Abstract
The CYP3A locus encodes hepatic enzymes that metabolize many clinically used drugs. However, there is marked interindividual variability in enzyme expression and clearance of drugs metabolized by these enzymes. We utilized comparative genomics and computational prediction of transcriptional factor binding sites to evaluate regions within CYP3A that were most likely to contribute to this variation. We then used a haplotype tagging single-nucleotide polymorphisms (htSNPs) approach to evaluate the entire locus with the fewest number of maximally informative SNPs. We investigated the association between these htSNPs and in vivo CYP3A enzyme activity using a single-point IV midazolam clearance assay. We found associations between the midazolam phenotype and age, diagnosis of hypertension and one htSNP (141689) located upstream of CYP3A4. 141689 lies near the xenobiotic responsive enhancer module (XREM) regulatory region of CYP3A4. Cell-based studies show increased transcriptional activation with the minor allele at 141689, in agreement with the in vivo association study findings. This study marks the first systematic evaluation of coding and noncoding variation that may contribute to CYP3A phenotypic variability.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 6 print issues and online access
$259.00 per year
only $43.17 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Guengerich FP . Cytochrome P-450 3A4: regulation and role in drug metabolism. Annu Rev Pharmacol Toxicol 1999; 39: 1–17.
Wrighton SA, Stevens JC . The human hepatic cytochromes P450 involved in drug metabolism. Crit Rev Toxicol 1992; 22: 1–21.
Wrighton SA, Brian WR, Sari MA, Iwasaki M, Guengerich FP, Raucy JL et al. Studies on the expression and metabolic capabilities of human liver cytochrome P450IIIA5 (HLp3). Mol Pharmacol 1990; 38: 207–213.
Haehner BD, Gorski JC, Vandenbranden M, Wrighton SA, Janardan SK, Watkins PB et al. Bimodal distribution of renal cytochrome P450 3A activity in humans. Mol Pharmacol 1996; 50: 52–59.
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.
Westlind-Johnsson A, Malmebo S, Johansson A, Otter C, Andersson TB, Johansson I et al. Comparative analysis of CYP3A expression in human liver suggests only a minor role for CYP3A5 in drug metabolism. Drug Metab Dispos 2003; 31: 755–761.
Shimada T, Yamazaki H, Mimura M, Inui Y, Guengerich FP . Interindividual variations in human liver cytochrome P-450 enzymes involved in the oxidation of drugs, carcinogens and toxic chemicals: studies with liver microsomes of 30 Japanese and 30 Caucasians. J Pharmacol Exp Ther 1994; 270: 414–423.
Westlind A, Lofberg L, Tindberg N, Andersson TB, Ingelman-Sundberg M . Interindividual differences in hepatic expression of CYP3A4: relationship to genetic polymorphism in the 5′-upstream regulatory region. Biochem Biophys Res Commun 1999; 259: 201–205.
Lin YS, Dowling AL, Quigley SD, Farin FM, Zhang J, Lamba J et al. Co-regulation of CYP3A4 and CYP3A5 and contribution to hepatic and intestinal midazolam metabolism. Mol Pharmacol 2002; 62: 162–172.
Schellens JH, Soons PA, Breimer DD . Lack of bimodality in nifedipine plasma kinetics in a large population of healthy subjects. Biochem Pharmacol 1988; 37: 2507–2510.
Wilkinson GR . Cytochrome P4503A (CYP3A) metabolism: prediction of in vivo activity in humans. J Pharmacokinet Biopharm 1996; 24: 475–490.
Ozdemir V, Kalowa 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.
Chung E, Nafziger AN, Kazierad DJ, Bertino Jr JS . Comparison of midazolam and simvastatin as cytochrome P450 3A probes. Clin Pharmacol Ther 2006; 79: 350–361.
Prueksaritanont T, Vega JM, Rogers JD, Gagliano K, Greenberg HE, Gillen L et al. Simvastatin does not affect CYP3A activity, quantified by the erythromycin breath test and oral midazolam pharmacokinetics, in healthy male subjects. J Clin Pharmacol 2000; 40: 1274–1279.
Thompson EE, Kuttab-Boulos H, Yang L, Roe BA, Di Rienzo A . Sequence diversity and haplotype structure at the human CYP3A cluster. Pharmacogenomics J 2006; 6: 105–114.
Krupka E, Venisse N, Lafay C, Gendre D, Diquet B, Bouquet S et al. Probe of CYP3A by a single-point blood measurement after oral administration of midazolam in healthy elderly volunteers. Eur J Clin Pharmacol 2006; 62: 653–659.
Lepper ER, Baker SD, Permenter M, Ries N, van Schaik RH, Schenk PW et al. Effect of common CYP3A4 and CYP3A5 variants on the pharmacokinetics of the cytochrome P450 3A phenotyping probe midazolam in cancer patients. Clin Cancer Res 2005; 11: 7398–7404.
Chaobal HN, Kharasch ED . Single-point sampling for assessment of constitutive, induced, and inhibited cytochrome P450 3A activity with alfentanil or midazolam. Clin Pharmacol Ther 2005; 78: 529–539.
Thummel KE, Shen DD, Podoll TD, Kunze KL, Trager WF, Bacchi CE et al. Use of midazolam as a human cytochrome P450 3A probe: II. Characterization of inter- and intraindividual hepatic CYP3A variability after liver transplantation. J Pharmacol Exp Ther 1994; 271: 557–566.
Carrillo JA, Ramos SI, Agundez JA, Martinez C, Benitez J . Analysis of midazolam and metabolites in plasma by high-performance liquid chromatography: probe of CYP3A. Ther Drug Monit 1998; 20: 319–324.
Fellay J, Marzolini C, Decosterd L, Golay KP, Baumann P, Buclin T et al. Variations of CYP3A activity induced by antiretroviral treatment in HIV-1 infected patients. Eur J Clin Pharmacol 2005; 60: 865–873.
Gurley BJ, Gardner SF, Hubbard MA, Williams DK, Gentry WB, Khan IA et al. In vivo effects of goldenseal, kava kava, black cohosh, and valerian on human cytochrome P450 1A2, 2D6, 2E1, and 3A4/5 phenotypes. Clin Pharmacol Ther 2005; 77: 415–426.
Eap CB, Fellay J, Buclin T, Bleiber G, Golay KP, Brocard M et al. CYP3A activity measured by the midazolam test is not related to 3435 C >T polymorphism in the multiple drug resistance transporter gene. Pharmacogenetics 2004; 14: 255–260.
Huang P, Zhu B, Wang LS, Ouyang DS, Huang SL, Chen XP et al. Relationship between CYP3A activity and breast cancer susceptibility in Chinese Han women. Eur J Clin Pharmacol 2003; 59: 471–476.
Zhu B, Liu ZQ, Chen GL, Chen XP, Ou-Yang DS, Wang LS et al. The distribution and gender difference of CYP3A activity in Chinese subjects. Br J Clin Pharmacol 2003; 55: 264–269.
Villeneuve JP, L’Ecuyer L, De Maeght S, Bannon P . Prediction of cyclosporine clearance in liver transplant recipients by the use of midazolam as a cytochrome P450 3A probe. Clin Pharmacol Ther 2000; 67: 242–248.
Zeigler-Johnson C, Friebel T, Walker AH, Wang Y, Spangler E, Panossian S et al. CYP3A4, CYP3A5, and CYP3A43 genotypes and haplotypes in the etiology and severity of prostate cancer. Cancer Res 2004; 64: 8461–8467.
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.
Goodwin B, Hodgson E, D’Costa DJ, Robertson GR, Liddle C . Transcriptional regulation of the human CYP3A4 gene by the constitutive androstane receptor. Mol Pharmacol 2002; 62: 359–365.
Xie W, Barwick JL, Simon CM, Pierce AM, Safe S, Blumberg B et al. Reciprocal activation of xenobiotic response genes by nuclear receptors SXR/PXR and CAR. Genes Dev 2000; 14: 3014–3023.
Lehmann JM, McKee DD, Watson MA, Willson TM, Moore JT, Kliewer SA . The human orphan nuclear receptor PXR is activated by compounds that regulate CYP3A4 gene expression and cause drug interactions. J Clin Invest 1998; 102: 1016–1023.
Bertilsson G, Heidrich J, Svensson K, Asman M, Jendeberg L, Sydow-Backman M et al. Identification of a human nuclear receptor defines a new signaling pathway for CYP3A induction. Proc Natl Acad Sci USA 1998; 95: 12208–12213.
Thummel KE, Brimer C, Yasuda K, Thottassery J, Senn T, Lin Y et al. Transcriptional control of intestinal cytochrome P-4503A by 1alpha,25-dihydroxy vitamin D3. Mol Pharmacol 2001; 60: 1399–1406.
Pascussi JM, Drocourt L, Gerbal-Chaloin S, Fabre JM, Maurel P, Vilarem MJ . Dual effect of dexamethasone on CYP3A4 gene expression in human hepatocytes. Sequential role of glucocorticoid receptor and pregnane X receptor. Eur J Biochem 2001; 268: 6346–6358.
Cai Y, Konishi T, Han G, Campwala KH, French SW, Wan YJ . The role of hepatocyte RXR alpha in xenobiotic-sensing nuclear receptor-mediated pathways. Eur J Pharm Sci 2002; 15: 89–96.
Lee SS, Pineau T, Drago J, Lee EJ, Owens JW, Kroetz DL et al. Targeted disruption of the alpha isoform of the peroxisome proliferator-activated receptor gene in mice results in abolishment of the pleiotropic effects of peroxisome proliferators. Mol Cell Biol 1995; 15: 3012–3022.
Johnson EF, Hsu MH, Savas U, Griffin KJ . Regulation of P450 4A expression by peroxisome proliferator activated receptors. Toxicology 2002; 181–182: 203–206.
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.
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.
Wang JC, Stafford JM, Scott DK, Sutherland C, Granner DK . The molecular physiology of hepatic nuclear factor 3 in the regulation of gluconeogenesis. J Biol Chem 2000; 275: 14717–14721.
Bombail V, Taylor K, Gibson GG, Plant N . Role of Sp1, C/EBP alpha, HNF3, and PXR in the basal- and xenobiotic-mediated regulation of the CYP3A4 gene. Drug Metab Dispos 2004; 32: 525–535.
Lamba JK, Lin YS, Thummel K, Daly A, Watkins PB, Strom S et al. Common allelic variants of cytochrome P4503A4 and their prevalence in different populations. Pharmacogenetics 2002; 12: 121–132.
Roy JN, Lajoie J, Zijenah LS, Barama A, Poirier C, Ward BJ et al. CYP3A5 genetic polymorphisms in different ethnic populations. Drug Metab Dispos 2005; 33: 884–887.
Yamaori S, Yamazaki H, Iwano S, Kiyotani K, Matsumura K, Honda G et al. CYP3A5 Contributes significantly to CYP3A-mediated drug oxidations in liver microsomes from Japanese subjects. Drug Metab Pharmacokinet 2004; 19: 120–129.
Shih PS, Huang JD . Pharmacokinetics of midazolam and 1′-hydroxymidazolam in Chinese with different CYP3A5 genotypes. Drug Metab Dispos 2002; 30: 1491–1496.
Floyd MD, Gervasini G, Masica AL, Mayo G, George Jr AL, Bhat K et al. Genotype-phenotype associations for common CYP3A4 and CYP3A5 variants in the basal and induced metabolism of midazolam in European- and African-American men and women. Pharmacogenetics 2003; 13: 595–606.
He P, Court MH, Greenblatt DJ, Von Moltke LL . Genotype-phenotype associations of cytochrome P450 3A4 and 3A5 polymorphism with midazolam clearance in vivo. Clin Pharmacol Ther 2005; 77: 373–387.
Kharasch ED . Every breath you take, we’ll be watching you. Anesthesiology 2007; 106: 652–654.
Thummel KE . Does the CYP3A5*3 polymorphism affect in vivo drug elimination? Pharmacogenetics 2003; 13: 585–587.
Givens RC, Lin YS, Dowling AL, Thummel KE, Lamba JK, Schuetz EG et al. CYP3A5 genotype predicts renal CYP3A activity and blood pressure in healthy adults. J Appl Physiol 2003; 95: 1297–1300.
Ho H, Pinto A, Hall SD, Flockhart DA, Li L, Skaar TC et al. Association between the CYP3A5 genotype and blood pressure. Hypertension 2005; 45: 294–298.
Bochud M, Eap CB, Elston RC, Bovet P, Maillard M, Schild L et al. Association of CYP3A5 genotypes with blood pressure and renal function in African families. J Hypertens 2006; 24: 923–929.
Young JH, Chang YP, Kim JD, Chretien JP, Klag MJ, Levine MA et al. Differential susceptibility to hypertension is due to selection during the out-of-Africa expansion. PLoS Genet 2005; 1: e82.
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.
Maruyama M, Matsunaga T, Harada E, Ohmori S . Comparison of basal gene expression and induction of CYP3As in HepG2 and human fetal liver cells. Biol Pharm Bull 2007; 30: 2091–2097.
Frerichs VA, Zaranek C, Haas CE . Analysis of omeprazole, midazolam and hydroxy-metabolites in plasma using liquid chromatography coupled to tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 824: 71–80.
Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA . Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 2004; 74: 106–120.
Eap CB, Bochud M, Elston RC, Bovet P, Maillard MP, Nussberger J et al. CYP3A5 and ABCB1 genes influence blood pressure and response to treatment, and their effect is modified by salt. Hypertension 2007; 49: 1007–1014.
Stephens M, Smith NJ, Donnelly P . A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001; 68: 978–989.
Kel AE, Gossling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E . MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 2003; 31: 3576–3579.
Acknowledgements
This work was made possible with the assistance in statistical and computational analysis by David Witonski and Cheryl Roe, LC/MS/MS assistance by Larry House, and genotyping via dHPLC by Pei Xian Chen. Special thanks go to Dr Emma Thompson for her instruction in population genetics and enlightening conversations and theories. This study was supported by NIH grants GM60346, GM61393 and GM07019.
Author information
Authors and Affiliations
Corresponding author
Additional information
Supplementary Information accompanies the paper on the The Pharmacogenomics Journal website (http://www.nature.com/tpj)
Supplementary information
Rights and permissions
About this article
Cite this article
Perera, M., Thirumaran, R., Cox, N. et al. Prediction of CYP3A4 enzyme activity using haplotype tag SNPs in African Americans. Pharmacogenomics J 9, 49–60 (2009). https://doi.org/10.1038/tpj.2008.13
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/tpj.2008.13
Keywords
This article is cited by
-
Rate of onset of inhibition of gut-wall and hepatic CYP3A by clarithromycin
European Journal of Clinical Pharmacology (2013)
-
PPARA: A Novel Genetic Determinant of CYP3A4 In Vitro and In Vivo
Clinical Pharmacology & Therapeutics (2012)
-
Intronic polymorphism in CYP3A4 affects hepatic expression and response to statin drugs
The Pharmacogenomics Journal (2011)
-
The Missing Association: Sequencing-Based Discovery of Novel SNPs in VKORC1 and CYP2C9 That Affect Warfarin Dose in African Americans
Clinical Pharmacology & Therapeutics (2011)