Utilizing toxicogenomic data to understand chemical mechanism of action in risk assessment

Toxicology and Applied Pharmacology

Volumn 271, Issue 3, 2013, Pages 299-308

  Wilson, Vickie S ^a   Keshava, Nagalakshmi ^b   Hester, Susan ^a   Segal, Deborah ^b   Chiu, Weihsueh ^b   Thompson, Chad M ^c   Euling, Susan Y ^b  

^a U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^b U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

^c ToxStrategies Inc   (United States)

Author keywords

Mechanism of action; Risk assessment; Toxicogenomics

Indexed keywords

ACETOCHLOR; ALACHLOR; BUTOCLOR; ENVIRONMENTAL CHEMICAL; FORMALDEHYDE; GLUTARALDEHYDE; KETOCONAZOLE; MYCLOBUTANIL; ORGANOARSENIC DERIVATIVE; PESTICIDE; PHENOBARBITAL; PROPICONAZOLE; TRIADIMEFON; UNCLASSIFIED DRUG;

ARTICLE; CARCINOGENESIS; CARCINOGENICITY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC SCREENING; GENOTYPE; HEALTH HAZARD; HUMAN; HYPOTHESIS; METABOLOMICS; MICROARRAY ANALYSIS; PROTEOMICS; REGULATORY MECHANISM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RISK ASSESSMENT; TOXICOGENETICS; TOXICOKINETICS; TRANSCRIPTOMICS;

MECHANISM OF ACTION; RISK ASSESSMENT; TOXICOGENOMICS;

ANIMALS; DRUG TOXICITY; HUMANS; RISK ASSESSMENT; TOXICOGENETICS;

EID: 84883741862     PISSN: 0041008X     EISSN: 10960333     Source Type: Journal    
DOI: 10.1016/j.taap.2011.01.017     Document Type: Article

References (73)

1. Allen J.W., Wolf D.C., George M.H., Hester S.D., Sun G., Thai S.F., Delker D.A., Moore T., Jones C., Nelson G., Roop B.C., Leavitt S., Winkfield E., Ward W.O., Nesnow S. Toxicity profiles in mice treated with hepatotumorigenic and non-hepatotumorigenic triazole conazole fungicides: propiconazole, triadimefon, and myclobutanil. Toxicol. Pathol. 2006, 34:853-862.
2. Ball C.A., Brazma A., Causton H., Chervitz S., Edgar R., Hingamp P., Matese J.C., Parkinson H., Quackenbush J., Ringwald M., Sansone S.A., Sherlock G., Spellman P., Stoeckert C., Tateno Y., Taylor R., White J., Winegarden N. Submission of microarray data to public repositories. PLoS Biol. 2004, 2:E317.
3. Bodin L., Beaune P.H., Loriot M.A. Determination of cytochrome P450 2D6 (CYP2D6) gene copy number by real-time quantitative PCR. J. Biomed. Biotechnol. 2005, 2005:248-253.
4. Boverhof D.R., Zacharewski T.R. Toxicogenomics in risk assessment: applications and needs. Toxicol. Sci. 2006, 89:352-360.
5. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C.A., Causton H.C., Gaasterland T., Glenisson P., Holstege F.C., Kim I.F., Markowitz V., Matese J.C., Parkinson H., Robinson A., Sarkans U., Schulze-Kremer S., Stewart J., Taylor R., Vilo J., Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 2001, 29:365-371.
6. Buckley P.G., Mantripragada K.K., Piotrowski A., Diaz de Stahl T., Dumanski J.P. Copy-number polymorphisms: mining the tip of an iceberg. Trends Genet. 2005, 21:315-317.
7. Canales R.D., Luo Y., Willey J.C., Austermiller B., Barbacioru C.C., Boysen C., Hunkapiller K., Jensen R.V., Knight C.R., Lee K.Y., Ma Y., Maqsodi B., Papallo A., Peters E.H., Poulter K., Ruppel P.L., Samaha R.R., Shi L., Yang W., Zhang L., Goodsaid F.M. Evaluation of DNA microarray results with quantitative gene expression platforms. Nat. Biotechnol. 2006, 24:1115-1122.
8. Carlson E.A., Silkworth J.B. Toxicogenomics in human health risk assessment. Toxicol. Appl. Pharmacol. 2009, 236:254-256. author reply 257-260.
9. Casciano D.A., Woodcock J. Empowering microarrays in the regulatory setting. Nat. Biotechnol. 2006, 24:1103.
10. Chan V.S., Theilade M.D. The use of toxicogenomic data in risk assessment: a regulatory perspective. Clin. Toxicol. (Phila) 2005, 43:121-126.
11. Chen M., Martin J., Fang H., Isukapalli S., Georgopoulos P.G., Welsh W.J., Tong W. ebTrack: an environmental bioinformatics system built upon ArrayTrack. BMC Proc. 2009, 3(Suppl 2):S5.
12. Chiu W.A., Euling S.Y., Scott C.S., Subramaniam R.P. Approaches to advancing quantitative human health risk assessment of environmental chemicals in the post-genomic era. Toxicol. Appl. Pharmacol. 2013, 271:309-323. (this issue).
13. Daston G.P. Gene expression, dose-response, and phenotypic anchoring: applications for toxicogenomics in risk assessment. Toxicol. Sci. 2008, 105:233-234.
14. Dix D.J., Gallagher K., Benson W.H., Groskinsky B.L., McClintock J.T., Dearfield K.L., Farland W.H. A framework for the use of genomics data at the EPA. Nat. Biotechnol. 2006, 24:1108-1111.
15. Ekins S., Nikolsky Y., Nikolskaya T. Techniques: application of systems biology to absorption, distribution, metabolism, excretion and toxicity. Trends Pharmacol. Sci. 2005, 26:202-209.
16. Euling S.Y., Thompson C.M., Benson R., Chiu W.A. An approach for integrating toxicogenomic data in risk assessment: The dibutyl phthalate case study. Toxicol. Appl. Pharmacol. 2013, 271:324-335. (this issue).
17. European Medicines Agency Scientific Guidelines for Human Medicinal Products 2009, eEuropean Medicines Agency. http://www.emea.europa.eu/htms/human/humanguidelines/multidiscipline.htm.
18. FDA Guidance for industry: Pharmacogenomic Data Submissions 2005, eFood and Drug Administration. http://www.fda.gov/downloads/RegulatoryInformation/Guidances/ucm126957.pdf.
19. FDA Guidance for Industry: Pharmacogenomic Data Submissions - Companion Guidance 2007, eFood and Drug Administration, Rockville, MD. http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/ucm079855.pdf.
20. FDA Genomic Data Submission 2009, eFood and Drug Administration. http://www.fda.gov/Drugs/ScienceResearch/ResearchAreas/Pharmacogenetics/ucm083641.htm.
21. Frueh F.W. Impact of microarray data quality on genomic data submissions to the FDA. Nat. Biotechnol. 2006, 24:1105-1107.
22. Gatti D.M., Shabalin A.A., Lam T.C., Wright F.A., Rusyn I., Nobel A.B. FastMap: fast eQTL mapping in homozygous populations. Bioinformatics 2009, 25:482-489.
23. Gatti D.M., Sypa M., Rusyn I., Wright F.A., Barry W.T. SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy. Bioinformatics 2009, 25:541-542.
24. Genter M.B., Burman D.M., Bolon B. Progression of alachlor-induced olfactory mucosal tumours. Int. J. Exp. Pathol. 2002, 83:303-308.
25. Ginsberg G., Smolenski S., Hattis D., Sonawane B. Population distribution of aldehyde dehydrogenase-2 genetic polymorphism: implications for risk assessment. Regul. Toxicol. Pharmacol. 2002, 36:297-309.
26. Ginsberg G., Neafsey P., Hattis D., Guyton K.Z., Johns D.O., Sonawane B. Genetic polymorphism in paraoxonase 1 (PON1): population distribution of PON1 activity. J. Toxicol. Environ. Health B Crit. Rev. 2009, 12:473-507.
27. Ginsberg G., Smolenski S., Hattis D., Guyton K.Z., Johns D.O., Sonawane B. Genetic polymorphism in glutathione transferases (GST): population distribution of GSTM1, T1, and P1 conjugating activity. J. Toxicol. Environ. Health B Crit. Rev. 2009, 12:389-439.
28. Ginsberg G., Smolensk i.S., Neafsey P., Hattis D., Walker K., Guyton K., Johns D., Sonawane B. The influence of genetic polymorphisms on population variability in six xenobiotic-metabolizing enzymes. J. Toxicol. Environ. Health B Crit. Rev. 2009, 12:307-333.
29. Ginsberg G., Guyton K., Johns D., Schimek J., Angle K., Sonawane B. Genetic polymorphism in metabolism and host defense enzymes: implications for human health risk assessment. Crit. Rev. Toxicol. 2010, 40:575-619.
30. Guo L., Lobenhofer E.K., Wang C., Shippy R., Harris S.C., Zhang L., Mei N., Chen T., Herman D., Goodsaid F.M., Hurban P., Phillips K.L., Xu J., Deng X., Sun Y.A., Tong W., Dragan Y.P., Shi L. Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat. Biotechnol. 2006, 24:1162-1169.
31. Hackett J.L., Lesko L.J. Microarray data - the USFDA, industry and academia. Nat. Biotechnol. 2003, 21:742-743.
32. Hamadeh H.K., Bushel P.R., Jayadev S., DiSorbo O., Bennett L., Li L., Tennant R., Stoll R., Barrett J.C., Paules R.S., Blanchard K., Afshari C.A. Prediction of compound signature using high density gene expression profiling. Toxicol. Sci. 2002, 67:232-240.
33. Hamadeh H.K., Bushel P.R., Jayadev S., Martin K., DiSorbo O., Sieber S., Bennett L., Tennant R., Stoll R., Barrett J.C., Blanchard K., Paules R.S., Afshari C.A. Gene expression analysis reveals chemical-specific profiles. Toxicol. Sci. 2002, 67:219-231.
34. Hedberg J.J., Grafstrom R.C., Vondracek M., Sarang Z., Warngard L., Hoog J.O. Micro-array chip analysis of carbonyl-metabolising enzymes in normal, immortalised and malignant human oral keratinocytes. Cell. Mol. Life Sci. 2001, 58:1719-1726.
35. Hester S.D., Benavides G.B., Yoon L., Morgan K.T., Zou F., Barry W., Wolf D.C. Formaldehyde-induced gene expression in F344 rat nasal respiratory epithelium. Toxicology 2003, 187:13-24.
36. Hester S.D., Barry W.T., Zou F., Wolf D.C. Transcriptomic analysis of F344 rat nasal epithelium suggests that the lack of carcinogenic response to glutaraldehyde is due to its greater toxicity compared to formaldehyde. Toxicol. Pathol. 2005, 33:415-424.
37. Holsapple M.P., Pitot H.C., Cohen S.M., Boobis A.R., Klaunig J.E., Pastoor T., Dellarco V.L., Dragan Y.P. Mode of action in relevance of rodent liver tumors to human cancer risk. Toxicol. Sci. 2006, 89:51-56.
38. IARC Phenobarbital and its sodium salts. IARC Monographs, Some Thyrotropic Agents 2001, 161-288. IARC Press, Lyon, France.
39. Ji H., Davis R.W. Data quality in genomics and microarrays. Nat. Biotechnol. 2006, 24:1112-1113.
40. Kedderis G.L., Elmore A.R., Crecelius E.A., Yager J.W., Goldsworthy T.L. Kinetics of arsenic methylation by freshly isolated B6C3F1 mouse hepatocytes. Chem. Biol. Interact. 2006, 161:139-145.
41. Mortensen H.M., Euling S.Y. Integrating mechanistic and polymorphism data to characterize human genetic susceptibility for environmental chemical risk assessment in the 21st century. Toxicol. Appl. Pharmacol. 2013, 271:381-390. (this issue).
42. Neafsey P., Ginsberg G., Hattis D., Johns D.O., Guyton K.Z., Sonawane B. Genetic polymorphism in CYP2E1: population distribution of CYP2E1 activity. J. Toxicol. Environ. Health B Crit. Rev. 2009, 12:362-388.
43. Neafsey P., Ginsberg G., Hattis D., Sonawane B. Genetic polymorphism in cytochrome P450 2D6 (CYP2D6): population distribution of CYP2D6 activity. J. Toxicol. Environ. Health B Crit. Rev. 2009, 12:334-361.
44. Nesnow S., Ward W., Moore T., Ren H., Hester S.D. Discrimination of tumorigenic triazole conazoles from phenobarbital by transcriptional analyses of mouse liver gene expression. Toxicol. Sci. 2009, 110:68-83.
45. NRC, 2007a. Applications of toxicogenomic technologies to predictive toxicology and risk assessment. (N. R. Council, Ed.). National Academy Press, Washington, DC.
46. NRC, 2007b. Toxicity testing in the 21st century. (N. R. Council, Ed.). National Academy Press, Washington, DC.
47. Oberemm A., Onyon L., Gundert-Remy U. How can toxicogenomics inform risk assessment?. Toxicol. Appl. Pharmacol. 2005, 207:592-598.
48. Ovacik M.A., Sen B., Euling S.Y., Gaido K.W., Ierapetritou M.G., Androulakis I.P. Pathway modeling of microarray data: a case study of pathway activity changes in the testis following in utero exposure to dibutyl phthalate (DBP). Toxicol. Appl. Pharmacol. 2010, 271:372-380. (this issue).
49. Pandey A., Mann M. Proteomics to study genes and genomes. Nature 2000, 405:837-846.
50. Patterson T.A., Lobenhofer E.K., Fulmer-Smentek S.B., Collins P.J., Chu T.M., Bao W., Fang H., Kawasaki E.S., Hager J., Tikhonova I.R., Walker S.J., Zhang L., Hurban P., de Longueville F., Fuscoe J.C., Tong W., Shi L., Wolfinger R.D. Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat. Biotechnol. 2006, 24:1140-1150.
51. Pettit S., des Etages S.A., Mylecraine L., Snyder R., Fostel J., Dunn R.T., Haymes K., Duval M., Stevens J., Afshari C., Vickers A. Current and future applications of toxicogenomics: results summary of a survey from the HESI Genomics State of Science Subcommittee. Environ. Health Perspect. 2010, 118:992-997.
52. Sen B., Wang A., Hester S.D., Robertson J.L., Wolf D.C. Gene expression profiling of responses to dimethylarsinic acid in female F344 rat urothelium. Toxicology 2005, 215:214-226.
53. Sen B., Wolf D.C., Turpaz Y., Bugrim A., Retief J., Hester S.D. Identification of interspecies concordance of mechanisms of arsenic-induced bladder cancer. Toxicol. In Vitro 2007, 21:1513-1529.
54. Shi L., Reid L.H., Jones W.D., Shippy R., Warrington J.A., Baker S.C., Collins P.J., de Longueville F., Kawasaki E.S., Lee K.Y., Luo Y., Sun Y.A., Willey J.C., Setterquist R.A., Fischer G.M., Tong W., Dragan Y.P., Dix D.J., Frueh F.W., Goodsaid F.M., Herman D., Jensen R.V., Johnson C.D., Lobenhofer E.K., Puri R.K., Schrf U., Thierry-Mieg J., Wang C., Wilson M., Wolber P.K., Zhang L., Amur S., Bao W., Barbacioru C.C., Lucas A.B., Bertholet V., Boysen C., Bromley B., Brown D., Brunner A., Canales R., Cao X.M., Cebula T.A., Chen J.J., Cheng J., Chu T.M., Chudin E., Corson J., Corton J.C., Croner L.J., Davies C., Davison T.S., Delenstarr G., Deng X., Dorris D., Eklund A.C., Fan X.H., Fang H., Fulmer-Smentek S., Fuscoe J.C., Gallagher K., Ge W., Guo L., Guo X., Hager J., Haje P.K., Han J., Han T., Harbottle H.C., Harris S.C., Hatchwell E., Hauser C.A., Hester S., Hong H., Hurban P., Jackson S.A., Ji H., Knight C.R., Kuo W.P., LeClerc J.E., Levy S., Li Q.Z., Liu C., Liu Y., Lombardi M.J., Ma Y., Magnuson S.R., Maqsodi B., McDaniel T., Mei N., Myklebost O., Ning B., Novoradovskaya N., Orr M.S., Osborn T.W., Papallo A., Patterson T.A., Perkins R.G., Peters E.H., Peterson R., et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol. 2006, 24:1151-1161.
55. Shi L., Campbell G., Jones W.D., Campagne F., Wen Z., Walker S.J., Su Z., Chu T.M., Goodsaid F.M., Pusztai L., Shaughnessy J.D., Oberthuer A., Thomas R.S., Paules R.S., Fielden M., Barlogie B., Chen W., Du P., Fischer M., Furlanello C., Gallas B.D., Ge X., Megherbi D.B., Symmans W.F., Wang M.D., Zhang J., Bitter H., Brors B., Bushel P.R., Bylesjo M., Chen M., Cheng J., Chou J., Davison T.S., Delorenzi M., Deng Y., Devanarayan V., Dix D.J., Dopazo J., Dorff K.C., Elloumi F., Fan J., Fan S., Fan X., Fang H., Gonzaludo N., Hess K.R., Hong H., Huan J., Irizarry R.A., Judson R., Juraeva D., Lababidi S., Lambert C.G., Li L., Li Y., Li Z., Lin S.M., Liu G., Lobenhofer E.K., Luo J., Luo W., McCall M.N., Nikolsky Y., Pennello G.A., Perkins R.G., Philip R., Popovici V., Price N.D., Qian F., Scherer A., Shi T., Shi W., Sung J., Thierry-Mieg D., Thierry-Mieg J., Thodima V., Trygg J., Vishnuvajjala L., Wang S.J., Wu J., Wu Y., Xie Q., Yousef W.A., Zhang L., Zhang X., Zhong S., Zhou Y., Zhu S., Arasappan D., Bao W., Lucas A.B., Berthold F., Brennan R.J., Buness A., Catalano J.G., Chang C., Chen R., Cheng Y., Cui J., et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat. Biotechnol. 2010, 28:827-838.
56. Shippy R., Fulmer-Smentek S., Jensen R.V., Jones W.D., Wolber P.K., Johnson C.D., Pine P.S., Boysen C., Guo X., Chudin E., Sun Y.A., Willey J.C., Thierry-Mieg J., Thierry-Mieg D., Setterquist R.A., Wilson M., Lucas A.B., Novoradovskaya N., Papallo A., Turpaz Y., Baker S.C., Warrington J.A., Shi L., Herman D. Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nat. Biotechnol. 2006, 24:1123-1131.
57. Staab C.A., Ceder R., Roberg K., Grafstrom R.C., Hoog J.O. Serum-responsive expression of carbonyl-metabolizing enzymes in normal and transformed human buccal keratinocytes. Cell. Mol. Life Sci. 2008, 65:3653-3663.
58. Staab J.M., O'Connell T.M., Gomez S.M. Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS). BMC Bioinform. 2010, 11:123.
59. Thybaud V., Le Fevre A.C., Boitier E. Application of toxicogenomics to genetic toxicology risk assessment. Environ. Mol. Mutagen. 2007, 48:369-379.
60. Tong W., Lucas A.B., Shippy R., Fan X., Fang H., Hong H., Orr M.S., Chu T.M., Guo X., Collins P.J., Sun Y.A., Wang S.J., Bao W., Wolfinger R.D., Shchegrova S., Guo L., Warrington J.A., Shi L. Evaluation of external RNA controls for the assessment of microarray performance. Nat. Biotechnol. 2006, 24:1132-1139.
61. U.S.EPA Interim Policy on Genomics. Prepared by the Science Policy Council 2002, eEnvironmental Protection Agency. http://www.epa.gov/osa/spc/genomics.htm.
62. U.S.EPA Interim guidance for microarray-based assays: data submission, quality, analysis, management and training considerations. External review draft. 2007, Tasks Force Workgroup, Science Policy Council, Environmental Protection Agency, Washington, DC. http://www.epa.gov/osa/spc/genomicsguidance.htm.
63. U.S.EPA The U.S. Environmental Protection Agency's Strategic Plan for Evaluating the Toxicity of Chemicals 2009, eEnvironmental Protection Agency, Washington, DC. http://www.epa.gov/spc/toxicitytesting/index.htm.
64. U.S.EPA Acetochlor Report of the Cancer Assessment Review Committee (CARC). Fourth Evaluation 2004, Office of Pesticide Programs, Environmental Protection Agency, Washington, DC.
65. U.S.EPA Potential Implications of Genomics for Regulatory and Risk Assessment Applications at EPA. eGenomics Tasks Force Workgroup, Science Policy Council 2004, US EPA. http://www.epa.gov/osa/genomics-external-review-draft.pdf.
66. U.S.EPA Revised Reregistration Eligibility Decision Document (RED) for MSMA; DSMA, and CAMA and Cacodylic Acid Washington, DC. http://www.epa.gov/oppsrrd1/REDs/organic_arsenicals_red.pdf.
67. U.S.EPA Proceedings of the Computational Toxicology Centers STAR Progress Review Workshop http://www.epa.gov/ncerqa/publications/workshop/10_01_09/comptoxproceedings100109.pdf.
68. Van Aggelen G., Ankley G.T., Baldwin W.S., Bearden D.W., Benson W.H., Chipman J.K., Collette T.W., Craft J.A., Denslow N.D., Embry M.R., Falciani F., George S.G., Helbing C.C., Hoekstra P.F., Iguchi T., Kagami Y., Katsiadaki I., Kille P., Liu L., Lord P.G., McIntyre T., O'Neill A., Osachoff H., Perkins E.J., Santos E.M., Skirrow R.C., Snape J.R., Tyler C.R., Versteeg D., Viant M.R., Volz D.C., Williams T.D., Yu L. Integrating omic technologies into aquatic ecological risk assessment and environmental monitoring: hurdles, achievements, and future outlook. Environ. Health Perspect. 2010, 118:1-5.
69. Vondracek M., Weaver D.A., Sarang Z., Hedberg J.J., Willey J.C., Warngard L., Grafstrom R.C. Transcript profiling of enzymes involved in detoxification of xenobiotics and reactive oxygen in human normal and simian virus 40 T antigen-immortalized oral keratinocytes. Int. J. Cancer 2002, 99:776-782.
70. Walker K., Ginsberg G., Hattis D., Johns D.O., Guyton K.Z., Sonawane B. Genetic polymorphism in N-Acetyltransferase (NAT): population distribution of NAT1 and NAT2 activity. J. Toxicol. Environ. Health B Crit. Rev. 2009, 12:440-472.
71. Ward W.O., Delker D.A., Hester S.D., Thai S.F., Wolf D.C., Allen J.W., Nesnow S. Transcriptional profiles in liver from mice treated with hepatotumorigenic and nonhepatotumorigenic triazole conazole fungicides: propiconazole, triadimefon, and myclobutanil. Toxicol. Pathol. 2006, 34:863-878.
72. Waters M.D., Fostel J.M. Toxicogenomics and systems toxicology: aims and prospects. Nat. Rev. Genet. 2004, 5:936-948.
73. Wolf D.C., Allen J.W., George M.H., Hester S.D., Sun G., Moore T., Thai S.F., Delker D., Winkfield E., Leavitt S., Nelson G., Roop B.C., Jones C., Thibodeaux J., Nesnow S. Toxicity profiles in rats treated with tumorigenic and nontumorigenic triazole conazole fungicides: propiconazole, triadimefon, and myclobutanil. Toxicol. Pathol. 2006, 34:895-902.