Intersection of toxicogenomics and high throughput screening in the Tox21 program: An NIEHS perspective

International Journal of Biotechnology

Volumn 14, Issue 1, 2015, Pages 7-27

  Merrick, B Alex ^a   Paules, Richard S ^a   Tice, Raymond R ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

High throughput screening; In vitro; NextGen sequencing; Pathways; Robotics; Tox21; Toxicogenomics; Toxicology

Indexed keywords

BIOHAZARDS; CHEMICALS; ROBOTICS;

HIGH THROUGHPUT SCREENING; IN-VITRO; NEXT-GEN SEQUENCING; PATHWAYS; TOX21; TOXICOGENOMICS; TOXICOLOGY;

CHEMICAL HAZARDS;

ANIMAL; BIOASSAY; GENE EXPRESSION; GENETIC ANALYSIS; GENOTOXICITY; HAZARD ASSESSMENT; NUMERICAL MODEL; PUBLIC HEALTH; ROBOTICS; TECHNOLOGICAL DEVELOPMENT; TOXICOLOGY;

EXPOSURE; GENOME; GOVERNMENT; HAZARD ASSESSMENT; HIGH THROUGHPUT SCREENING; HUMAN; IN VITRO STUDY; MODEL; TOXICOLOGY;

UNITED STATES;

ANIMALIA;

EID: 84959337867     PISSN: 09636048     EISSN: 17415020     Source Type: Journal    
DOI: 10.1504/IJBT.2015.074797     Document Type: Article

References (41)

1. Allard, P., Kleinstreuer, N.C., Knudsen, T.B. and Colaiacovo, M.P. (2013) 'A C. elegans screening platform for the rapid assessment of chemical disruption of germline function', Environmental Health Perspectives, Vol. 121, No. 6, pp. 717-724.
2. Attene-Ramos, M.S., Miller, N., Huang, R., Michael, S., Itkin, M., Kavlock, R.J., Austin, C.P., Shinn, P., Simeonov, A., Tice, R.R. and Xia, M. (2013) 'The Tox21 robotic platform for the assessment of environmental chemicals-from vision to reality', Drug Discovery Today, Vol. 18, Nos. 15-16, pp. 716-723.
3. Auerbach, S.S., Phadke, D.P., Mav, D., Holmgren, S., Gao, Y., Xie, B., Shin, J.H., Shah, R.R., Merrick, B.A. and Tice, R.R. (2014) 'RNA-Seq-based toxicogenomic assessment of fresh frozen and formalin-fixed tissues yields similar mechanistic insights', Journal of Applied Toxicology, in press, doi: 10.1002/jat.3068.
4. Boyd, W.A., McBride, S.J., Rice, J.R., Snyder, D.W. and Freedman, J.H. (2010) 'A high-throughput method for assessing chemical toxicity using a Caenorhabditis elegans reproduction assay', Toxicol. Appl. Pharmacol., Vol. 245, No. 2, pp. 153-159.
5. Ding, L., Wendl, M.C., Koboldt, D.C. and Mardis, E.R. (2010) 'Analysis of next-generation genomic data in cancer: accomplishments and challenges', Human Molecular Genetics, Vol. 19, No. R2, pp. R188-196.
6. Dix, D.J., Houck, K.A., Judson, R.S., Kleinstreuer, N.C., Knudsen, T.B., Martin, M.T., Reif, D.M., Richard, A.M., Shah, I., Sipes, N.S. and Kavlock, R.J. (2012) 'Incorporating biological, chemical, and toxicological knowledge into predictive models of toxicity', Toxicological sciences : an official journal of the Society of Toxicology, Vol. 130, No. 2, pp. 440-441; author reply pp. 442-443.
7. Elmore, S.A., Ryan, A.M., Wood, C.E., Crabbs, T.A. and Sills, R.C. (2014) 'FutureTox II: contemporary concepts in toxicology: 'pathways to prediction: in vitro and in silico models for predictive toxicology'', Toxicol. Pathol., Vol. 42, No. 5, pp. 940-942.
8. Forreryd, A., Johansson, H., Albrekt, A.S. and Lindstedt, M. (2014) 'Evaluation of high throughput gene expression platforms using a genomic biomarker signature for prediction of skin sensitization', BMC Genomics, Vol. 15, p.379.
9. Huang, R., Sakamuru, S., Martin, M.T., Reif, D.M., Judson, R.S., Houck, K.A., Casey, W., Hsieh, J.H., Shockley, K.R., Ceger, P., Fostel, J., Witt, K.L., Tong, W., Rotroff, D.M., Zhao, T., Shinn, P., Simeonov, A., Dix, D.J., Austin, C.P., Kavlock, R.J., Tice, R.R. and Xia, M. (2014) 'Profiling of the Tox21 10K compound library for agonists and antagonists of the estrogen receptor alpha signaling pathway', Scientific Reports, Vol. 4, p.5664.
10. Huang, R., Xia, M., Cho, M.H., Sakamuru, S., Shinn, P., Houck, K.A., Dix, D.J., Judson, R.S., Witt, K.L., Kavlock, R.J., Tice, R.R. and Austin, C.P. (2011) 'Chemical genomics profiling of environmental chemical modulation of human nuclear receptors', Environmental Health Perspectives, Vol. 119, No. 8, pp. 1142-1148.
11. Khan, S.R., Baghdasarian, A., Fahlman, R.P., Michail, K. and Siraki, A.G. (2014) 'Current status and future prospects of toxicogenomics in drug discovery', Drug Discovery Today, Vol. 19, No. 5, pp. 562-578.
12. Klein, S., Mueller, D., Schevchenko, V. and Noor, F. (2014) 'Long-term maintenance of HepaRG cells in serum-free conditions and application in a repeated dose study', Journal of Applied Toxicology: JAT, Vol. 34, No. 10, pp. 1078-1086.
13. Kleinstreuer, N.C., Dix, D.J., Houck, K.A., Kavlock, R.J., Knudsen, T.B., Martin, M.T., Paul, K.B., Reif, D.M., Crofton, K.M., Hamilton, K., Hunter, R., Shah, I. and Judson, R.S. (2013) 'In vitro perturbations of targets in cancer hallmark processes predict rodent chemical carcinogenesis', Toxicological Sciences : An Official Journal of the Society of Toxicology, Vol. 131, No. 1, pp. 40-55.
14. Kleinstreuer, N.C., Yang, J., Berg, E.L., Knudsen, T.B., Richard, A.M., Martin, M.T., Reif, D.M., Judson, R.S., Polokoff, M., Dix, D.J., Kavlock, R.J. and Houck, K.A. (2014) 'Phenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanisms', Nat. Biotechnol., Vol. 32, No. 6, pp. 583-591.
15. Koboldt, D.C., Steinberg, K.M., Larson, D.E., Wilson, R.K. and Mardis, E.R. (2013) 'The next-generation sequencing revolution and its impact on genomics', Cell, Vol. 155, No. 1, pp. 27-38.
16. Lantz-McPeak, S., Guo, X., Cuevas, E., Dumas, M., Newport, G.D., Ali, S.F., Paule, M.G. and Kanungo, J. (2015) 'Developmental toxicity assay using high content screening of zebrafish embryos', Journal of Applied Toxicology: JAT, Vol. 35, No. 3, pp. 261-272.
17. Li, H., Qiu, J. and Fu, X.D. (2012) 'RASL-seq for massively parallel and quantitative analysis of gene expression', Ausubel, F.M. et al. (Eds.): Current Protocols in Molecular Biology, Chapter 4, Unit 4, pp. pp. 11-19.
18. Li, L., Chen, E., Yang, C., Zhu, J., Jayaraman, P., De Pons, J., Kaczorowski, C.C., Jacob, H.J., Greene, A.S., Hodges, M.R., Cowley Jr., A.W., Liang, M., Xu, H., Liu, P. and Lu, Y. (2015) 'Improved rat genome gene prediction by integration of ESTs with RNA-Seq information', Bioinformatics, Vol. 31, No. 1, pp. 25-32.
19. Merrick, B.A., Phadke, D.P., Auerbach, S.S., Mav, D., Stiegelmeyer, S.M., Shah, R.R. and Tice, R.R. (2013) 'RNA-Seq profiling reveals novel hepatic gene expression pattern in aflatoxin B1 treated rats', PloS One, Vol. 8, No. 4, p.e61768.
20. Mueller, D., Kramer, L., Hoffmann, E., Klein, S. and Noor, F. (2014) '3D organotypic HepaRG cultures as in vitro model for acute and repeated dose toxicity studies', Toxicology In Vitro: An International Journal published in Association with BIBRA, Vol. 28, No. 1, pp. 104-112.
21. Nettles, J.H., Jenkins, J.L., Bender, A., Deng, Z., Davies, J.W. and Glick, M. (2006) 'Bridging chemical and biological space: 'target fishing' using 2D and 3D molecular descriptors', J. Med. Chem., Vol. 49, No. 23, pp. 6802-6810.
22. Ning, B., Su, Z., Mei, N., Hong, H., Deng, H., Shi, L., Fuscoe, J.C. and Tolleson, W.H. (2014) 'Toxicogenomics and cancer susceptibility: advances with next-generation sequencing', Journal of Environmental Science and Health. Part C, Environmental Carcinogenesis & Ecotoxicology Reviews, Vol. 32, No. 2, pp. 121-158.
23. NRC (2007) Toxicity Testing in the 21st Century: A Vision and a Strategy [online] http://www.nap.edu/openbook.php?record-id=11970 (accessed 3 October 2014).
24. NTP (2004) NTP Vision and Roadmap [online] http://ntp.niehs.nih.gov/ntp/about-ntp/ntpvision/ntproadmap-508.pdf (accessed 25 May 2015).
25. Nuwaysir, E.F., Bittner, M., Trent, J., Barrett, J.C. and Afshari, C.A. (1999) 'Microarrays and toxicology: the advent of toxicogenomics', Mol. Carcinog., Vol. 24, No. 3, pp. 153-159.
26. Pack, M., Solnica-Krezel, L., Malicki, J., Neuhauss, S.C., Schier, A.F., Stemple, D.L., Driever, W. and Fishman, M.C. (1996) 'Mutations affecting development of zebrafish digestive organs', Development, Vol. 123, No. 1, pp. 321-328.
27. Persson, M., Loye, A.F., Jacquet, M., Mow, N.S., Thougaard, A.V., Mow, T. and Hornberg, J.J. (2014) 'High-content analysis/screening for predictive toxicology: application to hepatotoxicity and genotoxicity', Basic Clin. Pharmacol. Toxicol., Vol. 115, No. 1, pp. 18-23.
28. Petit-Zeman, S. (2004) Exploring Biological Space [online] http://www.nature.com/horizon/chemicalspace/background/explore.html (accessed 25 May 2015).
29. Piersma, A.H., Ezendam, J., Luijten, M., Muller, J.J., Rorije, E., van der Ven, L.T. and van Benthem, J. (2014) 'A critical appraisal of the process of regulatory implementation of novel in vivo and in vitro methods for chemical hazard and risk assessment', Crit. Rev., Toxicol., Vol. 44, No. 10, pp. 876-894.
30. Shukla, S.J., Huang, R., Austin, C.P. and Xia, M. (2010) 'The future of toxicity testing: a focus on in vitro methods using a quantitative high-throughput screening platform', Drug Discovery Today, Vol. 15, Nos. 23-24, pp. 997-1007.
31. Sipes, N.S., Martin, M.T., Kothiya, P., Reif, D.M., Judson, R.S., Richard, A.M., Houck, K.A., Dix, D.J., Kavlock, R.J. and Knudsen, T.B. (2013) 'Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays', Chemical Research in Toxicology, Vol. 26, No. 6, pp. 878-895.
32. Sipes, N.S., Martin, M.T., Reif, D.M., Kleinstreuer, N.C., Judson, R.S., Singh, A.V., Chandler, K.J., Dix, D.J., Kavlock, R.J. and Knudsen, T.B. (2011) 'Predictive models of prenatal developmental toxicity from ToxCast high-throughput screening data', Toxicological Sciences: An Official Journal of the Society of Toxicology, Vol. 124, No. 1, pp. 109-127.
33. Tatum-Gibbs, K.R., McKee, J.M., Higuchi, M. and Bushnell, P.J. (2015) 'Effects of toluene, acrolein and vinyl chloride on motor activity of Drosophila melanogaster', Neurotoxicol. Teratol., January-February, Vol. 47, pp. 114-124.
34. Thomas, C.J., Auld, D.S., Huang, R., Huang, W., Jadhav, A., Johnson, R.L., Leister, W., Maloney, D.J., Marugan, J.J., Michael, S., Simeonov, A., Southall, N., Xia, M., Zheng, W., Inglese, J. and Austin, C.P. (2009) 'The pilot phase of the NIH chemical genomics center', Current Topics in Medicinal Chemistry, Vol. 9, No. 13, pp. 1181-1193.
35. Tice, R.R., Austin, C.P., Kavlock, R.J. and Bucher, J.R. (2013) 'Improving the human hazard characterization of chemicals: a Tox21 update', Environmental Health Perspectives, Vol. 121, No. 7, pp. 756-765.
36. Tolosa, L., Gomez-Lechon, M.J. and Donato, M.T. (2015) 'High-content screening technology for studying drug-induced hepatotoxicity in cell models', Arch. Toxicol., in press, doi: 10.1007/s00204-015-1503-z.
37. Truong, L., Reif, D.M., St Mary, L., Geier, M.C., Truong, H.D. and Tanguay, R.L. (2014) 'Multidimensional in vivo hazard assessment using zebrafish', Toxicological Sciences: An Official Journal of the Society of Toxicology, Vol. 137, No. 1, pp. 212-233.
38. Wang, C., Gong, B., Bushel, P.R., Thierry-Mieg, J., Thierry-Mieg, D., Xu, J., Fang, H., Hong, H., Shen, J., Su, Z., Meehan, J., Li, X., Yang, L., Li, H., Labaj, P.P., Kreil, D.P., Megherbi, D., Gaj, S., Caiment, F., van Delft, J., Kleinjans, J., Scherer, A., Devanarayan, V., Wang, J., Yang, Y., Qian, H.R., Lancashire, L.J., Bessarabova, M., Nikolsky, Y., Furlanello, C., Chierici, M., Albanese, D., Jurman, G., Riccadonna, S., Filosi, M., Visintainer, R., Zhang, K.K., Li, J., Hsieh, J.H., Svoboda, D.L., Fuscoe, J.C., Deng, Y., Shi, L., Paules, R.S., Auerbach, S.S. and Tong, W. (2014) 'The concordance between RNA-Seq and microarray data depends on chemical treatment and transcript abundance', Nat. Biotechnol., Vol. 32, No. 9, pp. 926-932.
39. Yu, Y., Fuscoe, J.C., Zhao, C., Guo, C., Jia, M., Qing, T., Bannon, D.I., Lancashire, L., Bao, W., Du, T., Luo, H., Su, Z., Jones, W.D., Moland, C.L., Branham, W.S., Qian, F., Ning, B., Li, Y., Hong, H., Guo, L., Mei, N., Shi, T., Wang, K.Y., Wolfinger, R.D., Nikolsky, Y., Walker, S.J., Duerksen-Hughes, P., Mason, C.E., Tong, W., Thierry-Mieg, J., Thierry-Mieg, D., Shi, L. and Wang, C. (2014) 'A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages', Nat. Commun., Vol. 5, p.3230, doi: 10.1038/ncomms4230.
40. Zeiger, E. and Margolin, B.H. (2000) 'The proportions of mutagens among chemicals in commerce', Regulatory Toxicology and Pharmacology: RTP, Vol. 32, No. 2, pp. 219-225.
41. Zhang, L., McHale, C.M., Greene, N., Snyder, R.D., Rich, I.N., Aardema, M.J., Roy, S., Pfuhler, S. and Venkatactahalam, S. (2014) 'Emerging approaches in predictive toxicology', Environ. Mol. Mutagen., Vol. 55, No. 9, pp. 679-688.