Isoform-level expression of the constitutive androstane receptor (CAR or NR1I3) transcription factor better predicts the mRNA expression of the cytochrome P450s in human liver samples.

Many factors cause interperson variability in the activity and expression of the cytochrome P450 (CYP) drug-metabolizing enzymes in the liver, leading to variable drug exposure and treatment outcomes. Several liver-enriched transcription factors are associated with CYP expression, with estrogen receptor α (ESR1) and constitutive androstane receptor (CAR or NR1I3) being the 2 top factors. ESR1 and NR1I3 undergo extensive alternative splicing that results in numerous splice isoforms, but how these splice isoforms associate with CYP expression is unknown. Here, we quantified 18 NR1I3 splice isoforms and the 3 most abundant ESR1 isoforms in 260 liver samples derived from African Americans (n = 125) and European Americans (n = 135). Our results showed variable splice isoform populations in the liver for both NR1I3 and ESR1. Multiple linear regression analyses revealed that compared with gene-level NR1I3, isoform-level NR1I3 expression better predicted the mRNA expression of most CYPs and 3 UDP-glucuronosyltransferases (UGTs), whereas ESR1 isoforms improved predictive models for the UGTs and CYP2D6 but not for most CYPs. Also, different NR1I3 isoforms were associated with different CYPs, and the associations varied depending on sample ancestry. Surprisingly, noncanonical NR1I3 isoforms having retained introns (introns 2 or 6) were abundantly expressed and associated with the expression of most CYPs and UGTs, whereas the reference isoform (NR1I3-205) was only associated with CYP2D6. Moreover, NR1I3 isoform diversity increased during the differentiation of induced pluripotent stem cells to hepatocytes, paralleling increasing CYP expression. These results suggest that isoform-level transcription factor expression may help to explain variation in CYP or UGT expression between individuals. SIGNIFICANCE STATEMENT: We quantified 18 NR1I3 splice isoforms and the 3 most abundant ESR1 splice isoforms in 260 liver samples derived from African American and European American donors and found variable NR1I3 and ESR1 splice isoform expression in the liver. Multiple linear regression analysis showed that, compared with gene-level expression, isoform-level expression of NR1I3 and ESR1 better predicted the mRNA expression of some cytochrome P450s and UDP-glucuronosyltransferases, highlighting the importance of isoform-level analyses to enhance our understanding of gene transcriptional regulatory networks controlling the expression of drug-metabolizing enzymes.