Transcription factors of the Nuclear Factor I (NFI) family control hepatocyte differentiation and cytochrome P450 activity in human liver

Interindividual variability in hepatic drug metabolism and transport is well-known, and genetic variation in pharmacogenes impacts the efficacy and safety of drug treatments. Recent reports have indicated that the minor allele of the nuclear transcription factor I/B (NFIB), rs28379954 T > C, affects the metabolism of risperidone and clozapine, which are mediated by CYP2D6 and CYP1A2, respectively. First, we reanalyzed the association between rs28379954 T > C and CYP2D6 activity in three independent cohorts exposed to CYP2D6 substrates (propafenone, tamoxifen, and sparteine) which revealed no association. Next, to investigate the effects of all four NFIs expressed in human livers more broadly, 150 well-characterized hepatic tissue samples, along with data on expression quantitative trait loci (eQTL) and genome-wide association (GWA), were used. NFI expression levels significantly correlated with the mRNA and/or protein expression of multiple CYP genes (e.g. CYP1A1, CYP1A2, CYP2A6, CYP2C8, CYP2C19) which was confirmed for NFIA with the metabolism of CYP2C19, CYP1A2, and CYP2A6 probe substrates. While non-genetic factors (e.g. age, inflammation) also control NFI expression, genetic polymorphisms did not reach genome-wide significance. To validate the identified associations, siRNA-mediated knockdowns were used in primary human hepatocytes, followed by RNA sequencing and evaluation of differentially regulated pathways. We identified significant downregulation of several metabolic pathways related to hepatic functionality, PPAR signaling, and drug metabolism for NFIB, NFIC, and NFIX, whereas pathways associated with cancer biology were significantly induced. In summary our findings provide further insight into hepatic CYP regulation via the NFI network with implications for the understanding of interindividual variability of drug metabolism.