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The human pregnane X receptor: genomic structure and identification and functional characterization of natural allelic variants

Zhang, Jionga,b*; Kuehl, Petera,c*; Green, Eric D.d,e; Touchman, Jeffery W.e; Watkins, Paul B.f; Daly, Anng; Hall, Stephen D.h; Maurel, Patricki; Relling, Maryj; Brimer, Cynthiaj; Yasuda, Kazutoj; Wrighton, Steven A.k; Hancock, Michaelj; Kim, Richard B.l; Strom, Stephenm; Thummel, Kennethn; Russell, Christopher G.o; Hudson, James R. Jro; Schuetz, Erin G.j; Boguski, Mark S.a

Pharmacogenetics and Genomics: October 2001 - Volume 11 - Issue 7 - p 555-572
Original Article

The pregnane X receptor (PXR)/steroid and xenobiotic receptor (SXR) transcriptionally activates cytochrome P4503A4 (CYP3A4) when ligand activated by endobiotics and xenobiotics. We cloned the human PXR gene and analysed the sequence in DNAs of individuals whose CYP3A phenotype was known. The PXR gene spans 35 kb, contains nine exons, and mapped to chromosome 13q11–13. Thirty-eight single nucleotide polymorphisms (SNPs) were identified including six SNPs in the coding region. Three of the coding SNPs are non-synonymous creating new PXR alleles [PXR*2, P27S (79C to T);PXR*3, G36R (106G to A); and PXR*4, R122Q (4321G to A)]. The frequency of PXR*2 was 0.20 in African Americans and was never found in Caucasians. Hepatic expression of CYP3A4 protein was not significantly different between African Americans homozygous for PXR*1 compared to those with one PXR*2 allele. PXR*4 was a rare variant found in only one Caucasian person. Homology modelling suggested that R122Q, (PXR*4) is a direct DNA contact site variation in the third alpha-helix in the DNA binding domain. Compared with PXR*1, and variants PXR*2 and PXR*3, only the variant PXR*4 protein had significantly decreased affinity for the PXR binding sequence in electromobility shift assays and attenuated ligand activation of the CYP3A4 reporter plasmids in transient transfection assays. However, the person heterozygous for PXR*4 is normal for CYP3A4 metabolism phenotype. The relevance of each of the 38 PXR SNPs identified in DNA of individuals whose CYP3A basal and rifampin-inducible CYP3A4 expression was determined in vivo and/or in vitro was demonstrated by univariate statistical analysis. Because ligand activation of PXR and upregulation of a system of drug detoxification genes are major determinants of drug interactions, it will now be useful to extend this work to determine the association of these common PXR SNPs to human variation in induction of other drug detoxification gene targets.

aNational Center for Biotechnology Information, National Institute of Health, Bethesda, MD, USA, bMcKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University, Baltimore, MD, USA, cDepartment of Molecular and Cell Biology, University of Maryland at Baltimore, Baltimore, MD, USA, dGenome Technology Branch, National Human Genome Research Institute, Bethesda, MD, USA, eNIH Intramural Sequencing Center, Bethesda, MD, USA, fUniversity of North Carolina, Chapel Hill, NC, USA, gDepartment of Pharmacological Sciences, University of Newcastle Upon Tyne, Newcastle, UK, hDepartment of Clinical Pharmacology, Indiana University, Indianapolis, IN, USA, iINSERM, Montpellier, France, jDepartment of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA, kDepartment of Drug Metabolism, Eli Lilly & Co., Indianapolis, IN, USA, lDepartment of Clinical Pharmacology, Vanderbilt University, Nashville, TN, USA, mDepartment of Pathology, University of Pittsburgh, Pittsburgh, PA, USA nDepartment of Pharmaceutics, University of Washington, Seattle, WA, USA and oResearch Genetics, Huntsville, AL, USA

Received 24 April 2001; accepted 21 May 2001

*These authors contributed equally to this work

Correspondence to Dr Mark Boguski, Rosetta Inpharmatics, Inc. 1304011 5th Avenue NE, Kirkland, WA 98034, USA Tel: +1 425 636 6347; fax: +1 425 562 0788; e-mail:

© 2001 Lippincott Williams & Wilkins, Inc.