Identification of polymorphisms in the 3′-untranslated region of the human pregnane X receptor (PXR) gene associated with variability in cytochrome P450 3A (CYP3A) metabolism

Abstract

1. Single nucleotide polymorphisms in the 3′-untranslated region (3′UTR) of the human pregnane X receptor (PXR) gene might contribute to interindividual variability in cytochrome P450 3A (CYP3A) activity.

2. Genotype–phenotype associations involving PXR-3′UTR single nucleotide polymorphisms were investigated through in vitro (53 human livers from primarily White donors) and in vivo (26 mainly White or African-American volunteers) studies using midazolam 1′-hydroxylation and midazolam apparent oral clearance (CL/F), respectively, as CYP3A-specific probes.

3. PXR-3′UTR resequencing identified twelve single nucleotide polymorphisms, including two that were novel. Although none of the single nucleotide polymorphisms evaluated were associated with altered midazolam 1′-hydroxylation in the liver bank, both rs3732359 homozygotes and rs3732360 carriers showed 80% higher (p < 0.05) CL/F compared with homozygous reference individuals. These differences in CL/F were even larger (100% and 120% higher, respectively; p < 0.01) when only African-American subjects (n = 14) were considered.

4. Five major haplotypes were identified containing the PXR-3′UTR single nucleotide polymorphisms and previously identified intron single nucleotide polymorphisms. Although CL/F differences were not statistically significant within the entire study cohort, African-American carriers of Haplotype-1 (which includes both rs3732359 and rs3732360 variants) exhibited 70% higher median CL/F compared with African-American non-carriers (p = 0.036).

5. The results identify rs3732359 and rs3732360 as PXR-3′UTR single nucleotide polymorphisms associated with higher CYP3A activity in vivo in African-Americans.

Keywords::

• Pregnane X receptor (PXR)
• single nucleotide polymorphism (SNP)
• 3′-untranslated region (UTR)
• haplotype
• cytochrome P450 (CYP) 3A (CYP3A)

Acknowledgements

This article was made possible by Grant Number F31-DA023861 from the National Institute on Drug Abuse (NIDA), National Institutes of Health, Bethesda, MD, USA, to L.O. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIDA, or the National Institutes of Health. Other support was provided by National Institutes of Health (Bethesda, MD) Grant Number R01-GM061834 to M.H.C and Grant Numbers R01-AG17880, R01-GM061834, and R01-AI58784 to D.J.G. The authors also acknowledge the contributions of Dr Ping He who generated some of the published data (including MDZ CL/F and liver bank 1′-OH-MDZ formation rates) used in this study.

Appendix

Table A1.  Oligonucleotide primer sets and real-time PCR probe used in this study.

Table A2.  Analysis of the effects of PXR-3′UTR genotype on MDZ-1′OH rates (nmole min⁻¹ mg⁻¹ protein) measured in human livers from 53 primarily white donors. A similar analysis in 47 livers identified as being from only white donors also failed to reveal any significant association (data not shown).

Table A3.  Analysis of effect of PXR-3′UTR haplotype on MDZ-1′OH rates (nmole min⁻¹ mg⁻¹ protein) in 53 human livers.