The CYP2C19 intron 2 branch point SNP is the ancestral polymorphism contributing to the poor metabolizer phenotype in livers with CYP2C19∗35 and CYP2C19∗2 alleles

Drug Metabolism and Disposition

Volumn 43, Issue 8, 2015, Pages 1226-1235

  Chaudhry, Amarjit S ^a   Prasad, Bhagwat ^b   Shirasaka, Yoshiyuki ^b   Fohner, Alison ^b   Finkelstein, David ^a   Fan, Yiping ^a   Wang, Shuoguo ^a   Wu, Gang ^a   Aklillu, Eleni ^c   Sim, Sarah C ^c   Thummel, Kenneth E ^b   Schuetz, Erin G ^a  

^a ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME P450 2C19; MEPHENYTOIN; COMPLEMENTARY DNA; CYP2C19 PROTEIN, HUMAN; ISOENZYME;

ALLELE; ARTICLE; CONTROLLED STUDY; DRUG DISPOSITION; ETHIOPIAN; ETHNIC DIFFERENCE; EXON; FEMALE; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE SEQUENCE; GENETIC POLYMORPHISM; GENOTYPE; HAPLOTYPE; HOMOZYGOSITY; HUMAN; HUMAN CELL; HUMAN TISSUE; INTRON; LIVER MICROSOME; MALE; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DEPLETION; PROTEOMICS; QUANTITATIVE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TANDEM MASS SPECTROMETRY; ACETYLATION; ADULT; BIOSYNTHESIS; ENZYMOLOGY; EPIDEMIOLOGY; ETHIOPIA; GENE FREQUENCY; GENETICS; LIVER; METABOLISM; RNA SPLICING;

ACETYLATION; ADULT; ALLELES; CYTOCHROME P-450 CYP2C19; DNA, COMPLEMENTARY; ETHIOPIA; EXONS; FEMALE; GENE FREQUENCY; HAPLOTYPES; HUMANS; ISOENZYMES; LIVER; MALE; MEPHENYTOIN; PHENOTYPE; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA SPLICING; TANDEM MASS SPECTROMETRY;

EID: 84940416896     PISSN: 00909556     EISSN: 1521009X     Source Type: Journal    
DOI: 10.1124/dmd.115.064428     Document Type: Article

References (38)

1. Aklillu E, Herrlin K, Gustafsson LL, Bertilsson L, and Ingelman-Sundberg M (2002) Evidence for environmental influence on CYP2D6-catalysed debrisoquine hydroxylation as demonstrated by phenotyping and genotyping of Ethiopians living in Ethiopia or in Sweden. Pharmacogenetics 12:375-383.
2. Anders S, Pyl PT, and Huber W (2015) HTSeq-a Python framework to work with highthroughput sequencing data. Bioinformatics 31:166-169.
3. Aten E, Sun Y, Almomani R, Santen GW, Messemaker T, Maas SM, Breuning MH, and den Dunnen JT (2013) Exome sequencing identifies a branch point variant in Aarskog-Scott syndrome. Hum Mutat 34:430-434.
4. Barrett JC, Fry B, Maller J, and Daly MJ (2005) Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics 21:263-265.
5. Chhibber A, French CE, Yee SW, Gamazon ER, Theusch E, Qin X, Webb A, Papp AC, Wang A, and Simmons CQ, et al. (2015) Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines. Pharmacogenomics J. (in Review).
6. Corvelo A, Hallegger M, Smith CW, and Eyras E (2010) Genome-wide association between branch point properties and alternative splicing. PLOS Comput Biol 6:e1001016.
7. De-Morais SM, Wilkinson GR, Blaisdell J, Meyer UA, Nakamura K, and Goldstein JA (1994a) Identification of a new genetic defect responsible for the polymorphism of (S)-mephenytoin metabolism in Japanese. Mol Pharmacol 46:594-598.
8. De-Morais SM, Wilkinson GR, Blaisdell J, Nakamura K, Meyer UA, and Goldstein JA (1994b) The major genetic defect responsible for the polymorphism of S-mephenytoin metabolism in humans. J Biol Chem 269:15419-15422.
9. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, and Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29: 15-21.
10. Downing JR, Wilson RK, Zhang J, Mardis ER, Pui CH, Ding L, Ley TJ, and Evans WE (2012) The Pediatric Cancer Genome Project. Nat Genet 44:619-622.
11. Desmet FO, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, and Béroud C (2009) Human Splicing Finder: An online bioinformatics tool to predict splicing signals. Nucleic Acids Res 37:e67.
12. Edson KZ, Prasad B, Unadkat JD, Suhara Y, Okano T, Guengerich FP, and Rettie AE (2013) Cytochrome P450-dependent catabolism of vitamin K: v-hydroxylation catalyzed by human CYP4F2 and CYP4F11. Biochemistry 52:8276-8285.
13. Gooding C, Clark F, Wollerton MC, Grellscheid SN, Groom H, and Smith CWJ (2006) A class of human exons with predicted distant branch points revealed by analysis of AG dinucleotide exclusion zones. Genome Biol 7:R1.
14. Gordon AS, Tabor HK, Johnson AD, Snively BM, Assimes TL, Auer PL, Ioannidis JP, Peters U, Robinson JG, and Sucheston LE, et al.; NHLBI GO Exome Sequencing Project (2014) Quantifying rare, deleterious variation in 12 human cytochrome P450 drug-metabolism genes in a large-scale exome dataset. Hum Mol Genet 23:1957-1963.
15. Hicks JK, Swen JJ, Thorn CF, Sangkuhl K, Kharasch ED, Ellingrod VL, Skaar TC, Müller DJ, Gaedigk A, and Stingl JC; Clinical Pharmacogenetics Implementation Consortium (2013) Clinical Pharmacogenetics Implementation Consortium guideline for CYP2D6 and CYP2C19 genotypes and dosing of tricyclic antidepressants. Clin Pharmacol Ther 93:402-408.
16. Hirota T, Eguchi S, and Ieiri I (2013) Impact of genetic polymorphisms in CYP2C9 and CYP2C19 on the pharmacokinetics of clinically used drugs. Drug Metab Pharmacokinet 28: 28-37.
17. Janha RE, Worwui A, Linton KJ, Shaheen SO, Sisay-Joof F, and Walton RT (2014) Inactive alleles of cytochrome P450 2C19 may be positively selected in human evolution. BMC Evol Biol 14:71.
18. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, and Salzberg SL (2013) TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36.
19. Kuehl P, Zhang J, Lin Y, Lamba J, Assem M, Schuetz J, Watkins PB, Daly A, Wrighton SA, and Hall SD, et al. (2001) Sequence diversity in CYP3A promoters and characterization of the genetic basis of polymorphic CYP3A5 expression. Nat Genet 27:383-391.
20. Lamba V, Lamba J, Yasuda K, Strom S, Davila J, Hancock ML, Fackenthal JD, Rogan PK, Ring B, and Wrighton SA, et al. (2003) Hepatic CYP2B6 expression: gender and ethnic differences and relationship to CYP2B6 genotype and CAR (constitutive androstane receptor) expression. J Pharmacol Exp Ther 307:906-922.
21. Li-Wan-Po A, Girard T, Farndon P, Cooley C, and Lithgow J (2010) Pharmacogenetics of CYP2C19: functional and clinical implications of a new variant CYP2C19∗17. Br J Clin Pharmacol 69:222-230.
22. McGraw J and Waller D (2012) Cytochrome P450 variations in different ethnic populations. Expert Opin Drug Metab Toxicol 8:371-382.
23. Owusu Obeng A, Egelund EF, Alsultan A, Peloquin CA, and Johnson JA (2014) CYP2C19 polymorphisms and therapeutic drug monitoring of voriconazole: Are we ready for clinical implementation of pharmacogenomics? Pharmacotherapy 34:703-718.
24. Persson I, Aklillu E, Rodrigues F, Bertilsson L, and Ingelman-Sundberg M (1996) S-mephenytoin hydroxylation phenotype and CYP2C19 genotype among Ethiopians. Pharmacogenetics 6: 521-526.
25. Prasad B and Unadkat JD (2014) Optimized approaches for quantification of drug transporters in tissues and cells by MRM proteomics. AAPS J 16:634-648.
26. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, and Mesirov JP (2011) Integrative genomics viewer. Nat Biotechnol 29:24-26.
27. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, and McDonald GJ, et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419:832-837.
28. Sakabe NJ and de-Souza SJ (2007) Sequence features responsible for intron retention in human. BMC Genomics 8:59.
29. Sanz EJ, Villén T, Alm C, and Bertilsson L (1989) S-mephenytoin hydroxylation phenotypes in a Swedish population determined after coadministration with debrisoquin. Clin Pharmacol Ther 45:495-499.
30. Scott SA, Sangkuhl K, Stein CM, Hulot JS, Mega JL, Roden DM, Klein TE, Sabatine MS, Johnson JA, and Shuldiner AR; Clinical Pharmacogenetics Implementation Consortium (2013) Clinical Pharmacogenetics Implementation Consortium guidelines for CYP2C19 genotype and clopidogrel therapy: 2013 update. Clin Pharmacol Ther 94:317-323.
31. Shah BS, Parmar SA, Mahajan S, and Mehta AA (2012) An insight into the interaction between clopidogrel and proton pump inhibitors. Curr Drug Metab 13:225-235.
32. Shirasaka Y, Sager JE, Lutz JD, Davis C, and Isoherranen N (2013) Inhibition of CYP2C19 and CYP3A4 by omeprazole metabolites and their contribution to drug-drug interactions. Drug Metab Dispos 41:1414-1424.
33. Sim SC, Risinger C, Dahl ML, Aklillu E, Christensen M, Bertilsson L, and Ingelman-Sundberg M (2006) A common novel CYP2C19 gene variant causes ultrarapid drug metabolism relevant for the drug response to proton pump inhibitors and antidepressants. Clin Pharmacol Ther 79: 103-113.
34. Singh G and Cooper TA (2006) Minigene reporter for identification and analysis of cis elements and trans factors affecting pre-mRNA splicing. Biotechniques 41:177-181.
35. Taggart AJ, DeSimone AM, Shih JS, Filloux ME, and Fairbrother WG (2012) Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo. Nat Struct Mol Biol 19: 719-721.
36. Tybring G and Bertilsson L (1992) A methodological investigation on the estimation of the S-mephenytoin hydroxylation phenotype using the urinary S/R ratio. Pharmacogenetics 2: 241-243.
37. Wang L, Prasad B, Salphati L, Chu X, Gupta A, Hop CE, Evers R, and Unadkat JD (2015) Interspecies variability in expression of hepatobiliary transporters across human, dog, monkey, and rat as determined by quantitative proteomics. Drug Metab Dispos 43:367-374.
38. Wedlund PJ (2000) The CYP2C19 enzyme polymorphism. Pharmacology 61:174-183.