EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences最新文献

{"title":"Application of toxicogenomic analysis to risk assessment of delayed long-term effects of multiple chemicals, including endocrine disruptors in human fetuses.","authors":"Chisato Mori,&nbsp;Masatoshi Komiyama,&nbsp;Tetsuya Adachi,&nbsp;Kenichi Sakurai,&nbsp;Daisuke Nishimura,&nbsp;Kyoka Takashima,&nbsp;Emiko Todaka","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Our previous studies analyzing umbilical cords show that human fetuses in Japan are exposed to multiple chemicals. Because of these findings, we believe it is necessary to establish a new strategy for examining the possible delayed long-term effects caused by prenatal exposure to multiple chemical combinations and evaluating the health risk to human fetuses. In this commentary we describe our attempts to apply toxicogenomic analysis of umbilical cords, using DNA microarray for future risk assessment. Because the umbilical cord is part of the fetal tissue, it is possible to estimate the effects of chemicals on the fetus by analyzing alteration of the gene expression. This type of toxicogenomic analysis could be a powerful and effective tool for developing a new risk assessment strategy to help investigators understand and possibly prevent long-term effects caused by fetal exposure to multiple chemicals. Worldwide cooperation is needed to establish a new stragegy for risk assessment using toxicogenomic analysis that focuses on the human fetus.</p>","PeriodicalId":84641,"journal":{"name":"EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences","volume":"111 1T","pages":"7-13"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22374943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expression profiling of estrogenic compounds using a sheepshead minnow cDNA macroarray.","authors":"Patrick Larkin,&nbsp;Leroy C Folmar,&nbsp;Michael J Hemmer,&nbsp;Arianna J Poston,&nbsp;Nancy D Denslow","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A variety of anthropogenic compounds are capable of binding to the estrogen receptor (ER) of vertebrate species. Binding of these chemicals to the ER can interfere with homeostasis by altering normal gene expression patterns. The purpose of this study was to characterize the expression of 30 genes using a sheepshead minnow (Cyprinodon variegatus) cDNA macroarray. Many of the genes on the array were previously identified by differential display reverse transcriptase-polymerase chain reaction to be upregulated or downregulated in sheepshead minnows treated through aqueous exposure to known or suspected estrogenic chemicals. The results of this study show that 17 beta-estradiol (E2), 17 alpha-ethinyl estradiol (EE2), diethylstilbestrol (DES), and methoxychlor (MXC) have similar genetic signatures for the 30 genes examined. The genetic signature of fish treated with p-nonylphenol was identical in pattern to that in fish treated with E2, EE2, DES, and MXC except for the additional upregulation of a cDNA clone that shares similarity to ubiquitin-conjugating enzyme 9. Endosulfan produced results that resembled the gene expression patterns of untreated control fish with exception of the upregulation of estrogen receptor alpha and the downregulation of a cDNA clone that shares similarity to 3-hydroxy-3-methylglutaryl-coenzyme A reductase. We show that our estrogen-responsive cDNA macroarray can detect dose-dependent changes in gene expression patterns in fish treated with EE2.</p>","PeriodicalId":84641,"journal":{"name":"EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences","volume":"111 1T","pages":"29-36"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22374945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a DNA microarray for toxicology based on hepatotoxin-regulated sequences.","authors":"Jeffrey F Waring,&nbsp;Guy Cavet,&nbsp;Robert A Jolly,&nbsp;Jeff McDowell,&nbsp;Hongye Dai,&nbsp;Rita Ciurlionis,&nbsp;Chunsheng Zhang,&nbsp;Roland Stoughton,&nbsp;Pek Lum,&nbsp;Allan Ferguson,&nbsp;Christopher J Roberts,&nbsp;Roger G Ulrich","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Toxicogenomics is an emerging field combining genomics and bioinformatics to identify and characterize mechanisms of toxicity of compounds. One of the main tools used in toxicogenomics is DNA microarrays. We have used a novel strategy to create a library highly enriched for genes expressed in the liver under hepatotoxic conditions. Using this library, we have created a new oligonucleotide microarray dedicated to the study of rat liver function. Oligonucleotide probes for these genes were designed and used in experimental hybridization studies to deduce the correct sequence orientation and to determine those sequences exhibiting differential regulation under a variety of toxicity-related treatments and conditions. The final array was benchmarked on treatments with 3-methylcholanthrene, Aroclor 1254, and cyclopropane carboxylic acid. Our results showed that the subtractive hybridization greatly enriched for genes regulated during a hepatotoxic response. Overall, our strategy for design of a new rat toxicology microarray can be applied to other systems as well and should aid greatly in the development of microarrays targeted for specific scientific areas.</p>","PeriodicalId":84641,"journal":{"name":"EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences","volume":"111 1T","pages":"53-60"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22375442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"EHP Toxicogenomics: a publication forum in the postgenome era.","authors":"Kenneth S Ramos","doi":"10.1289/ehp.111t-a13","DOIUrl":"https://doi.org/10.1289/ehp.111t-a13","url":null,"abstract":"","PeriodicalId":84641,"journal":{"name":"EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences","volume":"111 1T","pages":"A13"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22374935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intrinsic hepatic phenotype associated with the Cyp1a2 gene as shown by cDNA expression microarray analysis of the knockout mouse.","authors":"Andrew G Smith,&nbsp;Reginald Davies,&nbsp;Timothy P Dalton,&nbsp;Marian L Miller,&nbsp;David Judah,&nbsp;Joan Riley,&nbsp;Timothy Gant,&nbsp;Daniel W Nebert","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Several forms of cytochrome P450 (CYP) appear to metabolize principally pharmaceutical agents, as well as other dietary and plant chemicals. Other CYP forms have major roles in steroid, sterol, and bile acid metabolism. CYP1A2 expression is constitutively high in mouse liver and is well known for metabolizing several drugs and many procarcinogens to reactive intermediates that can cause toxicity or cancer. CYP1A2 is also known to carry out several endogenous functions such as uroporphyrinogen and melatonin oxidation and the 2- and 4-hydroxylations of estradiol. We have used cDNA microarray analysis of the untreated Cyp1a2(-/-) knockout mouse to search for changes in gene expression that might indicate important intrinsic roles for this enzyme. For 15 of the up- or downregulated genes, these increases or decreases were corroborated by reverse-transcription real-time polymerase chain reaction. Other than upregulation of the Hprt gene (used in the selection procedure for disrupting the Cyp1a2 gene), we found several genes upregulated that are associated with cell-cycle regulation and lipid metabolism. Besides Cyp1a2, the gene exhibiting the greatest downregulation was Igfbp1 (insulin-like growth factor binding protein-1), showing only 12% expression of that in the Cyp1a2(+/+) wild-type liver. Recurrent themes between both up- and downregulated genes include cell-cycle control, insulin action, lipogenesis, and fatty acid and cholesterol biosynthetic pathways. Histologically, the Cyp1a2(-/-) mouse exhibited an approximately 50% decrease in lipid stored in hepatocytes, and 50% increase in lipid present in interstitial fat-storing cells compared with that in the Cyp1a2(+/+) wild-type. These data suggest that the CYP1A2 enzyme might perform additional hepatic endogenous functions heretofore not appreciated.</p>","PeriodicalId":84641,"journal":{"name":"EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences","volume":"111 1T","pages":"45-51"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22374947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploiting genome data to understand the function, regulation, and evolutionary origins of toxicologically relevant genes.","authors":"Nazzareno Ballatori,&nbsp;James L Boyer,&nbsp;John C Rockett","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The wealth of new information coming from the many genome sequencing projects is providing unprecedented opportunities for major advances in all areas of biology, including the environmental health sciences. To facilitate this discovery process, experts in the fields of functional genomics and informatics and the emerging field of toxicogenomics recently gathered at the Mount Desert Island Biological Laboratory in Salisbury Cove, Maine, site of a National Institute of Environmental Health Sciences Marine and Freshwater Biomedical Science Center, to share their ideas and latest research findings. The goal of the symposium was to highlight approaches that may be used to identify and characterize toxicologically relevant genes being discovered in the genome sequencing projects. Many of the approaches rely heavily on comparative models as a way of identifying gene homology, ontology, and physiologic function, and on the availability of databases that facilitate storage, analysis, interpretation, and widespread dissemination of relevant data.</p>","PeriodicalId":84641,"journal":{"name":"EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences","volume":"111 1T","pages":"61-5"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22375443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The new biology.","authors":"Tina Adler","doi":"10.1289/ehp.111t-a14","DOIUrl":"https://doi.org/10.1289/ehp.111t-a14","url":null,"abstract":"","PeriodicalId":84641,"journal":{"name":"EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences","volume":"111 1T","pages":"A14-5"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22374936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Systems toxicology and the Chemical Effects in Biological Systems (CEBS) knowledge base.","authors":"Michael Waters,&nbsp;Gary Boorman,&nbsp;Pierre Bushel,&nbsp;Michael Cunningham,&nbsp;Rick Irwin,&nbsp;Alex Merrick,&nbsp;Kenneth Olden,&nbsp;Richard Paules,&nbsp;James Selkirk,&nbsp;Stanley Stasiewicz,&nbsp;Brenda Weis,&nbsp;Ben Van Houten,&nbsp;Nigel Walker,&nbsp;Raymond Tennant","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The National Center for Toxicogenomics is developing the first public toxicogenomics knowledge base that combines molecular expression data sets from transcriptomics, proteomics, metabonomics, and conventional toxicology with metabolic, toxicologcal pathway, and gene regulatory network information relevant to environmental toxicology and human disease. It is called the Chemical Effects in Biological Systems (CEBS) knowledge base and is designed to meet the information needs of \"systems toxicology,\" involving the study of perturbation by chemicals and stressors, monitoring changes in molecular expression and conventional toxicological parameters, and iteratively integrating biological response data to describe the functioning organism. Based upon functional genomics approaches used successfully in analyzing yeast gene expression data sets, relational and descriptive compendia will be assembled for toxicologically important genes, groups of genes, single nucleotide polymorphisms (SNPs), and mutant and knockout phenotypes. CEBS data sets will be fully documented in the experimental protocol and therefore searchable by compound, structure, toxicity end point, pathology and point, gene, gene group, SNP, pathway, and network as a function of dose, time, and the phenotype of the target tissue. A knowledge base is being developed by assimilating toxicological, biological, and chemical information from multiple public domain databases and by progressively refining that information about gene, protein, and metabolite expression for classes of chemicals and their biological effects in various species. By analogy to the GenBank database for genome sequences, researchers will globally query (or BLAST) CEBS using a transcriptome of a tissue of interest (or a list of outliers) to have the knowledge base return information on genes, groups of genes, metabolic and toxicological pathways, and contextually associated phenotypic information for compounds that display similar response profiles. With high-quality data content, CEBS will ultimately become a resource to support hypothesis-driven and discovery research that contributes effectively to drug safety and the improvement of risk assessments for chemicals in the environment. The CEBS development effort will span a decade or more.</p>","PeriodicalId":84641,"journal":{"name":"EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences","volume":"111 1T","pages":"15-28"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22374944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HapMap: building a database with blocks.","authors":"Charles W Schmidt","doi":"10.1289/ehp.111t-a16","DOIUrl":"https://doi.org/10.1289/ehp.111t-a16","url":null,"abstract":"","PeriodicalId":84641,"journal":{"name":"EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences","volume":"111 1T","pages":"A16"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22374937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"National Center for Toxicogenomics: an introduction.","authors":"James K Selkirk","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":84641,"journal":{"name":"EHP toxicogenomics : journal of the National Institute of Environmental Health Sciences","volume":"111 1T","pages":"A18-9"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"22374938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}