The unique complexity of the CYP3A4 upstream region suggests a nongenetic explanation of its expression variability

Pharmacogenetics and Genomics

Volumn 20, Issue 3, 2010, Pages 167-178

  Qiu, Huan ^a   Mathäs, Marianne ^a   Nestler, Sebastian ^a   Bengel, Christopher ^a   Nem, Dieudonne ^a   Gödtel Armbrust, Ute ^a   Lang, Thomas ^a   Taudien, Stefan ^b   Burk, Oliver ^c   Wojnowski, Leszek ^a  

^a JOHANNES GUTENBERG UNIVERSITY   (Germany)

^b FRITZ LIPMANN INSTITUTE   (Germany)

^c UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

CAR; CYP3A; CYP3A4; CYP3A5; Induction; Phylogenetics; PXR,transcription; Variability

Indexed keywords

CYTOCHROME P450 3A4;

ARTICLE; GENE EXPRESSION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIMATE; PRIORITY JOURNAL; TRANSCRIPTION REGULATION;

BASE SEQUENCE; BINDING SITES; CYTOCHROME P-450 CYP3A; GENE EXPRESSION REGULATION, ENZYMOLOGIC; HUMANS; LIGANDS; LUCIFERASES, FIREFLY; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; RECEPTORS, CYTOPLASMIC AND NUCLEAR; RECEPTORS, STEROID; SEQUENCE ANALYSIS; TRANSFECTION; XENOBIOTICS;

EUTHERIA; PRIMATES;

EID: 76749152935     PISSN: 17446872     EISSN: 17446880     Source Type: Journal    
DOI: 10.1097/FPC.0b013e328336bbeb     Document Type: Article

References (41)

1. Nelson DR, Zeldin DC, Hoffman SM, Maltais LJ, Wain HM, Nebert DW. Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants. Pharmacogenetics 2004; 14:1-18.
2. Wilkinson GR. Drug metabolism and variability among patients in drug response. N Engl J Med 2005; 352:2211-2221.
3. Schirmer M, Toliat MR, Haberl M, Suk A, Kamdem LK, Klein K, et al. Genetic signature consistent with selection against the CYP3A4*1B allele in non-African populations. Pharmacogenet Genomics 2006; 16:59-71.
4. Ozdemir V, Kalow W, Tang BK, Paterson AD, Walker SE, Endrenyi L, et al. Evaluation of the genetic component of variability in CYP3A4 activity: a repeated drug administration method. Pharmacogenetics 2000; 10:373-388.
5. Wojnowski L, Kamdem LK. Clinical implications of CYP3A polymorphisms. Expert Opin Drug Metab Toxicol 2006; 2:171-182.
6. Schirmer M, Rosenberger A, Klein K, Kulle B, Toliat MR, Nurnberg P, et al. Sex-dependent genetic markers of CYP3A4 expression and activity in human liver microsomes. Pharmacogenomics 2007; 8:443-453.
7. Lamba JK, Lin YS, Schuetz EG, Thummel KE. Genetic contribution to variable human CYP3-Amediated metabolism. Adv Drug Deliv Rev 2002; 54:1271-1294.
8. Thompson EE, Kuttab-Boulos H, Witonsky D, Yang L, Roe BA, Di Rienzo A. CYP3A variation and the evolution of salt-sensitivity variants. Am J Hum Genet 2004; 75:1059-1069.
9. Backman JT, Kivisto KT, Olkkola KT, Neuvonen PJ. The area under the plasma concentration-time curve for oral midazolam is 400-fold larger during treatment with itraconazole than with rifampicin. Eur J Clin Pharmacol 1998; 54:53-58.
10. Burk O, Wojnowski L. Cytochrome P450 3A and their regulation. Naunyn Schmiedebergs Arch Pharmacol 2004; 369:105-124.
11. Timsit YE, Negishi M. CAR and PXR: the xenobiotic-sensing receptors. Steroids 2007; 72:231-246.
12. Koch I, Weil R, Wolbold R, Brockmoller J, Hustert E, Burk O, et al. Interindividual variability and tissue-specificity in the expression of cytochrome P450 3A mRNA. Drug Metab Dispos 2002; 30:1108-1114.
13. Kuehl P, Zhang J, Lin Y, Lamba J, Assem M, Schuetz J, et al. Sequence diversity in CYP3A promoters and characterization of the genetic basis of polymorphic CYP3A5 expression. Nat Genet 2001; 27:383-391.
14. Hustert E, Haberl M, Burk O, Wolbold R, He YQ, Klein K, et al. The genetic determinants of the CYP3A5 polymorphism. Pharmacogenetics 2001; 11:773-779.
15. Burk O, Tegude H, Koch I, Hustert E, Wolbold R, Glaeser H, et al. Molecular mechanisms of polymorphic CYP3A7 expression in adult human liver and intestine. J Biol Chem 2002; 277:24280-24288.
16. Burk O, Koch I, Raucy J, Hustert E, Eichelbaum M, Brockmoller J, et al. The induction of cytochrome P450 3A5 (CYP3A5) in the human liver and intestine is mediated by the xenobiotic sensors pregnane X receptor (PXR) and constitutively activated receptor (CAR). J Biol Chem 2004; 279:38379-38385.
17. Liu FJ, Song X, Yang D, Deng R, Yan B. The far and distal enhancers in the CYP3A4 gene coordinate the proximal promoter in responding similarly to the pregnane X receptor but differentially to hepatocyte nuclear factor-4alpha. Biochem J 2008; 409:243-250.
18. Frank C, Gonzalez MM, Oinonen C, Dunlop TW, Carlberg C. Characterization of DNA complexes formed by the nuclear receptor constitutive androstane receptor. J Biol Chem 2003; 278:43299-43310.
19. Frank C, Makkonen H, Dunlop TW, Matilainen M, Vaisanen S, Carlberg C. Identification of pregnane X receptor binding sites in the regulatory regions of genes involved in bile acid homeostasis. J Mol Biol 2005; 346:505-519.
20. Qiu H, Taudien S, Herlyn H, Schmitz J, Zhou Y, Chen G, et al. CYP3 phylogenomics: evidence for positive selection of CYP3A4 and CYP3A7. Pharmacogenet Genomics 2008; 18:53-66.
21. Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. Multiple sequence alignment with Clustal X. Trends Biochem Sci 1998; 23:403-405.
22. Eddy SR. Profile hidden Markov models. Bioinformatics 1998; 14:755-763.
23. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, et al. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 2003; 13:721-731.
24. Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, et al. VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 2000; 16:1046-1047.
25. Sandelin A, Wasserman WW. Prediction of nuclear hormone receptor response elements. Mol Endocrinol 2005; 19:595-606.
26. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 2002; 12:1611-1618.
27. Tegude H, Schnabel A, Zanger UM, Klein K, Eichelbaum M, Burk O. Molecular mechanism of basal CYP3A4 regulation by hepatocyte nuclear factor 4alpha: evidence for direct regulation in the intestine. Drug Metab Dispos 2007; 35:946-954.
28. Gellner K, Eiselt R, Hustert E, Arnold H, Koch I, Haberl M, et al. Genomic organization of the human CYP3A locus: identification of a new, inducible CYP3A gene. Pharmacogenetics 2001; 11:111-121.
29. Tom BH, Rutzky LP, Jakstys MM, Oyasu R, Kaye CI, Kahan BD. Human colonic adenocarcinoma cells. I. Establishment and description of a new line. In Vitro 1976; 12:180-191.
30. Geick A, Eichelbaum M, Burk O. Nuclear receptor response elements mediate induction of intestinal MDR1 by rifampin. J Biol Chem 2001; 276:14581-14587.
31. Miao J, Fang S, Bae Y, Kemper JK. Functional inhibitory cross-talk between constitutive androstane receptor and hepatic nuclear factor-4 in hepatic lipid/glucose metabolism is mediated by competition for binding to the DR1 motif and to the common coactivators, GRIP-1 and PGC1alpha. J Biol Chem 2006; 281:14537-14546.
32. Goodwin B, Hodgson E, Liddle C. The orphan human pregnane X receptor mediates the transcriptional activation of CYP3A4 by rifampicin through a distal enhancer module. Mol Pharmacol 1999; 56:1329-1339.
33. Baes M, Gulick T, Choi HS, Martinoli MG, Simha D, Moore DD. A new orphan member of the nuclear hormone receptor superfamily that interacts with a subset of retinoic acid response elements. Mol Cell Biol 1994; 14:1544-1552.
34. Kast HR, Goodwin B, Tarr PT, Jones SA, Anisfeld AM, Stoltz CM, et al. Regulation of multidrug resistance-associated protein 2 (ABCC2) by the nuclear receptors pregnane X receptor, farnesoid X-activated receptor, and constitutive androstane receptor. J Biol Chem 2002; 277:2908-2915.
35. Harmsen S, Koster AS, Beijnen JH, Schellens JH, Meijerman I. Comparison of two immortalized human cell lines to study nuclear receptor-mediated CYP3A4 induction. Drug Metab Dispos 2008; 36:1166-1171.
36. Hay CW, Docherty K. Comparative analysis of insulin gene promoters: implications for diabetes research. Diabetes 2006; 55:3201-3213.
37. Matsumura K, Saito T, Takahashi Y, Ozeki T, Kiyotani K, Fujieda M, et al. Identification of a novel polymorphic enhancer of the human CYP3A4 gene. Mol Pharmacol 2004; 65:326-334.
38. Daly AK. Significance of the minor cytochrome P450 3A isoforms. Clin Pharmacokinet 2006; 45:13-31.
39. Williams ET, Schouest KR, Leyk M, Strobel HW. The chimpanzee cytochrome P450 3A subfamily: is our closest related species really that similar? Comp Biochem Physiol D Genom Proteom 2007; 2:91-100.
40. Williams JA, Ring BJ, Cantrell VE, Jones DR, Eckstein J, Ruterbories K, et al. Comparative metabolic capabilities of CYP3A4, CYP3A5, and CYP3A7. Drug Metab Dispos 2002; 30:883-891.
41. Kuppens IE, Breedveld P, Beijnen JH, Schellens JH. Modulation of oral drug bioavailability: from preclinical mechanism to therapeutic application. Cancer Invest 2005; 23:443-464.