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

Abstract

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.

Associations of ABCB1, NFKB1, CYP3A, and NR1I2 polymorphisms with cyclosporine trough concentrations in Chinese renal transplant recipients

“…Although they were reported to be functional in previous studies, none of the NR1I2 SNPs were found to be correlated with CsA concentrations in our study [5,6,8] . However, most of these studies were in vitro, without the consideration of many possible influences caused by other factors in vivo.…”

“…The NFKB1 -94ins/del ATTG polymorphism was detected by TaqMan ® SNP Genotyping Assay. Polymorphisms of NR1I2, including T25385C, A24622T, C24446A, G24113A, C4356T, A601G, G7635A, A11156C, and C6994T, were genotyped by direct sequencing [5][6][7][8] .…”

“…Factors affecting the expression or function of PXR, such as single nucleotide polymorphisms (SNPs), may influence the expression of downstream target genes. T25385C, G24113A, C6994T, C4356T, and G7635A have been reported to be associated with CYP3A4 phenotype, activity and content, whereas A11156C has been associated with variable P-gp levels [5][6][7] . A24622T and C24446A in exon1 have been found to be associated with PXR levels in previous studies from our laboratory [8] , suggesting that these two SNPs may also be correlated with the expression of CYP3A4, CYP3A5, or ABCB1.…”

Pharmacogenomics and personalized medicine: a review focused on their application in the Chinese population

“…The pregnane X receptor (PXR, encoded by NR1I2) is reported to be the key nuclear receptor regulating the expression of CYP3A4, CYP3A5, and ABCB1 [29] . Several PXR SNPs have been reported to be associated with the CYP3A4 or P-gp/MDR1 expression level or activity in vitro [29][30][31] . Differences in the distribution of PXR SNPs were found when comparing the Han Chinese of South China and Caucasian Americans [31] .…”

Genotyping of the PXR A11156C polymorphism with locked nucleic acid containing fluorogenic probes

“…Hence, knowledge with regard to known PXR polymorphisms, which influence the expression of MDR1 and/or CYP3A4, is therefore relevant to understand the interindividual responses towards drugs. [3][4][5] One of the putative relevant polymorphisms is PXR A11156C, because it has been shown that the presence of the 11156C allele is associated with a decreased expression of MDR1-mRNA in intestinal villi cells derived from gut biopsies. 4 In order to determine the genotype of the PXR A11156C polymorphism, we developed a real-time PCR fluorescence resonance energy transfer (FRET) assay.…”