Received for publication May 11, 2007.
Revised October 4, 2007.
Accepted for publication October 5, 2007.

Novel SNPs in the Promoter and Intron 1 of Human PXR/NR1I2 and Their Association with CYP3A4 Expression

Abstract

The hypothesis was tested that sequence diversity in PXR cis-regulatory regions are significant determinants of variation in inducible and constitutive CYP3A4 expression. A combination of comparative genomics and computational algorithms were used to select regions of the human PXR promoter and intron 1 that were resequenced in the polymorphism discovery resource 24 DNA subset. PXR SNPs were then genotyped in donor human livers phenotyped for CYP3A4 and MDR1 mRNAs and primary human hepatocytes phenotyped for basal and rifampin inducible CYP3A4 activity. The human PXR promoter (16.9 kb) was significantly larger than in rodents (2.9 kb). Eighty-nine SNPs were identified in the promoter and intron 1 of PXR. The SNPs most consistently associated with CYP3A4 phenotypic measures were a 44477T>C (-1359) promoter SNP (in LD with SNP 463170, a 6 bp deletion in intron 1a, and SNP 46551, a C nucleotide insertion in intron 1b); SNP 63396C>T in intron 1 (in LD with SNPs 63704A>G, 63813(CAAA)(CA) variable repeat, and 65104T>C); and SNPs 56348C>A; 69789A>G and 66034T>C. Donor livers with the variant PXR alleles had altered hepatic expression of PXR targets compared to livers with PXR wild-type alleles. These results identified PXR promoter and intron 1 SNPs associated with PXR target gene expression (CYP3A4) in donor livers and cultured hepatocytes and that a striking number of the linked intron1 SNPs will affect putative binding sites for hepatic HNF3beta (FOXA2), a transcription factor linked with PXR expression.

Key words: CYP3A, p-glycoprotein, pharmacogenetics, PXR, SXR