RT Journal Article SR Electronic T1 Modeling Corticosteroid Pharmacogenomics and Proteomics in Rat Liver JF Journal of Pharmacology and Experimental Therapeutics JO J Pharmacol Exp Ther FD American Society for Pharmacology and Experimental Therapeutics SP jpet.118.251959 DO 10.1124/jpet.118.251959 A1 Vivaswath S. Ayyar A1 Siddharth Sukumaran A1 Debra C. DuBois A1 Richard R. Almon A1 William J. Jusko YR 2018 UL http://jpet.aspetjournals.org/content/early/2018/08/07/jpet.118.251959.abstract AB Corticosteroids (CS) regulate the expression of numerous genes at the mRNA and protein levels. The time-course of CS pharmacogenomics and proteomics were examined in livers obtained from adrenalectomized rats given a 50 mg/kg bolus dose of methylprednisolone. Microarrays and mass-spectrometry based proteomics were employed to quantify hepatic transcript and protein dynamics. A total of 163 differentially expressed mRNA and their corresponding proteins (163 genes) were clustered into two dominant groups. The temporal profiles of most proteins were delayed compared to its mRNA, attributable to synthesis delays and slower degradation kinetics. Based upon our fifth-generation model of CS, mathematical models were developed to simultaneously describe the emergent time-patterns for an array of steroid-responsive mRNA and proteins. The majority of genes showed time-dependent increases in mRNA and protein expression before returning to baseline. A model assuming direct, steroid-mediated stimulation of mRNA synthesis was applied. Some mRNAs and their proteins displayed down-regulation following CS. A model assuming receptor-mediated inhibition of mRNA synthesis was utilized. More complex patterns were observed for other genes (e.g. biphasic behaviors and opposite directionality in mRNA and protein). Models assuming either stimulation or inhibition of mRNA synthesis coupled with dual secondarily-induced regulatory mechanisms affecting mRNA or protein turnover were derived. These findings indicate that CS-regulated gene expression manifested at the mRNA and protein levels are controlled via mechanisms affecting key turnover processes. Our quantitative models of CS pharmacogenomics were expanded from mRNA to proteins and provide extended hypotheses for understanding the direct, secondary, and downstream mechanisms of CS actions.