View source for Toxicogenomics

<p><strong>Toxicogenomics</strong> is a field of science that deals with the collection, interpretation, and storage of information about gene and protein activity within particular cell or tissue of an organism in response to toxic substances. Toxicogenomics combines toxicology with <font color="#810081">genomics</font> or other high throughput molecular profiling technologies such as transcriptomics, proteomics and metabolomics<sup class="reference" id="cite_ref-0"><span>[</span>1<span>]</span></sup><sup class="reference" id="cite_ref-1"><span>[</span>2<span>]</span></sup>. Toxicogenomics endeavors to elucidate molecular mechanisms evolved in the expression of toxicity, and to derive molecular expression patterns (i.e., molecular biomarkers) that predict toxicity or the genetic susceptibility to it.</p>
<p>This broad definition is supported by the United States Environmental Protection Agency stating that &quot;the term &quot;genomics&quot; encompasses a broader scope of scientific inquiry and associated technologies than when genomics was initially considered. A genome is the sum total of all an individual organism's genes. Thus, genomics is the study of all the genes of a cell, or tissue, at the DNA (genotype), mRNA (transcriptome), or protein (proteome) levels. Genomics methodologies are expected to provide valuable insights for evaluating how environmental stressors affect cellular/tissue function and how changes in gene expression may relate to adverse effects. However, the relationships between changes in gene expression and adverse effects are unclear at this time and may likely be difficult to elucidate.&quot;<sup class="reference" id="cite_ref-2"><span>[</span>3<span>]</span></sup></p>
<p>In pharmaceutical research toxicogenomics is more narrowly defined as the study of the structure and function of the genome as it responds to adverse xenobiotic exposure. It is the toxicological subdiscipline of pharmacogenomics, which is broadly defined as the study of inter-individual variations in whole-genome or candidate gene single-nucleotide polymorphism maps, haplotype markers, and alterations in gene expression that might correlate with drug responses (Lesko and Woodcock 2004, Lesko et al 2003). Though the term toxicogenomics first appeared in the literature in 1999 (Nuwaysir et al) it was already in common use within the pharmaceutical industry as its origin was driven by marketing strategies from vendor companies. The term is still not universal accepted, and others have offered alternative terms such as chemogenomics to describe essentially the same area (Fielden et al., 2005).</p>
<p>The nature and complexity of the data (in volume and variability) demands highly developed processes for of automated handling and storage. The analysis usually involves a wide array of bioinformatics and statistics.<sup class="reference" id="cite_ref-3"><span>[</span>4<span>]</span></sup>, regularly involving classification approaches<sup class="reference" id="cite_ref-4"><span>[</span>5<span>]</span></sup>.</p>
<p>In pharmaceutical Drug discovery and development toxicogenomics is used to study adverse, i.e. toxic, effects, of pharmaceutical drugs in defined model systems in order to draw conclusions on the toxic risk to patients or the environment. Both the EPA and the U.S. Food and Drug Administration currently preclude basing regulatory decision making on genomics data alone. However, they do encourage the voluntary submission of well-documented, quality genomics data. Both agencies are considering the use of submitted data on a case-by-case basis for assessment purposes (e.g., to help elucidate mechanism of action or contribute to a weight-of-evidence approach) or for populating relevant comparative databases by encouraging parallel submissions of genomics data and traditional toxicologic test results.<sup class="reference" id="cite_ref-5"><span>[</span>6<span>]</span></sup></p>

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<h2><span class="mw-headline">Public Toxicogenomics Projects</span></h2>
<ul>
    <li>Chemical Effects in Biological Systems (CEBS) - Project hosted by the National Institute of Environmental Health Sciences (NIEHS) building a knowledgebase of toxicology studies including study design, clinical pathology, and histopathology and toxicogenomics data.<sup class="reference" id="cite_ref-6"><span>[</span>7<span>]</span></sup> </li>
    <li>InnoMed PredTox assessing the value of combining results from omics technologies together with the results from more conventional toxicology methods in more informed decision making in preclinical safety evaluation.<sup class="reference" id="cite_ref-Mattes_7-0"><span>[</span>8<span>]</span></sup> </li>
    <li>Predictive Safety Testing Consortium aiming to identify and clinically qualify safety biomarkers for regulatory use as part of the FDA's Critical Path Initiative<sup class="reference" id="cite_ref-Mattes_7-1"><span>[</span>8<span>]</span></sup> </li>
    <li>ToxCast program for Predicting Hazard, Characterizing Toxicity Pathways, and Prioritizing the Toxicity Testing of Environmental Chemicals at the United States Environmental Protection Agency<sup class="reference" id="cite_ref-8"><span>[</span>9<span>]</span></sup> </li>
</ul>
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<h2><span class="mw-headline">References</span></h2>
<div class="references-small">
<ol class="references">
    <li id="cite_note-0"><strong>^</strong> The National Academies Press: Communicating Toxicogenomics Information to Nonexperts: A Workshop Summary (2005) [1] </li>
    <li id="cite_note-1"><strong>^</strong> <cite class="book" id="CITEREFed._by_Hisham_K._Hamadeh.3B_Cynthia_A._Afshari.2004" style="FONT-STYLE: normal">ed. by Hisham K. Hamadeh; Cynthia A. Afshari. (2004). Hamadeh HK, Afshari CA. ed.. <em>Toxicogenomics: Principles and Applications</em>. Hoboken, NJ: Wiley-Liss. ISBN 0-471-43417-5.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Abook&amp;rft.genre=book&amp;rft.btitle=Toxicogenomics%3A+Principles+and+Applications&amp;rft.aulast=ed.+by+Hisham+K.+Hamadeh%3B+Cynthia+A.+Afshari.&amp;rft.au=ed.+by+Hisham+K.+Hamadeh%3B+Cynthia+A.+Afshari.&amp;rft.date=2004&amp;rft.place=Hoboken%2C+NJ&amp;rft.pub=Wiley-Liss&amp;rft.isbn=0-471-43417-5&amp;rfr_id=info:sid/en.wikipedia.org:Toxicogenomics"><span style="DISPLAY: none">&nbsp;</span></span><br />
    <cite class="Journal" id="CITEREFOmenn_GS2004" style="FONT-STYLE: normal">Omenn GS (November 2004). &quot;Book Review: Toxicogenomics: Principles and Applications&quot;. <em>Environ Health Perspect.</em> <strong>112</strong> (16): A962.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Book+Review%3A+Toxicogenomics%3A+Principles+and+Applications&amp;rft.jtitle=Environ+Health+Perspect.&amp;rft.aulast=Omenn+GS&amp;rft.au=Omenn+GS&amp;rft.date=November+2004&amp;rft.volume=112&amp;rft.issue=16&amp;rft.pages=A962&amp;rfr_id=info:sid/en.wikipedia.org:Toxicogenomics"><span style="DISPLAY: none">&nbsp;</span></span> </li>
    <li id="cite_note-2"><strong>^</strong> EPA Interim Genomics Policy </li>
    <li id="cite_note-3"><strong>^</strong> <cite class="Journal" id="CITEREFMattes_WB.2C_Pettit_SD.2C_Sansone_SA.2C_Bushel_PR.2C_Waters_MD2004" style="FONT-STYLE: normal">Mattes WB, Pettit SD, Sansone SA, Bushel PR, Waters MD (March 2004). &quot;Database development in toxicogenomics: issues and efforts&quot;. <em>Environ. Health Perspect.</em> <strong>112</strong> (4): 495&ndash;505. PMID 15033600. PMC: 1241904<span class="printonly">. http://ehp.niehs.nih.gov/txg/members/2004/6697/6697.html</span>.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Database+development+in+toxicogenomics%3A+issues+and+efforts&amp;rft.jtitle=Environ.+Health+Perspect.&amp;rft.aulast=Mattes+WB%2C+Pettit+SD%2C+Sansone+SA%2C+Bushel+PR%2C+Waters+MD&amp;rft.au=Mattes+WB%2C+Pettit+SD%2C+Sansone+SA%2C+Bushel+PR%2C+Waters+MD&amp;rft.date=March+2004&amp;rft.volume=112&amp;rft.issue=4&amp;rft.pages=495%E2%80%93505&amp;rft_id=info:pmid/15033600&amp;rft_id=http%3A%2F%2Fehp.niehs.nih.gov%2Ftxg%2Fmembers%2F2004%2F6697%2F6697.html&amp;rfr_id=info:sid/en.wikipedia.org:Toxicogenomics"><span style="DISPLAY: none">&nbsp;</span></span> </li>
    <li id="cite_note-4"><strong>^</strong> <cite class="Journal" id="CITEREFEllinger-Ziegelbauer_H.2C_Gmuender_H.2C_Bandenburg_A.2C_Ahr_HJ2008" style="FONT-STYLE: normal">Ellinger-Ziegelbauer H, Gmuender H, Bandenburg A, Ahr HJ (January 2008). &quot;Prediction of a carcinogenic potential of rat hepatocarcinogens using toxicogenomics analysis of short-term in vivo studies&quot;. <em>Mutat. Res.</em> <strong>637</strong> (1-2): 23&ndash;39. doi:<span class="neverexpand">10.1016/j.mrfmmm.2007.06.010</span>. PMID 17689568.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Prediction+of+a+carcinogenic+potential+of+rat+hepatocarcinogens+using+toxicogenomics+analysis+of+short-term+in+vivo+studies&amp;rft.jtitle=Mutat.+Res.&amp;rft.aulast=Ellinger-Ziegelbauer+H%2C+Gmuender+H%2C+Bandenburg+A%2C+Ahr+HJ&amp;rft.au=Ellinger-Ziegelbauer+H%2C+Gmuender+H%2C+Bandenburg+A%2C+Ahr+HJ&amp;rft.date=January+2008&amp;rft.volume=637&amp;rft.issue=1-2&amp;rft.pages=23%E2%80%9339&amp;rft_id=info:doi/10.1016%2Fj.mrfmmm.2007.06.010&amp;rft_id=info:pmid/17689568&amp;rfr_id=info:sid/en.wikipedia.org:Toxicogenomics"><span style="DISPLAY: none">&nbsp;</span></span> </li>
    <li id="cite_note-5"><strong>^</strong> <cite class="Journal" id="CITEREFCorvi_R.2C_Ahr_HJ.2C_Albertini_S.2C_.27.27et_al.27.272006" style="FONT-STYLE: normal">Corvi R, Ahr HJ, Albertini S, <em>et al</em> (March 2006). &quot;Meeting report: Validation of toxicogenomics-based test systems: ECVAM-ICCVAM/NICEATM considerations for regulatory use&quot;. <em>Environ Health Perspect.</em> <strong>114</strong> (3): 420&ndash;9. PMID 16507466. PMC: 1392237<span class="printonly">. http://www.ehponline.org/members/2005/8247/8247.html</span>.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Meeting+report%3A+Validation+of+toxicogenomics-based+test+systems%3A+ECVAM-ICCVAM%2FNICEATM+considerations+for+regulatory+use&amp;rft.jtitle=Environ+Health+Perspect.&amp;rft.aulast=Corvi+R%2C+Ahr+HJ%2C+Albertini+S%2C+%27%27et+al%27%27&amp;rft.au=Corvi+R%2C+Ahr+HJ%2C+Albertini+S%2C+%27%27et+al%27%27&amp;rft.date=March+2006&amp;rft.volume=114&amp;rft.issue=3&amp;rft.pages=420%E2%80%939&amp;rft_id=info:pmid/16507466&amp;rft_id=http%3A%2F%2Fwww.ehponline.org%2Fmembers%2F2005%2F8247%2F8247.html&amp;rfr_id=info:sid/en.wikipedia.org:Toxicogenomics"><span style="DISPLAY: none">&nbsp;</span></span> </li>
    <li id="cite_note-6"><strong>^</strong> <cite class="Journal" id="CITEREFCollins_BC.2C_Clarke_A.2C_Kitteringham_NR.2C_Gallagher_WM.2C_Pennington_SR2007" style="FONT-STYLE: normal">Collins BC, Clarke A, Kitteringham NR, Gallagher WM, Pennington SR (October 2007). &quot;Use of proteomics for the discovery of early markers of drug toxicity&quot;. <em>Expert Opin Drug Metab Toxicol</em> <strong>3</strong> (5): 689&ndash;704. doi:<span class="neverexpand">10.1517/17425225.3.5.689</span>. PMID 17916055.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Use+of+proteomics+for+the+discovery+of+early+markers+of+drug+toxicity&amp;rft.jtitle=Expert+Opin+Drug+Metab+Toxicol&amp;rft.aulast=Collins+BC%2C+Clarke+A%2C+Kitteringham+NR%2C+Gallagher+WM%2C+Pennington+SR&amp;rft.au=Collins+BC%2C+Clarke+A%2C+Kitteringham+NR%2C+Gallagher+WM%2C+Pennington+SR&amp;rft.date=October+2007&amp;rft.volume=3&amp;rft.issue=5&amp;rft.pages=689%E2%80%93704&amp;rft_id=info:doi/10.1517%2F17425225.3.5.689&amp;rft_id=info:pmid/17916055&amp;rfr_id=info:sid/en.wikipedia.org:Toxicogenomics"><span style="DISPLAY: none">&nbsp;</span></span> </li>
    <li id="cite_note-Mattes-7">^ <sup><em><strong>a</strong></em></sup> <sup><em><strong>b</strong></em></sup> <cite class="Journal" id="CITEREFMattes_WB2008" style="FONT-STYLE: normal">Mattes WB (2008). &quot;Public consortium efforts in toxicogenomics&quot;. <em>Methods Mol Biol.</em> <strong>460</strong>: 221&ndash;38. doi:<span class="neverexpand">10.1007/978-1-60327-048-9_11</span>. PMID 18449490.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=Public+consortium+efforts+in+toxicogenomics&amp;rft.jtitle=Methods+Mol+Biol.&amp;rft.aulast=Mattes+WB&amp;rft.au=Mattes+WB&amp;rft.date=2008&amp;rft.volume=460&amp;rft.pages=221%E2%80%9338&amp;rft_id=info:doi/10.1007%2F978-1-60327-048-9_11&amp;rft_id=info:pmid/18449490&amp;rfr_id=info:sid/en.wikipedia.org:Toxicogenomics"><span style="DISPLAY: none">&nbsp;</span></span> </li>
    <li id="cite_note-8"><strong>^</strong> <cite class="Journal" id="CITEREFDix_DJ.2C_Houck_KA.2C_Martin_MT.2C_Richard_AM.2C_Setzer_RW.2C_Kavlock_RJ2007" style="FONT-STYLE: normal">Dix DJ, Houck KA, Martin MT, Richard AM, Setzer RW, Kavlock RJ (January 2007). &quot;The ToxCast program for prioritizing toxicity testing of environmental chemicals&quot;. <em>Toxicol. Sci.</em> <strong>95</strong> (1): 5&ndash;12. doi:<span class="neverexpand">10.1093/toxsci/kfl103</span>. PMID 16963515.</cite><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.atitle=The+ToxCast+program+for+prioritizing+toxicity+testing+of+environmental+chemicals&amp;rft.jtitle=Toxicol.+Sci.&amp;rft.aulast=Dix+DJ%2C+Houck+KA%2C+Martin+MT%2C+Richard+AM%2C+Setzer+RW%2C+Kavlock+RJ&amp;rft.au=Dix+DJ%2C+Houck+KA%2C+Martin+MT%2C+Richard+AM%2C+Setzer+RW%2C+Kavlock+RJ&amp;rft.date=January+2007&amp;rft.volume=95&amp;rft.issue=1&amp;rft.pages=5%E2%80%9312&amp;rft_id=info:doi/10.1093%2Ftoxsci%2Fkfl103&amp;rft_id=info:pmid/16963515&amp;rfr_id=info:sid/en.wikipedia.org:Toxicogenomics"><span style="DISPLAY: none">&nbsp;</span></span> </li>
</ol>
</div>
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<h2><span class="mw-headline">See also</span></h2>
<ul>
    <li>Comparative Toxicogenomics Database </li>
    <li><font color="#810081">Genomics</font>
    <ul>
        <li>Chemogenomics </li>
        <li>Structural genomics </li>
        <li>Pharmacogenetics </li>
        <li>Pharmacogenomics </li>
    </ul>
    </li>
    <li>Genevestigator </li>
    <li>InnoMed PredTox </li>
    <li>Toxicology </li>
</ul>
<p>&nbsp;</p>
<h2><span class="mw-headline">External links</span></h2>
<ul>
    <li><a class="external text" title="http://ctd.mdibl.org/" rel="nofollow" href="http://ctd.mdibl.org/">Comparative Toxicogenomics Database</a> - a public database that integrates toxicogenomic data for chemicals, genes, and diseases from the scientific literature. </li>
    <li><a class="external text" title="http://www.ohsu.edu/croet/research/centers/toxicogenomics/whatis.html" rel="nofollow" href="http://www.ohsu.edu/croet/research/centers/toxicogenomics/whatis.html">Center for Research on Occupational and Environmental Toxicology</a> definition by the CROET Research Centers: (Neuro)toxicogenomics and Child Health Research Center. </li>
    <li><a class="external text" title="http://www.innomed-predtox.com/" rel="nofollow" href="http://www.innomed-predtox.com/">InnoMed PredTox</a> - official project website </li>
    <li><a class="external text" title="http://www.epa.gov/ncct/toxcast/" rel="nofollow" href="http://www.epa.gov/ncct/toxcast/">ToxCast</a> - official project website </li>
</ul>
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