Abstract
Pharmacoepigenetics is an emerging field, which can be studied by several approaches. Addressing DNA methylation status of drug-metabolizing enzymes and transporters (DMET) is challenging and might provide answers in relation to interindividual differences in pharmacokinetics and pharmacodynamics. Studying genetic variation in DMET genes in relation to drug response has been the main focus of pharmacogenetics laboratories; it is, however, expected that epigenetic modifications will play a role in drug responses as well. Some of the variations in drug-responses cannot be explained by genetic variation in DMET genes. For those particular genes it might be interesting to examine the DNA methylation status in relation to pharmacokinetics. In this chapter we discuss the methods available and provide a protocol to quantify DNA methylation status of CpG sites in candidate genes, which can readily be applied to most pharmacogenetics laboratories. In addition, we provide details about optimization and validation of the method in terms of technical specificity and technical sensitivity and precision of the method.
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References
Russo VEA, Martienssen RA, Riggs AD (1996) Epigenetic mechanisms of gene regulation. Cold Spring Harbor Press, Cold Spring Harbor, NY
Chen ZX, Riggs AD (2011) DNA methylation and demethylation in mammals. J Biol Chem 286:18347–18353
Gomez A, Ingelman-Sundberg M (2009) Pharmacoepigenetics: its role in interindividual differences in drug response. Clin Pharmacol Ther 85:426–430
Ingelman-Sundberg M, Sim SC, Gomez A, Rodriguez-Antona C (2007) Influence of cytochrome P450 polymorphisms on drug therapies: pharmacogenetic, pharmacoepigenetic and clinical aspects. Pharmacol Ther 116:496–526
Shen L, Waterland RA (2007) Methods of DNA methylation analysis. Curr Opin Clin Nutr Metab Care 10:576–581
Laird PW (2010) Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 11:191–203
Kristensen LS, Hansen LL (2009) PCR-based methods for detecting single-locus DNA methylation biomarkers in cancer diagnostics, prognostics, and response to treatment. Clin Chem 55:1471–1483
Feinberg AP, Vogelstein B (1983) Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301:89–92
Frommer M et al (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 89:1827–1831
Eads CA et al (2000) MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res 28:E32
Colella S, Shen L, Baggerly KA, Issa JP, Krahe R (2003) Sensitive and quantitative universal Pyrosequencing methylation analysis of CpG sites. Biotechniques 35:146–150
Ehrich M et al (2005) Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci USA 102:15785–15790
Campan M, Weisenberger DJ, Trinh B, Laird PW (2009) MethyLight. Methods Mol Biol 507:325–337
http://www.urogene.org/methprimer/index1.html. Accessed 26 July 2011
http://www.gene-quantification.de/efficiency01.html#rebrikov. Accessed 26 July 2011
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25:402–408
Acknowledgment
The expert technical assistance of Mr. Pieter Griffioen is gratefully acknowledged.
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Heil, S.G. (2013). Epigenetic Techniques in Pharmacogenetics. In: Innocenti, F., van Schaik, R. (eds) Pharmacogenomics. Methods in Molecular Biology, vol 1015. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-435-7_11
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DOI: https://doi.org/10.1007/978-1-62703-435-7_11
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Publisher Name: Humana Press, Totowa, NJ
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