GASP and FASP are Complementary for LC-MS/MS Proteomic Analysis of Drug-Metabolizing Enzymes and Transporters in Pig Liver.

Sample preparation is a critical step in the proteomic workflow. Numerous different approaches are used, tailored to the type of sample, the aims of the experiment, analytical method, and to an extent, user preference. This has resulted in large variation in reported protein abundances. In this study, the complementarity of two different sample preparation techniques is demonstrated for the study of absorption, distribution, metabolism, and excretion (ADME) related proteins from pig liver tissue. Filter-aided sample preparation (FASP) is a well-established and widely used method, while gel-aided sample preparation (GASP) is a relatively new method optimized and simplified from previous gel-associated digestion techniques. To investigate each method, the number of peptides and proteins characterized, reproducibility of results, and their real-time application are examined. While both methods have their merits and limitations, for example, FASP is the less technical of the two methods, while GASP is time efficient, ultimately the two methods show significant differences in the peptides identified and therefore, the use of both methods should be considered when examining and quantifying ADME related proteins. Data are available via ProteomeXchange with identifier PXD011324.

Toward systems-informed models for biologics disposition: covariates of the abundance of the neonatal Fc Receptor (FcRn) in human tissues and implications for pharmacokinetic modelling.

Biologics are a fast-growing therapeutic class, with intertwined pharmacokinetics and pharmacodynamics, affected by the abundance and function of the FcRn receptor. While many investigators assume adequacy of classical models, such as allometry, for pharmacokinetic characterization of biologics, advocates of physiologically-based pharmacokinetics (PBPK) propose consideration of known systems parameters that affect the fate of biologics to enable a priori predictions, which go beyond allometry. The aim of this study was to deploy a systems-informed modelling approach to predict the disposition of Fc-containing biologics. We used global proteomics to quantify the FcRn receptor [p51 and ß2-microglobulin (B2M) subunits] in 167 samples of human tissue (liver, intestine, kidney and skin) and assessed covariates of its expression. FcRn p51 subunit was highest in liver relative to other tissues, and B2M was 1-2 orders of magnitude more abundant than FcRn p51 across all sets. There were no sex-related differences, while higher expression was confirmed in neonate liver compared with adult liver. Trends of expression in liver and kidney indicated a moderate effect of body mass index, which should be confirmed in a larger sample size. Expression of FcRn p51 subunit was approximately 2-fold lower in histologically normal liver tissue adjacent to cancer compared with healthy liver. FcRn mRNA in plasma-derived exosomes correlated moderately with protein abundance in matching liver tissue, opening the possibility of use as a potential clinical tool. Predicted effects of trends in FcRn abundance in healthy and disease (cancer and psoriasis) populations using trastuzumab and efalizumab PBPK models were in line with clinical observations, and global sensitivity analysis revealed endogenous IgG plasma concentration and tissue FcRn abundance as key systems parameters influencing exposure to Fc-conjugated biologics.

Mass spectrometry-based abundance atlas of ABC transporters in human liver, gut, kidney, brain and skin.

ABC transporters (ATP-binding cassette transporter) traffic drugs and their metabolites across membranes, making ABC transporter expression levels a key factor regulating local drug concentrations in different tissues and individuals. Yet, quantification of ABC transporters remains challenging because they are large and low-abundance transmembrane proteins. Here, we analysed 200 samples of crude and membrane-enriched fractions from human liver, kidney, intestine, brain microvessels and skin, by label-free quantitative mass spectrometry. We identified 32 (out of 48) ABC transporters: ABCD3 was the most abundant in liver, whereas ABCA8, ABCB2/TAP1 and ABCE1 were detected in all tissues. Interestingly, this atlas unveiled that ABCB2/TAP1 may have TAP2-independent functions in the brain and that biliary atresia (BA) and control livers have quite different ABC transporter profiles. We propose that meaningful biological information can be derived from a direct comparison of these data sets.

Quantitative mass spectrometry-based proteomics in the era of model-informed drug development: Applications in translational pharmacology and recommendations for best practice.

Quantitative translation of the fate and action of a drug in the body is facilitated by models that allow extrapolation of in vitro measurements (such as the rate of metabolism, active transport across membranes, inhibition of enzymes and receptor occupancy) to in vivo consequences (intensity and duration of drug effects). These models use various physiological parameters, including data that describe the expression levels of pharmacologically relevant enzymes, transporters and receptors in tissues and in vitro systems. Immunoquantification approaches have traditionally been used to determine protein expression levels, generally providing relative quantification data with compromised selectivity and reproducibility. More recently, the development of several quantitative proteomic techniques, fuelled by advances in state-of-the-art mass spectrometry, has led to generating a wealth of qualitative and quantitative data. These data are currently used for various quantitative systems pharmacology applications, with the ultimate goal of conducting virtual clinical trials to inform clinical studies, especially when assessments are difficult to conduct on patients. In this review, we explore available quantitative proteomic methods, discuss their main applications in translational pharmacology and offer recommendations for selecting and implementing proteomic techniques.

Dose adjustment in orphan disease populations: the quest to fulfill the requirements of physiologically based pharmacokinetics.

INTRODUCTION: While the media is engaged and fascinated by the idea of 'Precision Medicine', the nuances related to 'Precision Dosing' seem to be largely ignored. Assuming the 'right drug' is selected, clinicians still need to decide on the 'right dose' for individuals. Ideally, optimal dosing should be studied in clinical trials; however, many drugs on the market lack evidence-based dosing recommendations, and small groups of patients (orphan disease populations) are dependent on local guidance and clinician experience to determine drug dosage adjustments. Areas Covered: This report explores the current understanding of dosing adjustment in special populations and examines the requirements for developing 'in silico' models for pediatric, elderly and pregnant patients. The report also highlights current use of modeling to provide evidence-based recommendations for drug labeling in the absence of complete clinical trials in orphan disease populations. Expert Opinion: Physiologically based pharmacokinetics (PBPK) is an attractive prospect for determining the best drug dosage adjustments in special populations. However, it is not sufficient for individualized, or even stratified dosing, unless the systems (drug-independent) data required to build robust PBPK models are obtained. Such models are not a substitute for clinical trials, but they are an alternative to undocumented and inconsistent guesswork.

Hyperphosphorylation of CREB in human dopaminergic neurons: a kinetic study of cellular distribution of total CREB and phospho-CREB following oxidative stress.

The neurotoxin, 6-hydroxy dopamine (6-OHDA)-induced oxidative stress causes alterations in intracellular signalling events and activates cellular and molecular mechanisms leading to the degeneration of the dopamine-containing neurons (DCNs). The cyclic-AMP response element-binding protein (CREB) modulates the transcription of mitochondrial and nuclear genes upon phosphorylation. However, oxidative stress disrupts CREB functions and inhibits CREB signalling pathways. We have measured the activities and levels of both total CREB and its phosphorylated form (phospho-CREB) in cytosolic, mitochondrial and nuclear compartments in control (untreated) and stressed (6-OHDA-treated) DCN, differentiated from the ReNVM cell line (dDCN) at 0, 24 and 72 h time points following oxidative stress. Our results indicate that CREB phosphorylation occurs in all three subcellular locations. It further shows significant disruption of the phosphorylation process by 6-OHDA treatment and shows tridirectional trafficking of total CREB and phospho-CREB between cytosol, mitochondria and nucleus following oxidative stress induced by 6-OHDA treatment. In conclusion, our results indicate the presence of specific signalling molecules in all the compartments studied and their involvement in the signal transduction processes, where total CREB and phospho-CREB levels and activities are either upregulated or downregulated to balance each other for their roles.