The advent of system toxicology: aims and aspect of toxicogenomics

Authors

  • S. M. Neaz Mahmud Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
  • Shahin Mahmud Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
  • Tamanna Tazrin Tandra Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
  • Antora Kar Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
  • Elia Jahan Shathy Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
  • Nasreen Jahan Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh

DOI:

https://doi.org/10.18203/2319-2003.ijbcp20162422

Keywords:

Toxicogenomics, System toxicology, Proteomics, Genomics, Metabolomics

Abstract

Last fifty years a significant advancement has been established in biological science. It happened due to the discovery of gene, genome and genetic code, function of genes and mutation of genes. Through this, the scientists have discovered that genetic code is the building block and fundamental of all molecular activity in biological system. According to this, several molecular techniques have been established to prove molecular events, effects of chemical exposure within individuals and environment. For this evaluation, the necessary of toxicogenomics is crucial, that deals with the effects of chemical in changing the genetic pattern along with mutation into gene. Toxicogenomics also deals with transcription of proteins and metabolite profiling to investigate the interaction of genes and environment stress in disease. Toxicogenomics also described the altered expression of genes caused by mutation and chemical exposure that cause several disease and show toxicant functions in cell. The main objective of toxicogenomics is to remove this exposure and provide remedy of these toxical diseases. The use, application, correlation, combination and collaboration of different significant, major, modern biological fields like proteomics, transcriptomics, bioinformatics, microarray and several other molecular process is carried out by toxicogenomics that gradually evolving in systems toxicology. This review recovered the evolution and significant application of the different fields of toxicogenomics.

References

Nuwaysir EF, Bittner M, Trent J, Barrett JC, Afshari CA. Microarrays and toxicology: The advent of toxicogenomics. Mol Carcinog. 1999;24:153-9.

Hayes KR, Bradfield CA. Advances in toxicogenomics. Chem Res Toxicol. 2005;18:403-14.

Hamadeh HK, Todd M, Healy L, Meyer JT, Kwok AM, Higgins M, et al. Application of genomics for identification of systemic toxicity triggers associated with VEGF-R inhibitors. Chem. Res. Toxicol. 2010;23:1025-33.

Cunningham1 ML. Toxicological highlight putting the fun into functional toxicogenomics. Toxicological Sciences. 2006;92(2):347-8.

Hamadeh HK, Amin RP, Paules RS, Afshari CA. An overview of toxicogenomics. Curr Issues Mol Biol 2002;4:45-56.

DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, et al. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet. 1996;14:457-60.

Duggan DJ, Bittner ML, Chen Y, Meltzer PS, Trent JM. Expression profiling using cDNA microarrays. Nat Genet. 1999;21:10-4.

Huang Q, Dunn RT, Jayadev S, DiSorbo O, Pack FD, Farr SB, et al. Assessment of cisplatin-induced nephrotoxicity by microarray technology. Toxicol. Sci. 2001;63:196-207.

Lueking A, Horn M, Eickhoff H, Bussow K, Lehrach H, Walter G. Protein microarrays for gene expression and antibody screening. Anal Biochem. 1999;270:103-11.

Page MJ, Amess B, Rohlff C, Stubberfield C, Parekh R. Proteomics: a major new technology for the drug discovery process. Drug Discov Today. 1999;4:55-62.

Rubin RB, Merchant M. A rapid protein profiling system that speeds study of cancer and other diseases. Am Clin Lab. 2000;19:28-9.

Steiner S, Anderson NL. Pharmaceutical proteomics. Ann NY Acad Sci. 2000;919:48-51.

Weinberger SR, Morris TS, Pawlak M. Recent trends in protein biochip technology. Pharmacogenomics. 2000;1:395-416.

Richard A, Yang C, Judson R. Toxicity data informatics: supporting a new paradigm for toxicity prediction. Tox Mech Meth. 2008;18:103-18.

Martin MT, Mendez E, Corum DG, Judson RS, Kavlock RJ, Rotroff DM, et al. Profiling the reproductive toxicity of chemicals from multigeneration studies in the Toxicity Reference Database (ToxRefDB). Toxicol Sci. 2009;110:181-90.

Afshari CA, Nuwaysir EF, Barrett JC. Application of complementary DNA microarray technology to carcinogen identification, toxicology, and drug safety evaluation. Cancer Res. 1999;59:4759-60.

Farr SRND. Concise review: gene expression applied to toxicology. Toxicol Sci. 1999;50:1-9.

Henry CM. DNA microarrays in toxicology. Anal Chem. 1999;71:462A-464A.

Rockett JC, Dix DJ. Application of DNA arrays to toxicology. Environmental Health Perspectives. 1999;107:681-5.

Hamadeh H, Afshari CA. Gene chips and functional genomics. American Scientist. 2000;88:508-15.

Pennie WD, Tugwood JD, Oliver GJ, Kimber I. The principles and practice of toxigenomics: applications and opportunities. Toxicol Sci. 2000;54:277-83.

Rockett JC, Dix DJ. DNA arrays: technology, options and toxicological applications. Xenobiotica. 2000;30:155-77.

Hooker TM. The Brave New World of Toxicogenomics. Environmental Compliance Litigation; 2001:16-5

Iannaccone PM. Toxicogenomics: the call of the wild chip. Environ Health Perspectives. 2001;109:A8-A11.

Olden KG. Genomics: implications for toxicology. Mutation Res. 2001;473:3-10.

Smith LL. Key challenges for toxicologists in the 21st century. Trends Pharmacol Sciences. 2001;22:281-5.

Tennant RW. The National center for toxicogenomics: using new technologies to inform mechanistic toxicology. Environ. Health Perspect. 2002;110:A8-A10.

Hamadeh HK, Bushel P, Paules RS, Afshari CA. Discovery in toxicology: Mediation by gene expression array technology. J Biochem Mol Toxicol. 2001;15:231-42.

Hamadeh HK, Nuwaysir EF, Paules RS, Barrett JC, Afshari CA. cDNA microarray technology: Merging toxicology and genomics. Comments Toxicol; 2002. Available at http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.113.9327&rep=rep1&type=pdf.

Waters MD. Systems toxicology and the chemical effects in biological systems knowledge base. Environ Health Perspect. 2003;111:811-24.

Alwine JC, Kemp DJ, Stark GR. Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc Natl Acad Sci. U.S.A. 1977;74:5350-4.

Miles MF, Hung P, Jungmann RA. Cyclic AMP regulation of lactate dehydrogenase. Quantitation of lactate dehydrogenase M-subunit messenger RNA in isoproterenol-and N6, O2’-dibutyryl cyclic AMPstimulated rat C6 glioma cells by hybridization analysis using a cloned cDNA probe. J Biol Chem. 1981;256:12545-52.

Huang RP. Detection of multiple proteins in an antibodybased protein microarray system. J Immunol Methods. 2001;255:1-13.

Chee M, Yang R, Hubbell E, Berno A, Huang XC, Stern D, et al. Accessing genetic information with high-density DNA arrays. Science. 1996;274:610-4.

Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, et al. Functional discovery via a compendium of expression profiles. Cell. 2000;102:109-26.

Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995;270:467-70.

Brown PO, Botstein D. Exploring the new world of the genome with DNA microarrays. Nat Genet. 1999;21(Suppl 1):33-7.

National Research Council. Committee on applications of toxicogenomics technologies to predictive toxicology, ‘‘applications of toxicogenomic technologies to predictive toxicology and risk assessment. National Academies Press, Washington DC; 2007.

Afshari CA, Hamadeh HK, Bushel† PR. The evolution of bioinformatics in toxicology:advancing toxicogenomics. Toxicological Sciences. 2011;120(S1):S225-S237.

Fostel WJM. Toxicogenomics and systems toxicology: aims and prospects, Nature Reviews; 2004:5.

Hamadeh HK. Methapyrilene toxicity: anchorage of pathologic observations to gene expression alterations. Toxicol Pathol. 2002;30:470-82.

Zweiger G. Knowledge discovery in gene-expressionmicroarray data: mining the information output of the genome. Trends Biotechnol. 1999;17:429-36.

Kaput J, Rodriguez RL. Nutritional genomics: the next frontier in the postgenomic era. Physiol -Genomics. 2004;16:166-77.

Mattes WB, Pettit SD, Sansone SA, Bushel PR, Waters MD. Database development in toxicogenomics: issues and efforts. Environ Health Perspect. 2004;112:495-505.

Xiao HS, Huang QH, Zhang FX, Bao L, Lu YJ, Guo C, et al. Identification of gene expression profile of dorsal root ganglion in the rat peripheral axotomy model of neuropathic pain. Proc Natl Acad Sci USA. 2002;99(12):8360-5.

Stoeckert CJ, Parkinson H. The MGED ontology: a framework for describing functional genomics experiments. Comp Funct Genom. 2003;4:127-32.

Tennant RW. The national center for toxicogenomics: using new technologies to inform mechanistic toxicology. Environ Health Perspectives. 2002;110(1):A8-10.

Morgan KT, Pino M, Crosby LM, Wang M, Elston TC, Jayyosi Z, et al. Complementary roles for toxicologic pathology and mathematics in toxicogenomics, with special reference to data interpretation and oscillatory dynamics. Toxicol. Pathol. 2004;32(Suppl 1):13-25.

Tsai YJ, Lin CT, Huang CT, Wang HY, Tien LT, Chen SH, et al. Neuropeptide Y modulates c-Fos protein expression in the cuneate nucleus and contributes to mechanical hypersensitivity following rat median nerve injury. Journal of neurotrauma. 2009;26(9):1609-21.

Fostel JM. Future of toxicogenomics and safety signatures: balancing public access to data with proprietary drug discovery. Pharmacogenomics. 2007;8(5):425-30.

Mattingly CJ, Rosenstein MC, Colby GT, Forrest J N, Boyer JL. The comparative toxicogenomics database (CTD): a resource for comparative toxicological studies. J Exp Zool A Comp Exp Biol. 2006;305:689-92.

Ellinger-Ziegelbauer H, Aubrecht J, Kleinjans JC, Ahr HJ. Application of toxicogenomics to study mechanisms of genotoxicity and carcinogenicity. Toxicol Lett. 2009;186:36-44.

Sawada H, Takami K, Asahi S. A toxicogenomic approach to drug-induced phospholipidosis: analysis of its induction mechanism and establishment of a novel in vitro screening system. Toxicol Sci. 2001;83:282-92.

Cai D, Deng K, Mellado W, Lee J, Ratan RR, Filbin MT. Arginase I and polyamines act downstream from cyclic AMP in overcoming inhibition of axonal growth MAG and myelin in vitro. Neuron. 2002;35(4):711-9.

Judson RS, Richard AM, Dix DJ, Houck K, Martin MT, Kavlock RJ, et al. The toxicity data landscape for environmental chemicals. Environ Health Perspect. 2009;117:685-95.

Kavlock RJ, Austin CP, Tice RR. Toxicity testing in the 21st century: implications for human health risk assessment. Risk Anal. 2009;29:485-7.

Ruepp SU, Tonge RP, Shaw J, Wallis N, Pognan F. Genomics and proteomics analysis of acetaminophen toxicity in mouse liver. Toxicol Sci. 2002;65:135-50.

Hogstrand C, Balesaria S, Glover CN. Application of genomics and proteomics for study of the integrated response to zinc exposure in a non-model fish species, the rainbow trout. Comp Biochem Physiol B. 2002;133:523-35.

Maine EM. Studying gene function in caenorhabditis elegans using RNA-mediated interference. Brief Funct. Genomic Proteomic. 2008;7:184-94.

Juan HF. Biomic study of human meyloid leukemia cells differentiation to macrophages using DNA array, proteomic, and bioinformatic analytical methods. Electrophoresis. 2002;23:2490-504.

Thomas RS, Pluta L, Yang L, Halsey TA. Application of genomic biomarkers to predict increased lung tumor incidence in 2-year rodent cancer bioassays. Toxicol Sci. 2007;97:55-64.

Hayes KR, Vollrath AL, Zastrow GM, McMillan BJ, Craven M, Jovanovich S, Rank DR, et al. EDGE: a centralized resource for the comparison, analysis, and distribution of toxicogenomic information. Mol. Pharmacol. 2005;67:1360-8.

Lindon JC. Contemporary issues in toxicology the role of metabonomics in toxicology and its evaluation by the COMET project. Toxicol Appl Pharmacol. 2003;187:137-46.

Amin RP. Genomic interrogation of mechanism(s) underlying cellular responses to toxicants. Toxicology. 2002;181-2:555-63.

Weinshilboum RM, Wang L. Pharmacogenetics and pharmacogenomics: development, science, and translation. Annu Rev Genomics Hum Genet. 2006;7:223-45.

Amin RP, Vickers AE, Sistare F, Thompson KL, Roman RJ, Lawton M, et al. Identification of putative gene-based markers of renal toxicity. Environ Health Perspect. 2004;112:465-79.

Kita Y. Implications of circadian gene expression in kidney, liver and the effects of fasting on pharmacogenomic studies. Pharmacogenetics. 2002;12:55-65.

Yang C, Arnby CH, Arvidson K, Aveston S, Benigni R, Benz RD, et al. Understanding genetic toxicity through data mining: The process of building knowledge by integrating multiple genetic toxicity databases. Tox Mech Meth. 2008;18:277-95.

Kramer JA, Pettit SD, Amin RP, Bertram TA, Car B, Cunningham M, et al. Overview of the application of transcription profiling using selected nephrotoxicants for toxicology assessment. Environ Health Perspect. 2004;112:460-4.

Bowtell DD. Options available-from start to finish-for obtaining expression data by microarray. Nat Genet. 1999;21(Suppl. 1):25-32.

Spellman PT, Miller M, Stewart J. Design and implementation of microarray gene expression mark-up language (MAGE-ML). Genome Biol. 2002;3(9):46.

Cunningham ML, Lehman-McKeeman L. Applying toxicogenomics in mechanistic and predictive toxicology. Toxicol Sci. 2005;83:205-6.

Wittliff JL, Erlander MG. Laser capture microdissection and its applications in genomics and proteomics. Methods Enzymol. 2002;356:12-25.

Kimura J, Nguyen ST, Liu H, Taira N, Miki Y, Yoshida K. A functional genome-wide RNAi screen identifies TAF1 as a regulator for apoptosis in response to genotoxic stress. Nucleic Acids Res. 2008;36:5250-9.

Harries HM, Fletcher ST, Duggan CM, Baker VA. The use of genomics technology to investigate gene expression changes in cultured human liver cells. Toxicol In Vitro. 2001;15(4-5):399-405.

Emmert-Buck MR. Laser capture microdissection. Science. 1996;274:998-1001.

Jain KK. Application of laser capture microdissection to proteomics. Methods Enzymol. 2002;356:157-67.

Karsten SL, Van Deerlin VM, Sabatti C, Gill LH, Geschwind DH. An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis. Nucleic Acids Res. 2002;30:E4.

Bonner RF. Laser capture microdissection: molecular analysis of tissue. Science. 1997;278:1481-3.

Venter JC, Adams MD, Myers EW. The sequence of the human genome. Science. 2011;291(5507):1304-51.

Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushel P, et al. Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol. 2001;8:625-37.

Quackenbush J. Computational analysis of microarray data. Nature Rev Genet. 2001;2:418-27.

Farland WH. Cancer risk assessment: evolution of the process. Prev Med. 1996;25:24-5.

Larsen JC, Farland W, Winters D. Current risk assessment approaches in different countries. Food Addit Contam. 2000;17:359-69.

Barry WT, Nobel AB, Wright FA. Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics. 2005;21(9):1943-9.

Ideker T, Galitski T, Hood L. A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet. 2001;2:343-72.

Xirasagar S, Gustafson SF, Huang CC, Pan Q, Fostel J, Boyer P, et al. Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application. Bioinformatics 2006;22:874-82.

Jeong SY, Park HJ, Oh JH, Kim CY, Yoon SJ. Gene expression profiling of doxifluridine treated liver, small and large intestine in cynomolgus (macaca fascicularis) monkeys. Molecularand Cellular Toxicology. 2007;3:137-44.

Wang EJ, Snyder RD, Fielden MR, Smith RJ, Gu YZ. Validation of putative genomic biomarkers of nephrotoxicity in rats. Toxicology. 2008;246:91-100.

Begley TJ, Rosenbach AS, Ideker T, Samson LD. Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. Mol Cancer Res. 2002;1:103-12.

Kim YJ, Song MK, Song M, Ryu JC. Toxicogenomic study to identify potential new mechanistic markers on direct-acting mutagens in human hepatocytes (THLE-3). Molecular and Cellular Toxicology. 2007;3:231-7.

Lewis F, Maughan NJ, Smith V, Hillan K, Quirke P. Unlocking the archive-gene expression in paraffinembedded tissue. J Pathol. 2001;195:66-71.

Farland WH. The U.S. environmental protection agency’s risk assessment guidelines: current status and future directions. Toxicol Ind Health 1992;8:205-12.

Wetmore BA, Merrick BA. Toxicoproteomics: proteomics applied to toxicology and pathology. Toxicol Pathol. 2004;32:619-42.

Stuart GW, Berry MW. A comprehensive whole genome bacterial phylogeny using correlated peptide motifs defined in a high dimensional vector space. J Bioinform Comput Biol. 2003;1:475-93.

Kazius J, McGuire R, Bursi R. Derivation and validation of toxicophores for mutagenicity prediction. J Med Chem. 2005;48:312-20.

Waring JF, Cavet G, Jolly RA, McDowell J, Dai H, Ciurlionis R, et al. Development of a DNA microarray for oxicology based on hepatotoxinregulate sequences. Environ Health Perspect. 2003;111:863-70.

Prelic A, Bleuler S, Zimmermann P, Wille A, Buhlmann P, Gruissem W, et al. A systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics. 2006;22:1122-9.

Foster WR, Chen SJ, He A, Truong A, Bhaskaran V, Nelson DM, et al. A retrospective analysis of toxicogenomics in the safety assessment of drug candidates. Toxicol Pathol. 2007;35:621-35.

Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995;270:467-70.

Watson JD, Crick FH. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature. 1953;171:737-8.

Downloads

Published

2017-01-05

How to Cite

Mahmud, S. M. N., Mahmud, S., Tandra, T. T., Kar, A., Shathy, E. J., & Jahan, N. (2017). The advent of system toxicology: aims and aspect of toxicogenomics. International Journal of Basic & Clinical Pharmacology, 5(4), 1164–1174. https://doi.org/10.18203/2319-2003.ijbcp20162422

Issue

Section

Review Articles