Precision Approaches for Assessing Complex Pharmacogenomic Traits in Vitamin K Metabolism

Abstract

The term “gene-environment interaction” accounts for various ways in which the effects of environmental exposures can be modified by our genetic variation. Of particular interest for this dissertation is the CYP4F2*3 coding variant, which has been shown to decrease vitamin K (VK) metabolic clearance in vitro and is associated with altered pharmacodynamic effects of coumarin based anticoagulant drugs (e.g., Warfarin) in vivo. On average, CYP4F2*3 carriers receiving coumarin-based anticoagulation therapy require higher doses to achieve a therapeutic INR. It is thought that increased hepatic VK levels caused by reduced VK metabolic clearance in CYP4F2*3 carriers antagonizes the effect of warfarin, explaining in part the wide range in warfarin dose requirements across the population. However, metabolic contributions from CYP4F11 toward VK metabolism and complex linkage disequilibrium (LD) patterns across the CYP4F gene loci make it challenging to quantify the true effect size of individual causal variant alleles. The overall objective of this dissertation was to develop and apply precision approaches for assessing pharmacogenomic traits in vitamin K metabolism. We hypothesized that the inclusion of diplotype data capturing linked genetic variability across the CYP4F2 and CYP4F11 locus can improve phenotype predictions, relative to the CYP4F2*3 V433M amino acid substitution data alone. In Chapter 1, we explore the role of VK, its disposition, and interaction with warfarin. In Chapter 2, we propose the use of non-linear mixed effect models (NLME) as an unconventional approach to evaluate the impact that complex genomic traits have on xenobiotics metabolism in-vitro. Here, we developed a novel population-based Michaelis-Menten Modeling approach (PopMM) that utilizes strategic sparse sampling allowing for approximation of individual parameter estimates using 50-70% less primary data. In Chapter 3, we evaluated the impact of CYP4F2/CYP4F11 diplotype on CYP4F2 and CYP4F11 mRNA abundance, protein abundance, and metabolic activity towards VK. Lastly, in Chapter 4 we assessed the modifying effect of the singular CYP4F2*3 variant on the relationship between dietary VK exposure and short-term biomarkers of VK status in healthy human subjects using a LC-MS/MS-based assay. Overall, this dissertation has advanced our understanding of the influence that genetic variability in VK metabolic pathways has on VK status. It applies novel tools to characterize the impact that complex genomic traits have on measures of VK metabolism in-vitro and examines the modifying effect that the CYP4F2*3 variant has on measures of VK exposure following dietary intake in vivo.