Universal Toxicity Gene Signatures for Early Identification of Drug-Induced Tissue Injuries in Rats.

A new safety testing paradigm that relies on gene expression biomarker panels was developed to easily and quickly identify drug-induced injuries across tissues in rats prior to drug candidate selection. Here, we describe the development, qualification, and implementation of gene expression signatures that diagnose tissue degeneration/necrosis for use in early rat safety studies. Approximately 400 differentially expressed genes were first identified that were consistently regulated across 4 prioritized tissues (liver, kidney, heart, and skeletal muscle), following injuries induced by known toxicants. Hundred of these "universal" genes were chosen for quantitative PCR, and the most consistent and robustly responding transcripts selected, resulting in a final 22-gene set from which unique sets of 12 genes were chosen as optimal for each tissue. The approach was extended across 4 additional tissues (pancreas, gastrointestinal tract, bladder, and testes) where toxicities are less common. Mathematical algorithms were generated to convert each tissue's 12-gene expression values to a single metric, scaled between 0 and 1, and a positive threshold set. For liver, kidney, heart, and skeletal muscle, this was established using a training set of 22 compounds and performance determined by testing a set of approximately 100 additional compounds, resulting in 74%-94% sensitivity and 94%-100% specificity for liver, kidney, and skeletal muscle, and 54%-62% sensitivity and 95%-98% specificity for heart. Similar performance was observed across a set of 15 studies for pancreas, gastrointestinal tract, bladder, and testes. Bundled together, we have incorporated these tissue signatures into a 4-day rat study, providing a rapid assessment of commonly seen compound liabilities to guide selection of lead candidates without the necessity to perform time-consuming histopathologic analyses.

Xenobiotic perturbation of ER stress and the unfolded protein response.

The proper folding, assembly, and maintenance of cellular proteins is a highly regulated process and is critical for cellular homeostasis. Multiple cellular compartments have adapted their own systems to ensure proper protein folding, and quality control mechanisms are in place to manage stress due to the accumulation of unfolded proteins. When the accumulation of unfolded proteins exceeds the capacity to restore homeostasis, these systems can result in a cell death response. Unfolded protein accumulation in the endoplasmic reticulum (ER) leads to ER stress with activation of the unfolded protein response (UPR) governed by the activating transcription factor 6 (ATF6), inositol requiring enzyme-1 (IRE1), and PKR-like endoplasmic reticulum kinase (PERK) signaling pathways. Many xenobiotics have been shown to influence ER stress and UPR signaling with either pro-survival or pro-death features. The ultimate outcome is dependent on many factors including the mechanism of action of the xenobiotic, concentration of xenobiotic, duration of exposure (acute vs. chronic), cell type affected, nutrient levels, oxidative stress, state of differentiation, and others. Assessing perturbations in activation or inhibition of ER stress and UPR signaling pathways are likely to be informative parameters to measure when analyzing mechanisms of action of xenobiotic-induced toxicity.

Phospholipidosis assay in HepG2 cells and rat or rhesus hepatocytes using phospholipid probe NBD-PE.

Phospholipidosis (PLD) is an accumulation of phospholipids in lysosome-derived multilamellar vesicles. More than 50 commercial drugs are known to cause PLD. In vitro screening assays were developed in HepG2 cells, rat primary hepatocytes, and rhesus monkey hepatocytes using the fluorescent-labeled phospholipid probe N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)-1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine (NBD-PE) or Nile Red lipid stain. The assays were qualified using amiodarone and fluoxetine as positive controls and precocene and valproic acid as negative controls. NBD-PE accumulation and Nile Red staining were first measured using fluorescence microscopy with morphometric analysis, and the throughput of the NBD-PE assay in HepG2 cells was increased by measuring fluorescence with a multiwell spectrofluorometer. The PLD potential values obtained for the tested compounds from the morphometric analysis were similar to the values obtained from the spectrofluorometer, suggesting the plate reader assay was effective at measuring the induction of NBD-PE accumulation. Fifteen commercial compounds were evaluated using the NBD-PE assay in HepG2 cells, rat primary hepatocytes, and rhesus monkey hepatocytes. The relative NBD-PE accumulation and PLD potentials of the evaluated compounds were similar and comparable to the values observed from other in vitro PLD assays referenced in the literature using different probes and cell lines. NBD-PE accumulations observed in rat hepatocytes after drug treatments were similar to those in HepG2 cells. NBD-PE accumulation potential observed in rhesus monkey hepatocytes after drug treatment was different for tamoxifen, perhexiline, clomipramine, and haloperidol. These agents caused potent NBD-PE accumulation in HepG2 cells, but minimal or no activity was observed in rhesus monkey hepatocytes. These data suggest that the NBD-PE spectrofluorometer assay in HepG2 cells has the speed and throughput to sensitively and quantitatively determine the PLD potential of various drug candidates. In addition, these data demonstrate the species differences in PLD potential between rat and monkey hepatocytes.

Use of metabonomics to identify impaired fatty acid metabolism as the mechanism of a drug-induced toxicity.

An increased diversity of therapeutic targets in the pharmaceutical industry in recent years has led to a greater diversity of toxicological effects. This, and the increased pace of drug discovery, leads to a need for new technologies for the rapid elucidation of toxicological mechanisms. As part of an evaluation of the utility of metabonomics in drug safety assessment, 1H NMR spectra were acquired on urine and liver tissue samples obtained from rats administered vehicle or a development compound (MrkA) previously shown to induce hepatotoxicity in several animal species. Multivariate statistical analysis of the urinary NMR data clearly discriminated drug-treated from control animals, due to a depletion in tricarboxylic acid cycle intermediates, and the appearance of medium chain dicarboxylic acids. High-resolution magic angle spinning NMR data acquired on liver samples exhibited elevated triglyceride levels that were correlated with changes in the urinary NMR data. Urinary dicarboxylic aciduria is associated with defective metabolism of fatty acids; subsequent in vitro experiments confirmed that MrkA impairs fatty acid metabolism. The successful application of metabonomics to characterize an otherwise ill-defined mechanism of drug-induced toxicity supports the practicality of this approach for resolving toxicity issues for drugs in discovery and development.