ABSTRACT:Identification of genetic variation predictive of clearance rate of a wide variety of prescription drugs could lead to cost-effective personalized medicine. Here we identify regulatory genes whose variable expression level among individuals may have widespread effects upon clearance rate of a variety of drugs. Twenty liver samples with variable CYP3A activity were profiled for expression level and activity of xenobiotic metabolism genes as well as genes involved in the regulation thereof. Regulatory genes whose expression level accounted for the highest degree of collinearity among expression levels of xenobiotic metabolism genes were identified as possible master regulators of drug clearance rate. Significant linear correlations (p < 0.05) were identified among mRNA levels of CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, MRP2, OATP2, P450 oxidoreductase (POR), and UDP-glucuronosyltranferase 1A1, suggesting that these xenobiotic metabolism genes are coregulated at the transcriptional level. Using partial regression analysis, constitutive androstane receptor (CAR) and hepatic nuclear factor 4␣ (HNF4␣) were identified as the nuclear receptors whose expression levels are most strongly associated with expression of coregulated xenobiotic metabolism genes. POR expression level, which is also associated with CAR and HNF4␣ expression level, was found to be strongly associated with the activity of many cytochromes P450. Thus, interindividual variation in the expression level of CAR, HNF4␣, and POR probably determines variation in expression and activity of a broad scope of xenobiotic metabolism genes and, accordingly, clearance rate of a variety of xenobiotics. Identification of polymorphisms in these candidate master regulator genes that account for their variable expression among individuals may yield readily detectable biomarkers that could serve as predictors of xenobiotic clearance rate.Interindividual variation in drug clearance rate is often responsible for toxicity or inefficacy of prescription drugs. Systemic drug clearance rate is determined by hepatic expression and activity of phase I oxidative cytochromes P450 (P450s), phase II conjugative enzymes, and transporter proteins. Expression of these metabolic enzymes is coordinately regulated by a network of transcription factors (Pascussi et al., 2004;Xu et al., 2005) exemplified in Fig. 1. The network is composed of ligand-activated nuclear receptors that recognize a variety of endogenous and xenobiotic compounds to activate transcription of metabolic enzymes involved in biotransformation and transport. Multiple nuclear receptors can recognize response elements of the same target gene (Fig. 1) and may control their own expression as well as the expression of other nuclear receptors in the pathway (Maglich et al., 2002;Pascussi et al., 2004). In addition, these regulatory proteins share a common pool of coregulators and the common heterodimeric partner, the retinoid X receptor (RXR).The role of xenobiotic metabolism gene polymorphisms in determining clearanc...