression for the study of the toxicity of new and existing chemical compounds. In the last few years the field has progressed from evaluating the potential of the technology to illustrating the practical use of gene expression profiling in toxicology. The application of gene expression profiling to ecotoxicology is at an earlier stage, mainly because of the the many variables involved in analyzing the status of natural populations. Nevertheless, significant studies have been carried out on the response to environmental stressors both in model and in nonmodel organisms. It can be easily predicted that the development of stressor-specific signatures in gene expression profiling in ecotoxicology will have a major impact on the ecotoxicology field in the near future. International collaborations could play an important role in accelerating the application of genomic approaches in ecotoxicology.

[1]  N. Neumann,et al.  DNA microarrays and toxicogenomics: applications for ecotoxicology? , 2002, Biotechnology advances.

[2]  D. Botstein,et al.  Genomic expression programs in the response of yeast cells to environmental changes. , 2000, Molecular biology of the cell.

[3]  M Schena,et al.  Microarrays: biotechnology's discovery platform for functional genomics. , 1998, Trends in biotechnology.

[4]  E. Lander,et al.  Remodeling of yeast genome expression in response to environmental changes. , 2001, Molecular biology of the cell.

[5]  J. Waring,et al.  Interlaboratory evaluation of rat hepatic gene expression changes induced by methapyrilene. , 2004, Environmental health perspectives.

[6]  E. Perkins,et al.  Playing in the Mud-Using Gene Expression to Assess Contaminant Effects on Sediment Dwelling Invertebrates , 2003, Ecotoxicology.

[7]  Russell D. Wolfinger,et al.  The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster , 2001, Nature Genetics.

[8]  R. Tennant,et al.  The National Center for Toxicogenomics: using new technologies to inform mechanistic toxicology. , 2002, Environmental health perspectives.

[9]  R G Ulrich,et al.  Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity. , 2001, Toxicology letters.

[10]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..

[11]  B. Koop,et al.  Microarray analyses identify molecular biomarkers of Atlantic salmon macrophage and hematopoietic kidney response to Piscirickettsia salmonis infection. , 2004, Physiological genomics.

[12]  Lee Bennett,et al.  Gene expression analysis reveals chemical-specific profiles. , 2002, Toxicological sciences : an official journal of the Society of Toxicology.

[13]  K. Morgan Gene expression analysis reveals chemical-specific profiles. , 2002, Toxicological sciences : an official journal of the Society of Toxicology.

[14]  G. Somero,et al.  Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[15]  D. Lockhart,et al.  Expression monitoring by hybridization to high-density oligonucleotide arrays , 1996, Nature Biotechnology.

[16]  Kazuho Ikeo,et al.  CIBEX: center for information biology gene expression database. , 2003, Comptes rendus biologies.

[17]  Frank D Sistare,et al.  Identification of platform-independent gene expression markers of cisplatin nephrotoxicity. , 2004, Environmental health perspectives.

[18]  R. Lovett Toxicologists Brace for Genomics Revolution , 2000, Science.

[19]  Janine Ezendam,et al.  Toxicogenomics of subchronic hexachlorobenzene exposure in Brown Norway rats. , 2004, Environmental health perspectives.

[20]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[21]  M Waters,et al.  Systems Toxicology and the Chemical Effects in Biological Systems (CEBS) Knowledge Base , 2003, EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences.

[22]  D. Hogness,et al.  Colony hybridization: a method for the isolation of cloned DNAs that contain a specific gene. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Jiasen Lu,et al.  Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. , 2000, Nucleic acids research.

[24]  Mark Schena,et al.  DNA microarrays : a practical approach , 1999 .

[25]  Jiri Aubrecht,et al.  The utility of DNA microarrays for characterizing genotoxicity. , 2004, Environmental health perspectives.

[26]  H. Iwahashi,et al.  Bioassay of cadmium using a DNA microarray: Genome‐wide expression patterns of Saccharomyces cerevisiae response to cadmium , 2001, Environmental toxicology and chemistry.

[27]  K. Thompson,et al.  Overview on the application of transcription profiling using selected nephrotoxicants for toxicology assessment. , 2004, Environmental health perspectives.

[28]  William Pennie,et al.  Toxicogenomics in risk assessment: an overview of an HESI collaborative research program. , 2004, Environmental health perspectives.

[29]  D. Hittel,et al.  Differential expression of adipose- and heart-type fatty acid binding proteins in hibernating ground squirrels. , 2001, Biochimica et biophysica acta.

[30]  J. Emery,et al.  Unique gene expression patterns in liver and kidney associated with exposure to chemical toxicants. , 2001, The Journal of pharmacology and experimental therapeutics.

[31]  L. Folmar,et al.  Expression Profiling of Estrogenic Compounds Using a Sheepshead Minnow cDNA Macroarray , 2003, EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences.

[32]  J. Trent,et al.  Microarrays and toxicology: The advent of toxicogenomics , 1999, Molecular carcinogenesis.

[33]  Justin C. Fay,et al.  Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae , 2004, Genome Biology.

[34]  E. Southern Detection of specific sequences among DNA fragments separated by gel electrophoresis. , 1975, Journal of molecular biology.

[35]  C. Ball,et al.  Submission of Microarray Data to Public Repositories , 2004, PLoS biology.

[36]  R. Dunn,et al.  Toxicogenomics-based discrimination of toxic mechanism in HepG2 human hepatoma cells. , 2000, Toxicological sciences : an official journal of the Society of Toxicology.

[37]  A. Andrew,et al.  Genomic and proteomic profiling of responses to toxic metals in human lung cells. , 2003, Environmental health perspectives.

[38]  Steen Knudsen,et al.  Guide to analysis of DNA microarray data , 2004 .

[39]  D. Dixon,et al.  Optimization of differential display polymerase chain reaction as a bioindicator for the cladoceran Daphnia magna , 2004, Environmental toxicology.

[40]  Joel S. Parker,et al.  Transcriptional Profiling of the Left and Median Liver Lobes of Male F344/N Rats Following Exposure to Acetaminophen , 2005, Toxicologic pathology.

[41]  A. Schulze,et al.  Navigating gene expression using microarrays — a technology review , 2001, Nature Cell Biology.

[42]  G. Gibson,et al.  Microarray Analysis , 2020, Definitions.

[43]  D. Hartl,et al.  Population genetic variation in genome-wide gene expression. , 2003, Molecular biology and evolution.

[44]  Colin D. Meiklejohn,et al.  Sex-Dependent Gene Expression and Evolution of the Drosophila Transcriptome , 2003, Science.

[45]  P. Brown,et al.  Yeast microarrays for genome wide parallel genetic and gene expression analysis. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[46]  D. Call,et al.  Detection of Pathogenic Vibrio spp. in Shellfish by Using Multiplex PCR and DNA Microarrays , 2004, Applied and Environmental Microbiology.

[47]  C. Perou,et al.  Prediction of Toxicant-Specific Gene Expression Signatures after Chemotherapeutic Treatment of Breast Cell Lines , 2022 .

[48]  S. Minchin,et al.  A DNA expression array to detect toxic stress response in European flounder (Platichthys flesus). , 2003, Aquatic toxicology.

[49]  Thomas H Hutchinson,et al.  Ecotoxicogenomics: the challenge of integrating genomics into aquatic and terrestrial ecotoxicology. , 2004, Aquatic toxicology.

[50]  E. Southern,et al.  Blotting at 25. , 2000, Trends in biochemical sciences.

[51]  K. Olden,et al.  Genomics: implications for toxicology. , 2001, Mutation research.

[52]  G. Churchill,et al.  Variation in gene expression within and among natural populations , 2002, Nature Genetics.

[53]  P. Brown,et al.  Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Nicholas H. Putnam,et al.  The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism , 2004, Science.

[55]  Stephen H. Friend,et al.  Toxicogenomics and drug discovery: will new technologies help us produce better drugs? , 2002, Nature Reviews Drug Discovery.

[56]  L. Penland,et al.  Use of a cDNA microarray to analyse gene expression patterns in human cancer , 1996, Nature Genetics.

[57]  K. Akiyama,et al.  Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. , 2002, The Plant journal : for cell and molecular biology.

[58]  Michael D Waters,et al.  Database development in toxicogenomics: issues and efforts. , 2004, Environmental health perspectives.

[59]  S. P. Fodor,et al.  High density synthetic oligonucleotide arrays , 1999, Nature Genetics.

[60]  Hongyue Dai,et al.  Widespread aneuploidy revealed by DNA microarray expression profiling , 2000, Nature Genetics.

[61]  Masakazu Satou,et al.  RIKEN Arabidopsis full-length (RAFL) cDNA and its applications for expression profiling under abiotic stress conditions. , 2003, Journal of experimental botany.

[62]  M. Greeley,et al.  DNA Microarrays Detect 4-Nonylphenol-induced Alterations in Gene Expression During Zebrafish Early Development , 2003, Ecotoxicology.

[63]  Sergio Contrino,et al.  ArrayExpress—a public repository for microarray gene expression data at the EBI , 2004, Nucleic Acids Res..

[64]  T R Zacharewski,et al.  Challenges and limitations of gene expression profiling in mechanistic and predictive toxicology. , 2001, Toxicological sciences : an official journal of the Society of Toxicology.

[65]  S W Burchiel,et al.  Analysis of genetic and epigenetic mechanisms of toxicity: potential roles of toxicogenomics and proteomics in toxicology. , 2001, Toxicological sciences : an official journal of the Society of Toxicology.

[66]  Weida Tong,et al.  Development of public toxicogenomics software for microarray data management and analysis. , 2004, Mutation research.

[67]  J. Barrett,et al.  Application of complementary DNA microarray technology to carcinogen identification, toxicology, and drug safety evaluation. , 1999, Cancer research.

[68]  J. Reindel,et al.  RNA expression in the early characterization of hepatotoxicants in Wistar rats by high‐density DNA microarrays , 2001, Hepatology.

[69]  Jan Sadowski,et al.  Ozone-induced oxidative stress response in Arabidopsis: transcription profiling by microarray approach. , 2004, Cellular & molecular biology letters.

[70]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[71]  武田 健,et al.  Toxicogenomics , 2003, Springer Japan.

[72]  J. Waring,et al.  Clofibrate-induced gene expression changes in rat liver: a cross-laboratory analysis using membrane cDNA arrays. , 2004, Environmental health perspectives.

[73]  Jennifer M Fostel,et al.  Towards standards for data exchange and integration and their impact on a public database such as CEBS (Chemical Effects in Biological Systems). , 2008, Toxicology and applied pharmacology.

[74]  N. Denslow,et al.  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). , 2004, Marine environmental research.

[75]  H. Iwahashi,et al.  Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. , 2002, Environmental science & technology.

[76]  R. Ulrich,et al.  Overview of an interlaboratory collaboration on evaluating the effects of model hepatotoxicants on hepatic gene expression. , 2004, Environmental health perspectives.

[77]  Timothy A Bertram,et al.  Identification of putative gene based markers of renal toxicity. , 2004, Environmental health perspectives.

[78]  T. Snell,et al.  Gene Expression Profiling in Ecotoxicology , 2003, Ecotoxicology.

[79]  Hans A Hofmann,et al.  Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray , 2004, BMC Genomics.

[80]  L. L. Smith,et al.  Key challenges for toxicologists in the 21st century. , 2001, Trends in pharmacological sciences.

[81]  Christopher J Portier,et al.  Toxicogenomics: the new frontier in risk analysis. , 2002, Carcinogenesis.