Pathway-Based Analysis of the Liver Response to Intravenous Methylprednisolone Administration in Rats: Acute Versus Chronic Dosing

Abstract

Pharmacological time-series data, from comparative dosing studies, are critical to characterizing drug effects. Reconciling the data from multiple studies is inevitably difficult; multiple in vivo high-throughput -omics studies are necessary to capture the global and temporal effects of the drug, but these experiments, though analogous, differ in (microarray or other) platforms, time-scales, and dosing regimens and thus cannot be directly combined or compared. This investigation addresses this reconciliation issue with a meta-analysis technique aimed at assessing the intrinsic activity at the pathway level. The purpose of this is to characterize the dosing effects of methylprednisolone (MPL), a widely used anti-inflammatory and immunosuppressive corticosteroid (CS), within the liver. A multivariate decomposition approach is applied to analyze acute and chronic MPL dosing in male adrenalectomized rats and characterize the dosing-dependent differences in the dynamic response of MPL-responsive signaling and metabolic pathways. We demonstrate how to deconstruct signaling and metabolic pathways into their constituent pathway activities, activities which are scored for intrinsic pathway activity. Dosing-induced changes in the dynamics of pathway activities are compared using a model-based assessment of pathway dynamics, extending the principles of pharmacokinetics/pharmacodynamics (PKPD) to describe pathway activities. The model-based approach enabled us to hypothesize on the likely emergence (or disappearance) of indirect dosing-dependent regulatory interactions, pointing to likely mechanistic implications of dosing of MPL transcriptional regulation. Both acute and chronic MPL administration induced a strong core of activity within pathway families including the following: lipid metabolism, amino acid metabolism, carbohydrate metabolism, metabolism of cofactors and vitamins, regulation of essential organelles, and xenobiotic metabolism pathway families. Pathway activities alter between acute and chronic dosing, indicating that MPL response is dosing dependent. Furthermore, because multiple pathway activities are dominant within a single pathway, we observe that pathways cannot be defined by a single response. Instead, pathways are defined by multiple, complex, and temporally related activities corresponding to different subgroups of genes within each pathway.

Modeling Pathway Dynamics of the Skeletal Muscle Response to Intravenous Methylprednisolone (MPL) Administration in Rats: Dosing and Tissue Effects

“…Based on our earlier studies which determined that acute and chronic MPL exposure impact differentially liver (Acevedo et al, 2019), we hypothesize the drug to induce dosing-dependent and tissue-specific effects, as earlier transcriptomic analyses indicate (Ballard et al, 1974;Sun et al, 1999;Yao et al, 2008; et al, 2014). When comparing liver and muscle effects, we determine that acute dosing elicits comparable dynamics in liver and muscle, as exemplified in Figure 8 for the peroxisome signaling pathway for which the dominant regulatory structure is receptor-mediated.…”

“…This statistic is the fraction of genes within a pathway for which gene profiles are available. To assess the confidence in the fractional coverage, an associated p-value (f c p-value) is determined using the 1-tail Fisher's Exact test such that the total rat genome is the set of unique rat genes in all KEGG's rat-relevant pathways (Acevedo et al, 2019). Pathways with low fractional occupancy yield inconclusive p-values as an artifact of the Fisher's Exact Test and were eliminated from the analysis.…”

“…The singular value associated with each singular vector expresses the fractional variability (f p ) captured by the corresponding PAL. In order to characterize the actual significance of a corresponding PAL, an associated f p p-value is evaluated using bootstrapping of the original gene set (see Supplementary Note) (Acevedo et al, 2019). Finally, all pathways yielding fractional coverage f c p-value ≤0.05 with at least one significant PAL profile f p p-value ≤0.05 are defined as significant.…”

“…We thus compare PAL dynamics across dosing, and tissues, in the space of pathway pharmacodynamic models. PAL profiles were captured by our "receptor-mediated" or "biosignal-mediated" model types as previously discussed in the context of liver (Acevedo et al, 2019) and developed as an extension of the concepts presented in Hazra et al (2008) and Yao et al (2008).…”

“…As previously discussed in Acevedo et al (2019), the parameter estimation was performed using MATLAB's optimization toolkit in a series of optimization stages. In all stages, we sought to minimize the residual sum of squares between the model prediction and the cluster centroid profile.…”