Omics in mechanistic and predictive toxicology

References

• Aardema MJ, MacGregor JT. 2002. Toxicology and genetic toxicology in the new era of ‘toxicogenomics’: impact of ‘-omics’ technologies. Mutat Res 499:13–25.
   PubMed Web of Science ®Google Scholar
• Ahmad I, Kumar A, Shukla S, Pandey HP, Singh C. 2008. The involvement of nitric oxide in maneb- and paraquat-induced oxidative stress in rat polymorphonuclear leukocytes. Free Radic Res 42:849–862.
   PubMed Web of Science ®Google Scholar
• Anderson L, Seilhamer J. 1997. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18:533–537.
   PubMed Web of Science ®Google Scholar
• Briefing. 1999. Proteomics, transcriptomics: what’s in a name? Nature 402:715. doi: 10.1038/45354.
   Web of Science ®Google Scholar
• Claudino WM, Quattrone A, Biganzoli L, Pestrin M, Bertini I, Di Leo A. 2007. Metabolomics: available results, current research projects in breast cancer, and future applications. J Clin Oncol 25:2840–2846.
   PubMed Web of Science ®Google Scholar
• Coulton G. 2004. Are histochemistry and cytochemistry ‘Omics’? J Mol Histol 35:603–613.
   PubMed Web of Science ®Google Scholar
• Farr S, Dunn RT 2nd. 1999. Gene expression applied to toxicology. Toxicol Sci 50:1–9.
   PubMed Web of Science ®Google Scholar
• Flora SJ. 2008. Status of toxicological research in India. Chem Res Toxicol 21:1317–1319.
   PubMed Web of Science ®Google Scholar
• Gatzidou ET, Zira AN, Theocharis SE. 2007. Toxicogenomics: a pivotal piece in the puzzle of toxicological research. J Appl Toxicol 27:302–309.
   PubMed Web of Science ®Google Scholar
• Ge F, He QY. 2009. Genomic and proteomic approaches for predicting toxicity and adverse drug reactions. Expert Opin Drug Metab Toxicol 5:29–37.
   PubMed Web of Science ®Google Scholar
• Hanash SM, Beretta LM. 2002. Operomics: integrated genomic and proteomic profiling of cells and tissues. Brief Funct Genomic Proteomic 1:10–22.
   PubMedGoogle Scholar
• Harrill AH, Rusyn I. 2008. Systems biology and functional genomics approaches for the identification of cellular responses to drug toxicity. Expert Opin Drug Metab Toxicol 4:1379–1389.
   PubMed Web of Science ®Google Scholar
• He QY, Chiu JF. 2003. Proteomics in biomarker discovery and drug development. J Cell Biochem 89:868–886.
   PubMed Web of Science ®Google Scholar
• Hegde PS, White IR, Debouck C. 2003. Interplay of transcriptomics and proteomics. Curr Opin Biotech 14:647–651.
   PubMed Web of Science ®Google Scholar
• Heijne WH, Kienhuis AS, van Ommen B, Stierum RH, Groten JP. 2005. Systems toxicology: applications of toxicogenomics, transcriptomics, proteomics and metabolomics in toxicology. Expert Rev Proteomics 2:767–780.
   PubMed Web of Science ®Google Scholar
• Inadera H, Uchida M, Shimomura A. 2007. Advances in ‘omics’ technologies for toxicological research. Nippon Eiseigaku Zasshi 62:18–31.
   PubMedGoogle Scholar
• Johri A, Yadav S, Dhawan A, Parmar D. 2007. Overexpression of cerebral and hepatic cytochrome P450s alters behavioral activity of rat offspring following prenatal exposure to lindane. Toxicol Appl Pharmacol 225:278–292.
   PubMed Web of Science ®Google Scholar
• Johri A, Yadav S, Dhawan A, Parmar D. 2008. Responsiveness of cerebral and hepatic cytochrome P450s in rat offspring prenatally exposed to lindane. Toxicol Appl Pharmacol 231:10–16.
   PubMed Web of Science ®Google Scholar
• Johri A, Yadav S, Singh RL, Dhawan A, Ali M, Parmar D. 2006. Long lasting effects of prenatal exposure to deltamethrin on cerebral and hepatic cytochrome P450s and behavioral activity in rat offspring. Eur J Pharmacol 544:58–68.
   PubMed Web of Science ®Google Scholar
• Kapoor N, Pant AB, Dhawan A, Dwievedi UN, Seth PK, Parmar D. 2007. Differences in the expression and inducibility of cytochrome P450 2B isoenzymes in cultured rat brain neuronal and glial cells. Mol Cell Biochem 305:199–207.
   PubMed Web of Science ®Google Scholar
• Khan AJ, Choudhuri G, Husain Q, Parmar D. 2009a. Polymorphism in glutathione-S-transferases: a risk factor in alcoholic liver cirrhosis. Drug Alcohol Depen 101:183–190.
   PubMed Web of Science ®Google Scholar
• Khan AJ, Ruwali M, Choudhuri G, Mathur N, Husain Q, Parmar D. 2009b. Polymorphism in cytochrome P450 2E1 and interaction with other genetic risk factors and susceptibility to alcoholic liver cirrhosis. Mutat Res 664:55–63.
   PubMed Web of Science ®Google Scholar
• Kumar A, Patel S, Gupta YK, Singh MP. 2006. Involvement of endogenous nitric oxide in myeloperoxidase mediated benzo (a) pyrene induced polymorphonuclear leukocytes injury. Mol Cell Biochem 286:43–51.
   PubMed Web of Science ®Google Scholar
• Kumar A, Upadhyay G, Modi DR, Singh MP. 2007. The involvement of secondary signaling molecules in cytochrome P-450 1A1-mediated inducible nitric oxide synthase expression in benzo(a)pyrene-treated rat polymorphonuclear leukocytes. Life Sci 81:1575–1584.
   PubMed Web of Science ®Google Scholar
• Kumar M, Agarwal SK, Goel SK. 2009. Lung cancer risk in north Indian population: role of genetic polymorphisms and smoking. Mol Cell Biochem 322:73–79.
   PubMed Web of Science ®Google Scholar
• Leighton JK. 2005. Application of emerging technologies in toxicology and safety assessment: regulatory perspectives. Int J Toxicol 24:153–155.
   PubMed Web of Science ®Google Scholar
• MacGregor JT. 2004. Biomarkers of cancer risk and therapeutic benefit: new technologies, new opportunities, and some challenges. Toxicol Pathol 32 (suppl 1):99–105.
   PubMedGoogle Scholar
• Merrick BA. 2008. The plasma proteome, adductome and idiosyncratic toxicity in toxicoproteomics research. Brief Funct Genomic Proteomic 7:35–49.
   PubMedGoogle Scholar
• Merrick BA, Madenspacher JH. 2005. Complementary gene and protein expression studies and integrative approaches in toxicogenomics. Toxicol Appl Pharmacol 207:189–194.
   PubMedGoogle Scholar
• Meyer UA. 2000. Pharmacogenetics and adverse drug reactions. Lancet 356:1667–1671.
   PubMed Web of Science ®Google Scholar
• Orphanides G, Kimber I. 2003. Toxicogenetics: applications and opportunities. Toxicol Sci 75:1–6.
   PubMed Web of Science ®Google Scholar
• Patel S, Parmar D, Gupta YK, Singh MP. 2005. Contribution of genomics, proteomics, and single-nucleotide polymorphism in toxicology research and Indian scenario. Indian J Hum Genet 11:61–75.
   Google Scholar
• Patel S, Singh K, Singh S, Singh MP. 2008. Gene expression profiles of mouse striatum in control and maneb + paraquat-induced Parkinson’s disease phenotype: validation of differentially expressed energy metabolizing transcripts. Mol Biotechnol 40:59–68.
   PubMed Web of Science ®Google Scholar
• Patel S, Singh V, Kumar A, Gupta YK, Singh MP. 2006. Status of antioxidant defense system and expression of toxicant responsive genes in striatum of maneb- and paraquat-induced Parkinson’s disease phenotype in mouse: mechanism of neurodegeneration. Brain Res 1081:9–18.
   PubMed Web of Science ®Google Scholar
• Patel S, Sinha A, Singh MP. 2007. Identification of differentially expressed proteins in striatum of maneb-and paraquat-induced Parkinson’s disease phenotype in mouse. Neurotoxicol Teratol 29:578–585.
   PubMed Web of Science ®Google Scholar
• Ruwali M, Pant MC, Shah PP, Mishra BN, Parmar D. 2009. Polymorphism in cytochrome P450 2A6 and glutathione S-transferase P1 modifies head and neck cancer risk and treatment outcome. Mutat Res 669:36–41.
   PubMed Web of Science ®Google Scholar
• Shah PP, Singh AP, Singh M, Mathur N, Mishra BN, Pant MC, Parmar D. 2008a. Association of functionally important polymorphisms in cytochrome P4501B1 with lung cancer. Mutat Res 643:4–10.
   PubMed Web of Science ®Google Scholar
• Shah PP, Singh AP, Singh M, Mathur N, Pant MC, Mishra BN, Parmar D. 2008b. Interaction of cytochrome P4501A1 genotypes with other risk factors and susceptibility to lung cancer. Mutat Res 639:1–10.
   PubMed Web of Science ®Google Scholar
• Singh C, Ahmad I, Kumar A. 2007a. Pesticides and metals induced Parkinson’s disease: involvement of free radicals and oxidative stress. Cell Mol Biol (Noisy-le-grand) 53:19–28.
   PubMed Web of Science ®Google Scholar
• Singh M, Khan AJ, Shah PP, Shukla R, Khanna VK, Parmar D. 2008b. Polymorphism in environment responsive genes and association with Parkinson disease. Mol Cell Biochem 312:131–138.
   PubMed Web of Science ®Google Scholar
• Singh M, Shah PP, Singh AP, Ruwali M, Mathur N, Pant MC, Parmar D. 2008a. Association of genetic polymorphisms in glutathione S-transferases and susceptibility to head and neck cancer. Mutat Res 638:184–194.
   PubMed Web of Science ®Google Scholar
• Singh MP, Patel S, Dikshit M, Gupta YK. 2006. Contribution of genomics and proteomics in understanding the role of modifying factors in Parkinson’s disease. Indian J Biochem Biophys 43:69–81.
   PubMed Web of Science ®Google Scholar
• Singh S, Singh K, Gupta SP, Patel DK, Singh VK, Singh RK, Singh MP. 2009a. Effect of caffeine on the expression of cytochrome P450 1A2, adenosine A2A receptor and dopamine transporter in control and 1-methyl 4-phenyl 1, 2, 3, 6-tetrahydropyridine treated mouse striatum. Brain Res 1283:115–126.
   PubMed Web of Science ®Google Scholar
• Singh S, Singh K, Patel DK, Singh C, Nath C, Singh VK, Singh RK, Singh MP. 2009b. The expression of CYP2D22, an ortholog of human CYP2D6, in mouse striatum and its modulation in 1-methyl 4-phenyl-1,2,3,6-tetrahydropyridine-induced parkinson’s disease phenotype and nicotine-mediated neuroprotection. Rejuvenation Res 12:185–197.
   PubMed Web of Science ®Google Scholar
• Singh S, Singh K, Patel S, Patel DK, Singh C, Nath C, Singh MP. 2008e. Nicotine and caffeine-mediated modulation in the expression of toxicant responsive genes and vesicular monoamine transporter-2 in 1-methyl 4-phenyl-1, 2, 3, 6-tetrahydropyridine-induced Parkinson’s disease phenotype in mouse. Brain Res 1207:193–206.
   PubMed Web of Science ®Google Scholar
• Singh V, Parmar D, Singh MP. 2008c. Do single nucleotide polymorphisms in xenobiotic metabolizing genes determine breast cancer susceptibility and treatment outcomes? Cancer Invest 26:769–783.
   PubMed Web of Science ®Google Scholar
• Singh V, Rastogi N, Mathur N, Singh K, Singh MP. 2008d. Association of polymorphism in MDM-2 and p53 genes with breast cancer risk in Indian women. Ann Epidemiol 18:48–57.
   PubMed Web of Science ®Google Scholar
• Singh V, Rastogi N, Sinha A, Kumar A, Mathur N, Singh MP. 2007b. A study on the association of cytochrome-P450 1A1 polymorphism and breast cancer risk in north Indian women. Breast Cancer Res Treat 101:73–81.
   PubMed Web of Science ®Google Scholar
• Sinha A, Patel S, Singh MP, Shukla R. 2007b. Blood proteome profiling in case controls and Parkinson’s disease patients in Indian population. Clin Chim Acta 380:232–234.
   PubMed Web of Science ®Google Scholar
• Sinha A, Singh C, Parmar D, Singh MP. 2007a. Proteomics in clinical interventions: achievements and limitations in biomarker development. Life Sci 80:1345–1354.
   PubMed Web of Science ®Google Scholar
• Sinha A, Srivastava N, Singh S, Singh AK, Bhushan S, Shukla R, Singh MP. 2009. Identification of differentially displayed proteins in cerebrospinal fluid of Parkinson’s disease patients: a proteomic approach. Clin Chim Acta 400:14–20.
   PubMed Web of Science ®Google Scholar
• Suter L, Babiss LE, Wheeldon EB. 2004. Toxicogenomics in predictive toxicology in drug development. Chem Biol 11:161–171.
   PubMed Web of Science ®Google Scholar
• Upadhyay G, Gupta SP, Prakash O, Singh MP. 2009. Pyrogallol-mediated toxicity and natural antioxidants: triumphs and pitfalls of preclinical findings and their translational limitations. Chem Biol Interact. doi:10.1016/j.cbi.2009.11.028.
   PubMed Web of Science ®Google Scholar
• Upadhyay G, Kumar A, Singh MP. 2007. Effect of silymarin on pyrogallol- and rifampicin-induced hepatotoxicity in mouse. Eur J Pharmacol 565:190–201.
   PubMed Web of Science ®Google Scholar
• Upadhyay G, Singh AK, Kumar A, Prakash O, Singh MP. 2008. Resveratrol modulates pyrogallol-induced changes in hepatic toxicity markers, xenobiotic metabolizing enzymes and oxidative stress. Eur J Pharmacol 596:146–152.
   PubMed Web of Science ®Google Scholar
• Yadav S, Singhal NK, Singh V, Rastogi N, Srivastava PK, Singh MP. 2009. Association of single nucleotide polymorphisms in CYP1B1 and COMT genes with breast cancer susceptibility in Indian women. Dis Markers 27:203–210.
   PubMed Web of Science ®Google Scholar