The impact of DNA methylation technologies on drug toxicology

Bibliography

• Brugsch J. Bases and clinical aspects of medicinal damages. Hippokrates 1959;30:541-4
   PubMedGoogle Scholar
• Bennet PN. Detecting adverse reactions to drugs. Hum Toxicol 1988;7:465-7
   PubMedGoogle Scholar
• Bracken MB. Why animal studies are often poor predictors of human reactions to exposure. J R Soc Med 2009;102:120-2
   PubMed Web of Science ®Google Scholar
• Olson H, Betton G, Robinson D, et al. Concordance of the toxicity of pharmaceuticals in humans and in animals. Regul Toxicol Pharmacol 2000;32:56-67
   PubMed Web of Science ®Google Scholar
• Knight A. Animal experiments scrutinised: systematic reviews demonstrate poor human clinical and toxicological utility. ALTEX 2007;24:320-5
   PubMed Web of Science ®Google Scholar
• Stevens JL. Future of toxicology – mechanisms of toxicity and drug safety: where do we go from here? Chem Res Toxicol 2006;19:1393-401
   PubMed Web of Science ®Google Scholar
• Koenig R. European researches grapple with animal rights. Science 1999;284(5420):1604-6
   PubMed Web of Science ®Google Scholar
• van Vliet E. Current standing and future prospects for the technologies proposed to transform toxicity testing in the 21st century. ALTEX 2011;28:17-44
   PubMed Web of Science ®Google Scholar
• Lockwood WW, Chari R, Chi B, et al. Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. Eur J Hum Genet 2006;14:139-48
   PubMed Web of Science ®Google Scholar
• Dong H, Wang S. Exploring the cancer genome in the era of next-generation sequencing. Front Med 2012;6:48-55
   Google Scholar
• Thomas RS, Rank DR, Penn SG, et al. Application of genomics to toxicology research. Environ Health Perspect 2002;110(Suppl 6):919-23
   PubMedGoogle Scholar
• Garte S, Taioli E, Popov T, et al. Genetic susceptibility to benzene toxicity in humans. J Toxicol Environ Health A 2008;71:1482-9
   PubMed Web of Science ®Google Scholar
• Jain KK. Applications of AmpliChip CYP450. Mol Diagn 2005;9:119-27
   PubMedGoogle Scholar
• Kronick MN. Creation of the whole human genome microarray. Expert Rev Proteomics 2004;1:19-28
   PubMed Web of Science ®Google Scholar
• Walker NJ. Real-time and quantitative PCR: applications to mechanism-based toxicology. J Biochem Mol Toxicol 2001;15:121-7
   PubMed Web of Science ®Google Scholar
• Zhou T, Chou J, Watkins PB, et al. Toxicogenomics: transcription profiling for toxicology assessment. EXS 2009;99:325-66
   PubMedGoogle Scholar
• Heinloth AN, Irwin RD, Boorman GA, et al. Gene expression profiling of rat livers reveals indicators of potential adverse effects. Toxicol Sci 2004;80:193-202
   PubMed Web of Science ®Google Scholar
• Hogberg HT, Kinsner-Ovaskainen A. Coecke S, et al. mRNA expression is a relevant tool to identify devel- opmental neurotoxicants using an in vitro approach. Toxicol Sci 2010;113:95-115
   PubMed Web of Science ®Google Scholar
• Ellinger-Ziegelbauer H, Fostel JM, Aruga C, et al. Characterization and interlaboratory comparison of a gene expression signature for differentiating genotoxic mechanisms. Toxicol Sci 2009;110:341-52
   PubMed Web of Science ®Google Scholar
• Ross JS, Hatzis C, Symans WF, et al. Commercialized multigene predictors of clinical outcome for breast cancer. Oncologist 2008;13:477-93
   PubMed Web of Science ®Google Scholar
• Peintinger F, Anderson K, Mazouni C, et al. Thirty-gene pharmacogenomic test correlates with residual cancer burden after preoperative chemotherapy for breast cancer. Clin Cancer Res 2007;13:4078-82
   PubMed Web of Science ®Google Scholar
• Yu LR. Pharmacoproteomics and toxicoproteomics: the field of dreams. J Proteomics 2011;74:2549-53
   PubMed Web of Science ®Google Scholar
• Garbis S, Lubec G, Fountoulakis M. Limitations of current proteomics technologies. J Chromatogr 2005;1077:1-18
   PubMed Web of Science ®Google Scholar
• Ross PL, Huang YN, Marchese JN, et al. Multiplexed protein quantitation in saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004;3:1154-69
   PubMed Web of Science ®Google Scholar
• George J, Singh R, Mahmood Z, et al. Toxicoproteomics: new paradigms in toxicology research. Toxicol Mech Methods 2010;20:415-23
   PubMed Web of Science ®Google Scholar
• Wetmore BA, Merrick BA. Toxicoproteomics: proteomics applied to toxicology and pathology. Toxicol Pathol 2004;32:619-42
   PubMed Web of Science ®Google Scholar
• Merrick BA, Witzmann FA. The role of toxicoproteomics in assessing organ specific toxicity. EXS 2009;99:367-400
   PubMedGoogle Scholar
• Yuan F, Lu J, You P, et al. Proteomic profiling of expression of proteasomal subunits from livers of mice treated with diethylnitrosamine. Proteomics 2013;13:389-97
   PubMed Web of Science ®Google Scholar
• Fernando H, Wiktorowicz JE, Soman KV, et al. Liver proteomics in progressive alcoholic steatosis. Toxicol Appl Pharmacol 2013;266:470-80
   PubMed Web of Science ®Google Scholar
• Hoogendoorn B, Berube K, Gregory C, et al. Gene and protein responses of human lung tissue explants exposed to ambient particulate matter of different sizes. Inhal Toxicol 2012;24:966-75
   PubMed Web of Science ®Google Scholar
• Benevento M, Munoz J. Role of mass spectrometry-based proteomics in the study of cellular reprogramming and induced pluripotent stem cells. Expert Rev Proteomics 2012;9:379-99
   PubMed Web of Science ®Google Scholar
• Usami M, Nakajima M, Mitsunaga K, et al. Proteomic analysis of indium embryotoxicity in cultured postimplantation rat embryos. Reprod Toxicol 2009;28:477-88
   PubMed Web of Science ®Google Scholar
• Ohtsuki S, Uchida Y, Kubo Y, et al. Quantitative targeted absolute proteomics-based ADME research as a new path to drug discovery and development: methodology, advantages, strategy, and prospects. J Pharm Sci 2011;100:3547-59
   PubMed Web of Science ®Google Scholar
• Robertson DG. Metabonomics in toxicology: a review. Toxicol Sci 2005;85:809-22
   PubMed Web of Science ®Google Scholar
• Dettmer K, Aronov PA, Hammock BD. Mass spectrometry-based metabolomics. Mass Spectrom Rev 2007;26:51-78
   PubMed Web of Science ®Google Scholar
• Wishart DS. Human metabolome database: completing the ‘human parts list’. Pharmacogenomics 2007;8:683-6
   PubMed Web of Science ®Google Scholar
• Smith CA, O'Maille G, Want EJ, et al. METLIN: a metabolite mass spectral database. Ther Drug Monit 2005;27:747-51
   PubMed Web of Science ®Google Scholar
• Lanza IR, Zhang S, Ward LE, et al. Quantitative metabolomics by H-NMR and LC-MS/MS confirms altered metabolic pathways in diabetes. PLoS One 2010;5:e10538
   PubMed Web of Science ®Google Scholar
• Lindon JC, Keun HC, Ebbels TM, et al. The consortium for metabonomic toxicology (COMET): aims, activities and achievements. Pharmacogenomics 2005;6:691-9
   PubMed Web of Science ®Google Scholar
• Ebbels TM, Keun HC, Beckonert OP, et al. Prediction and classification of drug toxicity using probabilistic modeling of temporal metabolic data: the consortium on metabonomic toxicology screening approach. J Proteome Res 2007;6:4407-22
   PubMed Web of Science ®Google Scholar
• Coen M. A metabonomic approach for mechanistic exploration of pre-clinical toxicology. Toxicology 2010;278:326-40
   PubMed Web of Science ®Google Scholar
• Nicholson JK, Lindon JC. Systems biology: metabonomics. Nature 2008;455:1054-6
   PubMed Web of Science ®Google Scholar
• Sumner S, Snyder R, Burgess J, et al. Metabolomics in the assessment of chemical-induced reproductive and developmental outcomes using non-invasive biological fluids: application to the study of butylbenzyl phthalate. J Appl Toxicol 2009;29:703-14
   PubMed Web of Science ®Google Scholar
• West PR, Weir AM, Smith AM, et al. Predicting human developmental toxicity of pharmaceuticals using human embryonic stem cells and metabolomics. Toxicol Appl Pharmacol 2010;247:18-27
   PubMed Web of Science ®Google Scholar
• Ramirez T, Daneshian M, Kamp H, et al. Metabolomics in toxicology and preclinical research. ALTEX 2013;30:209-25
   PubMedGoogle Scholar
• You JS, Jones PA. Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell 2012;22:9-2
   PubMed Web of Science ®Google Scholar
• Jurkowska RZ, Jurkowski TP, Jeltsch A. Structure and function of mammalian DNA methyltransferases. ChemBioChem 2011;12:206-22
   PubMed Web of Science ®Google Scholar
• Davie JR, Hendzel MJ. Multiple functions of dynamic histone acetylation. J Cell Biochem 1994;55:98-105
   PubMed Web of Science ®Google Scholar
• Heyn H, Esteller M. DNA methylation profiling in the clinic: applications and challenges. Nat Rev Genet 2012;13:679-92
   PubMed Web of Science ®Google Scholar
• Esteller M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 2007;8:286-98
   PubMed Web of Science ®Google Scholar
• Villar-Garea A, Imhof A. The analysis of histone modifications. Biochim Biophys Acta 2006;1764:1932-9
   PubMed Web of Science ®Google Scholar
• Cosgrove MS. Histone proteomics and the epigenetic regulation of nucleosome mobility. Expert Rev Proteomics 2007;4:465-78
   PubMed Web of Science ®Google Scholar
• Iorio MV, Piovan C, Croce CM. Interplay between microRNAs and the epigenetic machinery: an intricate network. Biochim Biophys Acta 2010;1799:694-701
   PubMed Web of Science ®Google Scholar
• Ito S, Shen L, Dai Q, et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 2011;333(6047):1300-3
   PubMed Web of Science ®Google Scholar
• Seisenberger S, Peat JR, Hore TA, et al. Reprogramming DNA methylation in the mammalian life cycle: building and breaking epigenetic barriers. Philos Trans R Soc Lond B Biol Sci 2013;368(1609):20110330
   PubMed Web of Science ®Google Scholar
• Hino S, Nagaoka K, Nakao M. Metabolism-epigenome crosstalk in physiology and diseases. J Hum Genet 2013;58:410-15
   PubMed Web of Science ®Google Scholar
• Jirtle RL, Skinner MK. Environmental epigenomics and disease susceptibility. Nat Rev Genet 2007;8:253-62
   PubMed Web of Science ®Google Scholar
• Costello JF, Fruhwald MC, Smiraglia DJ, et al. Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet 2000;24:132-8
   PubMed Web of Science ®Google Scholar
• Estécio MRH, Yan PS, Ibrahim AEK, et al. High-throughput methylation profiling by MCA coupled to CpG island microarray. Genome Res 2007;17:1529-36
   PubMed Web of Science ®Google Scholar
• Ibrahim AEK, Thorne NP, Baird K, et al. MMASS: an optimized array-based method for assessing CpG island methylation. Nucleic Acids Res 2006;34:e136
   PubMedGoogle Scholar
• Irizarry RA, Ladd-Acosta C, Wen B, et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 2009;41:178-86
   PubMed Web of Science ®Google Scholar
• Seifert M, Cortijo S, Colome-Tache M, et al. MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinformatics 2012;28:2930-9
   PubMed Web of Science ®Google Scholar
• Maunakea AK, Nagarajan RP, Bilenky M, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 2010;466(7303):253-7
   PubMed Web of Science ®Google Scholar
• Jacinto FV, Ballestar E, Ropero S, et al. Discovery of epigenetically silenced genes by methylated DNA immunoprecipitation in colon cancer cells. Cancer Res 2007;67:11481-6
   PubMed Web of Science ®Google Scholar
• Ballestar E, Paz MF, Valle L, et al. Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer. EMBO J 2003;22:6335-
   PubMed Web of Science ®Google Scholar
• Yegnasubramanian S, Wu Z, Haffner MC, et al. Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences. BMC Genomics 2011;12:313
   PubMed Web of Science ®Google Scholar
• Hiraoka D, Yoshida W, Abe K, et al. Development of a method to measure DNA methylation levels by using methyl CpG-binding protein and luciferase-fused zinc finger protein. Anal Chem 2012;84:8259-64
   PubMed Web of Science ®Google Scholar
• Frommer M, McDonal LE, Millar DS, et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 1992;89:1827-31
   PubMed Web of Science ®Google Scholar
• Kobayashi H, Kono T. DNA methylation analysis of germ cells by using bisulfite-based sequencing methods. Methods Mol Biol 2012;825:223-35
   PubMedGoogle Scholar
• Krueger F, Krek B, Franke A, et al. DNA methylome analysis using short bisulfite sequencing data. Nat Methods 2012;9:145-51
   PubMed Web of Science ®Google Scholar
• Beck S. Tacking the measure of the methylome. Nat Biotechnol 2010;28:1026-8
   PubMed Web of Science ®Google Scholar
• Bock C, Tomazou EM, Brinkman AB, et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 2010;28:1106-14
   PubMed Web of Science ®Google Scholar
• Harris RA, Wang T, Coarfa C, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 2010;28:1097-105
   PubMed Web of Science ®Google Scholar
• Marabita F, Almgren M, Lindholm ME, et al. An evaluation of analysis pipelines for DNA methylation profiling using the illumina humanmethylation450 beadchip platform. Epigenetics 2013;8:333-46
   PubMed Web of Science ®Google Scholar
• Ivanov M, Kacevska M, Ingelman-Sundberg M. Epigenomics and interindividual differences in drug response. Clin Pharmacol Ther 2012;92:727-36
   PubMed Web of Science ®Google Scholar
• Berghoff AS, Preusser M. Clinical neuropathology practice guide 06-2012: MGMT testing in elderly glioblastoma patients–yes, but how? Clin Neuropathol 2012;31:405-8
   PubMed Web of Science ®Google Scholar
• Chao C, Chi M, Preciado et al. Methylation markers for prostate cancer prognosis: a systematic review. Cancer Causes Control 2013;24:1615-41
   PubMed Web of Science ®Google Scholar
• Tóth K, Sipos F, Kalmár A, et al. Detection of methylated SEPT9 in plasma is a reliable screening method for both left- and right-sided colon cancers. PLoS One 2012;7:e46000
   PubMed Web of Science ®Google Scholar
• Darwiche K, Zarogoulidis P, Baehner K, et al. Assessment of SHOX2 methylation in EBUS-TBNA specimen improves accuracy in lung cancer staging. Ann Oncol 2013;24:2866-70
   PubMed Web of Science ®Google Scholar
• Ivanov M, Kals M, Kacevska M, et al. In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes. Nucleic Acids Res 2013;41:e72
   PubMed Web of Science ®Google Scholar
• Lutz P, Breitling LP, Yang R, et al. Tobacco-smoking-related differential DNA methylation: 27K discovery and replication. Am J Hum Genet 2011;88:450-7
   PubMed Web of Science ®Google Scholar
• Kim JH, Rozek LS, Soliman AS, et al. Bisphenol A-associated epigenomic changes in prepubescent girls: a cross-sectional study in Gharbiah, Egypt. Environ Health 2013;12:33
   PubMed Web of Science ®Google Scholar