Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism

Abstract

Corticosteroids (CS) are anti-inflammatory agents that cause extensive pharmacogenomic and proteomic changes in multiple tissues. An understanding of the proteome-wide effects of CS in liver and its relationships to altered hepatic and systemic physiology remains incomplete. Here, we report the application of a functional pharmacoproteomic approach to gain integrated insight into the complex nature of CS responses in liver in vivo. An in-depth functional analysis was performed using rich pharmacodynamic (temporal-based) proteomic data measured over 66 hours in rat liver following a single dose of methylprednisolone (MPL). Data mining identified 451 differentially regulated proteins. These proteins were analyzed on the basis of temporal regulation, cellular localization, and literature-mined functional information. Of the 451 proteins, 378 were clustered into six functional groups based on major clinically-relevant effects of CS in liver. MPL–responsive proteins were highly localized in the mitochondria (20%) and cytosol (24%). Interestingly, several proteins were related to hepatic stress and signaling processes, which appear to be involved in secondary signaling cascades and in protecting the liver from CS-induced oxidative damage. Consistent with known adverse metabolic effects of CS, several rate-controlling enzymes involved in amino acid metabolism, gluconeogenesis, and fatty-acid metabolism were altered by MPL. In addition, proteins involved in the metabolism of endogenous compounds, xenobiotics, and therapeutic drugs including cytochrome P450 and Phase-II enzymes were differentially regulated. Proteins related to the inflammatory acute-phase response were up-regulated in response to MPL. Functionally-similar proteins showed large diversity in their temporal profiles, indicating complex mechanisms of regulation by CS.

Modeling Corticosteroid Pharmacogenomics and Proteomics in Rat Liver

“…An extensive comparative analysis of our -omics data sets to those reported by others is also challenging, as most have investigated transcriptomics or proteomics at single time points after dosing. Nonetheless, changes in Tat protein were validated with measurements of enzyme activity in the same animals (Ayyar et al, 2018), and the pathways perturbed within our transcriptomic and proteomic data sets are, in terms of function, in agreement with recognized adverse and therapeutic effects of CS (Ayyar et al, 2017).…”

“…Within-class differential expression was employed to identify proteins that showed a differential expression profile over time. Only mRNA and proteins that varied significantly over time (P value ,0.05 and q-value ,0.01) were employed in the subsequent analysis (Kamisoglu et al, 2015;Ayyar et al, 2017). Temporal data for the differentially expressed genes identified at both transcriptomic and proteomic levels were concatenated and subjected to hierarchical clustering using the clustergram function in the Bioinformatics Toolbox of MATLAB (Mathworks, Natick, MA) as described previously (Kamisoglu et al, 2015).…”

“…Time-course data for 163 common genes that were available from both transcriptomic and proteomic data sets were concatenated and hierarchically clustered as described previously (Kamisoglu et al, 2015). Functional description and discussion of the proteomic data has been reported (Ayyar et al, 2017). On the basis of the analysis, cluster 1 was populated with 80 genes for which corresponding mRNA and protein expression profiles were essentially parallel in direction, whereas for 83 genes in cluster 2 the directionality between mRNA and protein was reversed (Fig.…”

A high resolution atlas of gene expression in the domestic sheep (Ovis aries)

“…AGXT, AGXT2 , ASPDH , ACY1 , EHHADH , DPYD , DAO , DDO , HAO1 , and HPD ) and the rate-limiting enzymes of gluconeogenesis ( PCK1 , PC , ALDOB and G6PC ). The contributions of kidney and liver to amino acid turnover and gluconeogenesis are well known in humans [41] and rodents [42]. These observations suggest that the shared catabolic pathways of liver and kidney cortex are largely conserved in sheep, but detailed curation of the genes in this cluster could provide further specific insights.…”

Methimazole-induced liver injury overshadowed by methylprednisolone pulse therapy

“…[ 31 ] MP is metabolized by CYP3A4 [ 34 , 35 ] and is a CYP inducer, [ 36 , 37 ] associated with differential regulation of 20 CYP enzymes (eg, CYP2C13, CYP2D10, and CYP3A2, and CYP2a1 and CYP2a2). [ 38 ] MP has been implicated in CYP3A4-mediated drug interactions with CYP3A4 inhibitors itraconazole and ketoconazole previously, [ 39 , 40 ] and inhibitory effects on CYP3A4 of methimazole have been described. [ 32 ] The cytochrome P450 (CYP)3A4-mediated drug interaction hypothesis is challenged by a study showing that the use of MP (32 mg once and 8 mg for 9 days) did not result in clinically significant induction of CYP3A4 [ 41 ] .…”