VIVD: Virtual in vitro distribution model for the mechanistic prediction of intracellular concentrations of chemicals in in vitro toxicity assays

Compound Absorption in Polymer Devices Impairs the Translatability of Preclinical Safety Assessments

Organotypic and microphysiological systems (MPS) that can emulate the molecular phenotype and function of human tissues, such as liver, are increasingly used in preclinical drug development. However, despite their improved predictivity, drug development success rates have remained low with most compounds failing in clinical phases despite promising preclinical data. Here, it is tested whether absorption of small molecules to polymers commonly used for MPS fabrication can impact preclinical pharmacological and toxicological assessments and contribute to the high clinical failure rates. To this end, identical devices are fabricated from eight different MPS polymers and absorption of prototypic compounds with different physicochemical properties are analyzed. It is found that overall absorption is primarily driven by compound hydrophobicity and the number of rotatable bonds. However, absorption can differ by >1000-fold between polymers with polydimethyl siloxane (PDMS) being most absorptive, whereas polytetrafluoroethylene (PTFE) and thiol-ene epoxy (TEE) absorbed the least. Strikingly, organotypic primary human liver cultures successfully flagged hydrophobic hepatotoxins in lowly absorbing TEE devices at therapeutically relevant concentrations, whereas isogenic cultures in PDMS devices are resistant, resulting in false negative safety signals. Combined, these results can guide the selection of MPS materials and facilitate the development of preclinical assays with improved translatability.

Novel Models for Accurate Estimation of Air-Blood Partitioning: Applications to Individual Compounds and Complex Mixtures of Neutral Organic Compounds

The air-blood partition coefficient (Kab) is extensively employed in human health risk assessment for chemical exposure. However, current Kab estimation approaches either require an extensive number of parameters or lack precision. In this study, we present two novel and parsimonious models to accurately estimate Kab values for individual neutral organic compounds, as well as their complex mixtures. The first model, termed the GC×GC model, was developed based on the retention times of nonpolar chemical analytes on comprehensive two-dimensional gas chromatography (GC×GC). This model is unique in its ability to estimate the Kab values for complex mixtures of nonpolar organic chemicals. The GC×GC model successfully accounted for the Kab variance (R2 = 0.97) and demonstrated strong prediction power (RMSE = 0.31 log unit) for an independent set of nonpolar chemical analytes. Overall, the GC×GC model can be used to estimate Kab values for complex mixtures of neutral organic compounds. The second model, termed the partition model (PM), is based on two types of partition coefficients: octanol to water (Kow) and air to water (Kaw). The PM was able to effectively account for the variability in Kab data (n = 344), yielding an R2 value of 0.93 and root-mean-square error (RMSE) of 0.34 log unit. The predictive power and explanatory performance of the PM were found to be comparable to those of the parameter-intensive Abraham solvation models (ASMs). Additionally, the PM can be integrated into the software EPI Suite, which is widely used in chemical risk assessment for initial screening. The PM provides quick and reliable estimation of Kab compared to ASMs, while the GC×GC model is uniquely suited for estimating Kab values for complex mixtures of neutral organic compounds. In summary, our study introduces two novel and parsimonious models for the accurate estimation of Kab values for both individual compounds and complex mixtures.

PBTK modeled perfluoroalkyl acid kinetics in zebrafish eleutheroembryos suggests impacts on bioconcentrations by chorion porosity dynamics

The zebrafish eleutheroembryo (zfe) is widely used as a model to characterize the toxicity of chemicals. However, analytical methods are still missing to measure organ concentrations. Therefore, physiologically-based toxicokinetic (PBTK) modeling may overcome current limitations to help understand the relationship between toxic effects and internal exposure in various organs. A previous PBTK model has been updated to include the chorionic transport barrier and its permeabilization, hatching dynamics within a zfe population over development, and active mediated transport mechanisms. The zfe PBTK model has been calibrated using measured time-dependent internal concentrations of PFBA, PFHxS, PFOA, and PFOS in a zfe population and evaluated using external datasets from the literature. Calibration was successful with 96% of the predictions falling within a 2-fold range of the observed concentrations. The external dataset was correctly estimated with about 50% of the predictions falling within a factor of 3 of the observed data and 10% of the predictions are out of the 10-fold error. The calibrated model suggested that active mediated transport differs between PFAS with a sulfonic and carboxylic acid functional end groups. This PBTK model predicts well the fate of PFAS with various physicochemical properties in zfe. Therefore, this model may improve the use of zfe as an alternative model in toxicokinetic-toxicodynamic studies and help to refine and reduce zfe-based experiments, while giving insights into the internal kinetics of chemicals.

Safety of elexacaftor/tezacaftor/ivacaftor dose reduction: Mechanistic exploration through physiologically based pharmacokinetic modeling and a clinical case series

INTRODUCTION

Elexacaftor/tezacaftor/ivacaftor (ETI) treatment is associated with significant improvement in lung function in people with cystic fibrosis (pwCF); however, some patients experience adverse effects (AEs) including hepatotoxicity. One potential strategy is dose reduction in ETI with the goal of maintaining therapeutic efficacy while resolving AEs. We report our experience of dose reduction in individuals who experienced AEs following ETI therapy. We provide mechanistic support for ETI dose reduction by exploring predicted lung exposures and underlying pharmacokinetics-pharmacodynamics (PK-PD) relationships.

METHOD

Adults prescribed ETI who underwent dose reduction due to the AEs were included in this case series, and their percent predicted forced expiratory volume in 1 s (ppFEV₁ ) and self-reported respiratory symptoms were collected. The full physiologically based pharmacokinetic (PBPK) models of ETI were developed incorporating physiological information and drug-dependent parameters. The models were validated against available pharmacokinetic and dose-response relationship data. The models were then used to predict lung concentrations of ETI at steady-state.

RESULTS

Fifteen patients underwent dose reduction in ETI due to AEs. Clinical stability without significant changes in ppFEV₁ after dose reduction was observed in all patients. Resolution or improvement of AEs occurred in 13 of the 15 cases. The model-predicted lung concentrations of reduced dose ETI exceeded the reported half maximal effective concentration (EC₅₀ ) from measurement of in vitro chloride transport, providing a hypothesis as to why therapeutic efficacy was maintained.

CONCLUSION

Albeit in a small number of patients, this study provides evidence that reduced ETI doses in pwCF who have experienced AEs may be effective. The PBPK models enable exploration of a mechanistic basis for this finding by simulating target tissue concentrations of ETI that can be compared with drug efficacy in vitro.

Mouse organoids as an in vitro tool to study the in vivo intestinal response to cytotoxicants

Cross-species comparison of drug responses at the organoid level could help to determine the human relevance of findings from animal studies. To this end, we first need to evaluate the in vitro to in vivo translatability of preclinical organoids. Here, we used 5-fluorouracil (5-FU) as an exemplar drug to test whether the in vivo gut response to this cytotoxicant was preserved in murine intestinal organoids. Mice treated with 5-FU at 20 or 50 mg/kg IV (low and high dose, respectively) displayed diarrhea at clinically relevant exposures. 5-FU also induced intestinal lesions, increased epithelial apoptosis, and decreased proliferation in a dose-dependent manner. To enable comparison between the in vitro and in vivo response, top nominal in vitro drug concentrations that caused significant cytotoxicity were chosen (dose range 1-1000 µM). The inferred intracellular concentration in organoids at 1000 µM was within the tissue exposure range related to intestinal toxicity in vivo. 5-FU at ≥ 100 µM decreased ATP levels and increased Caspase-3 activity in intestinal organoids. In keeping with the in vivo findings, 5-FU increased the percentage of Caspase-3-positive cells and reduced Ki67 staining. At the transcriptome level, there was an overlap in the activity of pathways related to 5-FU's mode of action, lipid and cholesterol metabolism and integrin signaling across in vivo gut and organoids. The predicted activity state of upstream regulators was generally well preserved between setups. Collectively, our results suggest that despite their inherent limitations, organoids represent an adequate tool to explore the intestinal response to cytotoxicants.

A PBPK model to evaluate zebrafish eleutheroembryos' actual exposure: bisphenol A and analogs' (AF, F, and S) case studies

The zebrafish eleutheroembryo model is increasingly used to assess the toxicity and developmental adverse effects of xenobiotics. However, the actual exposure is seldom measured (poorly accessible), while a predictive model could estimate these concentrations. The predictions with a new eleutheroembryo physiologically based pharmacokinetic (PBPK) model have been evaluated using datasets obtained from literature data for several bisphenols. The model simulated the toxicokinetics of bisphenols A (BPA), AF, F, and S through the eleutheroembryo tissues while considering the body and organ growth. We further improved the predictions by adding dynamic flows through the embryo and/or its chorion, impact of experimental temperature, metabolic clearance, and saturation of the absorption by Bayesian calibration. The model structure was determined using the BPA dataset and generalized to the other bisphenols. This model revealed the central role of the chorion in the compound uptake in the first 48 h post-fertilization. The predictions for the BPA substitutes estimated by our PBPK model were compared to available toxicokinetics data for zebrafish embryos, and 63% and 88% of them were within a twofold and fivefold error intervals of the corresponding experimental values, respectively. This model provides a tool to design new eleutheroembryo assays and evaluate the actual exposure.

Toward Realistic Dosimetry In Vitro: Determining Effective Concentrations of Test Substances in Cell Culture and Their Prediction by an In Silico Mass Balance Model

Nominal concentrations (C_Nom) in cell culture media are routinely used to define concentration-effect relationships in the in vitro toxicology. The actual concentration in the medium (C_Medium) can be affected by adsorption processes, evaporation, or degradation of chemicals. Therefore, we measured the total and free concentration of 12 chemicals, covering a wide range of lipophilicity (log K_OW -0.07-6.84), in the culture medium (C_Medium) and cells (C_Cell) after incubation with Balb/c 3T3 cells for up to 48 h. Measured values were compared to predictions using an as yet unpublished in silico mass balance model that combined relevant equations from similar models published by others. The total C_Medium for all chemicals except tamoxifen (TAM) were similar to the C_Nom. This was attributed to the cellular uptake of TAM and accumulation into lysosomes. The free (i.e., unbound) C_Medium for the low/no protein binding chemicals were similar to the C_Nom, whereas values of all moderately to highly protein-bound chemicals were less than 30% of the C_Nom. Of the 12 chemicals, the two most hydrophilic chemicals, acetaminophen (APAP) and caffeine (CAF), were the only ones for which the C_Cell was the same as the C_Nom. The C_Cell for all other chemicals tended to increase over time and were all 2- to 274-fold higher than C_Nom. Measurements of C_Cytosol, using a digitonin method to release cytosol, compared well with C_Cell (using a freeze-thaw method) for four chemicals (CAF, APAP, FLU, and KET), indicating that both methods could be used. The mass balance model predicted the total C_Medium within 30% of the measured values for 11 chemicals. The free C_Medium of all 12 chemicals were predicted within 3-fold of the measured values. There was a poorer prediction of C_Cell values, with a median overprediction of 3- to 4-fold. In conclusion, while the number of chemicals in the study is limited, it demonstrates the large differences between C_Nom and total and free C_Medium and C_Cell, which were also relatively well predicted by the mass balance model.

SimRFlow: An R-based workflow for automated high-throughput PBPK simulation with the Simcyp® simulator

SimRFlow is a high-throughput physiologically based pharmacokinetic (PBPK) modelling tool which uses Certara’s Simcyp® simulator. The workflow is comprised of three main modules: 1) a Data Collection module for automated curation of physicochemical (from ChEMBL and the Norman Suspect List databases) and experimental data (i.e.: clearance, plasma-protein binding, and blood-to-plasma ratio, from httk-R package databases), 2) a Simulation module which activates the Simcyp® simulator and runs Monte Carlo simulations on virtual subjects using the curated data, and 3) a Data Visualisation module for understanding the simulated compound-specific profiles and predictions. SimRFlow has three administration routes (oral, intravenous, dermal) and allows users to change some simulation parameters including the number of subjects, simulation duration, and dosing. Users are only expected to provide a file of the compounds they wish to simulate, and in return the workflow provides summary statistics, concentration-time profiles of various tissue types, and a database file (containing in-depth results) for each simulated compound. This is presented within a guided and easy-to-use R Shiny interface which provides many plotting options for the visualisation of concentration-time profiles, parameter distributions, trends between the different parameters, as well as comparison of predicted parameters across all batch-simulated compounds. The in-built R functions can be assembled in user-customised scripts which allows for the modification of the workflow for different purposes. SimRFlow proves to be a time-efficient tool for simulating a large number of compounds without any manual curation of physicochemical or experimental data necessary to run Simcyp® simulations.

Guide to development of compound files for PBPK modeling in the Simcyp population-based simulator

The Simcyp Simulator is a software platform for population physiologically‐based pharmacokinetic (PBPK) modeling and simulation. It links in vitro data to in vivo absorption, distribution, metabolism, excretion and pharmacokinetic/pharmacodynamic outcomes to explore clinical scenarios and support drug development decisions, including regulatory submissions and drug labels. This tutorial describes the different input parameters required, as well as the considerations needed when developing a PBPK model within the Simulator, for a small molecule intended for oral administration. A case study showing the development and application of a PBPK model for ondansetron is herein used to aid the understanding of different PBPK model development concepts.

Extension of the Virtual Cell Based Assay from a 2-D to a 3-D Cell Culture Model

Prediction of chemical toxicity is very useful in risk assessment. With the current paradigm shift towards the use of in vitro and in silico systems, we present herein a theoretical mathematical description of a quasi-diffusion process to predict chemical concentrations in 3-D spheroid cell cultures. By extending a 2-D Virtual Cell Based Assay (VCBA) model into a 3-D spheroid cell model, we assume that cells are arranged in a series of concentric layers within the sphere. We formulate the chemical quasi-diffusion process by simplifying the spheroid with respect to the number of cells in each layer. The system was calibrated and tested with acetaminophen (APAP). Simulated predictions of APAP toxicity were compared with empirical data from in vitro measurements by using a 3-D spheroid model. The results of this first attempt to extend the VCBA model are promising - they show that the VCBA model simulates close correlation between the influence of compound concentration and the viability of the HepaRG 3-D cell culture. The 3-D VCBA model provides a complement to current in vitro procedures to refine experimental setups, to fill data gaps and help in the interpretation of in vitro data for the purposes of risk assessment.

A Transcriptomic Approach to Elucidate the Mechanisms of Gefitinib-Induced Toxicity in Healthy Human Intestinal Organoids

Gefitinib is a tyrosine kinase inhibitor (TKI) that selectively inhibits the epidermal growth factor receptor (EGFR), hampering cell growth and proliferation. Due to its action, gefitinib has been used in the treatment of cancers that present abnormally increased expression of EGFR. However, side effects from gefitinib therapy may occur, among which diarrhoea is most common, that can lead to interruption of the planned therapy in the more severe cases. The mechanisms underlying intestinal toxicity induced by gefitinib are not well understood. Therefore, this study aims at providing insight into these mechanisms based on transcriptomic responses induced in vitro. A 3D culture of healthy human colon and small intestine (SI) organoids was exposed to 0.1, 1, 10 and 30 µM of gefitinib, for a maximum of three days. These drug concentrations were selected using physiologically-based pharmacokinetic simulation considering patient dosing regimens. Samples were used for the analysis of viability and caspase 3/7 activation, image-based analysis of structural changes, as well as RNA isolation and sequencing via high-throughput techniques. Differential gene expression analysis showed that gefitinib perturbed signal transduction pathways, apoptosis, cell cycle, FOXO-mediated transcription, p53 signalling pathway, and metabolic pathways. Remarkably, opposite expression patterns of genes associated with metabolism of lipids and cholesterol biosynthesis were observed in colon versus SI organoids in response to gefitinib. These differences in the organoids’ responses could be linked to increased activated protein kinase (AMPK) activity in colon, which can influence the sensitivity of the colon to the drug. Therefore, this study sheds light on how gefitinib induces toxicity in intestinal organoids and provides an avenue towards the development of a potential tool for drug screening and development.

Derivation of a Human In Vivo Benchmark Dose for Bisphenol A from ToxCast In Vitro Concentration Response Data Using a Computational Workflow for Probabilistic Quantitative In Vitro to In Vivo Extrapolation

A computational workflow which integrates physiologically based kinetic (PBK) modelling; global sensitivity analysis (GSA), Approximate Bayesian Computation (ABC), Markov Chain Monte Carlo (MCMC) simulation and the Virtual Cell Based Assay (VCBA) for the estimation of the active, free in vitro concentration of chemical in the reaction medium was developed to facilitate quantitative in vitro to in vivo extrapolation (QIVIVE). The workflow was designed to estimate parameter and model uncertainty within a computationally efficient framework. The workflow was tested using a human PBK model for bisphenol A (BPA) and high throughput screening (HTS) in vitro concentration-response data, for estrogen and pregnane X receptor activation determined in human liver and kidney cell lines, from the ToxCast/Tox21 database. In vivo benchmark dose 10% lower confidence limits (BMDL10) for oral uptake of BPA (ng/kg BW/day) were calculated from the in vivo dose-responses and compared to the human equivalent dose (HED) BMDL10 for relative kidney weight change in the mouse derived by European Food Safety Authority (EFSA). Three from four in vivo BMDL10 values calculated in this study were similar to the EFSA values whereas the fourth was much smaller. The derivation of an uncertainty factor (UF) to accommodate the uncertainties associated with measurements using human cell lines in vitro, extrapolated to in vivo, could be useful for the derivation of Health Based Guidance Values (HBGV).

Unravelling Mechanisms of Doxorubicin-Induced Toxicity in 3D Human Intestinal Organoids

Doxorubicin is widely used in the treatment of different cancers, and its side effects can be severe in many tissues, including the intestines. Symptoms such as diarrhoea and abdominal pain caused by intestinal inflammation lead to the interruption of chemotherapy. Nevertheless, the molecular mechanisms associated with doxorubicin intestinal toxicity have been poorly explored. This study aims to investigate such mechanisms by exposing 3D small intestine and colon organoids to doxorubicin and to evaluate transcriptomic responses in relation to viability and apoptosis as physiological endpoints. The in vitro concentrations and dosing regimens of doxorubicin were selected based on physiologically based pharmacokinetic model simulations of treatment regimens recommended for cancer patients. Cytotoxicity and cell morphology were evaluated as well as gene expression and biological pathways affected by doxorubicin. In both types of organoids, cell cycle, the p53 signalling pathway, and oxidative stress were the most affected pathways. However, significant differences between colon and SI organoids were evident, particularly in essential metabolic pathways. Short time-series expression miner was used to further explore temporal changes in gene profiles, which identified distinct tissue responses. Finally, in silico proteomics revealed important proteins involved in doxorubicin metabolism and cellular processes that were in line with the transcriptomic responses, including cell cycle and senescence, transport of molecules, and mitochondria impairment. This study provides new insight into doxorubicin-induced effects on the gene expression levels in the intestines. Currently, we are exploring the potential use of these data in establishing quantitative systems toxicology models for the prediction of drug-induced gastrointestinal toxicity.

PBPK Modeling to Simulate the Fate of Compounds in Living Organisms

Pharmacokinetics study the fate of xenobiotics in a living organism. Physiologically based pharmacokinetic (PBPK) models provide realistic descriptions of xenobiotics' absorption, distribution, metabolism, and excretion processes. They model the body as a set of homogeneous compartments representing organs, and their parameters refer to anatomical, physiological, biochemical, and physicochemical entities. They offer a quantitative mechanistic framework to understand and simulate the time-course of the concentration of a substance in various organs and body fluids. These models are well suited for performing extrapolations inherent to toxicology and pharmacology (e.g., between species or doses) and for integrating data obtained from various sources (e.g., in vitro or in vivo experiments, structure-activity models). In this chapter, we describe the practical development and basic use of a PBPK model from model building to model simulations, through implementation with an easily accessible free software.

Update and Evaluation of a High-Throughput In Vitro Mass Balance Distribution Model: IV-MBM EQP v2.0

This study demonstrates the utility of an updated mass balance model for predicting the distribution of organic chemicals in in vitro test systems (IV-MBM EQP v2.0) and evaluates its performance with empirical data. The IV-MBM EQP v2.0 tool was parameterized and applied to four independent data sets with measured ratios of bulk medium or freely-dissolved to initial nominal concentrations (e.g., C24/C0 where C24 is the measured concentration after 24 h of exposure and C0 is the initial nominal concentration). Model performance varied depending on the data set, chemical properties (e.g., "volatiles" vs. "non-volatiles", neutral vs. ionizable organics), and model assumptions but overall is deemed acceptable. For example, the r² was greater than 0.8 and the mean absolute error (MAE) in the predictions was less than a factor of two for most neutral organics included. Model performance was not as good for the ionizable organic chemicals included but the r² was still greater than 0.7 and the MAE less than a factor of three. The IV-MBM EQP v2.0 model was subsequently applied to several hundred chemicals on Canada's Domestic Substances List (DSL) with nominal effects data (AC50s) reported for two in vitro assays. We report the frequency of chemicals with AC50s corresponding to predicted cell membrane concentrations in the baseline toxicity range (i.e., >20-60 mM) and tabulate the number of chemicals with "volatility issues" (majority of chemical in headspace) and "solubility issues" (freely-dissolved concentration greater than water solubility after distribution). In addition, the predicted "equivalent EQP blood concentrations" (i.e., blood concentration at equilibrium with predicted cellular concentration) were compared to the AC50s as a function of hydrophobicity (log octanol-water partition or distribution ratio). The predicted equivalent EQP blood concentrations exceed the AC50 by up to a factor of 100 depending on hydrophobicity and assay conditions. The implications of using AC50s as direct surrogates for human blood concentrations when estimating the oral equivalent doses using a toxicokinetic model (i.e., reverse dosimetry) are then briefly discussed.

Mind the Exposure Gaps-Modeling Chemical Transport in Sediment Toxicity Tests

Chemical exposure in flow-through sediment toxicity tests can vary in time, between pore and overlying water, and amid free and bound states, complicating the link between toxicity and observable concentrations such as free pore (C_free,pore), free overlying (C_free,over), or the corresponding dissolved concentrations (C_diss, free + bound to dissolved organic carbon, DOC). We introduce a numerical model that describes the desorption from sediments to pore water, diffusion through pores and the sediment-water boundary, DOC-mediated transport, and mixing in and outflow from overlying water. The model explained both the experimentally measured gap between C_free,over and C_free,pore and the continuous decrease in overlying C_diss. Spatially resolved modeling suggested a steep concentration gradient present in the upper millimeter of the sediment due to slow chemical diffusion in sediment pores and fast outflux from the overlying water. In contrast to continuous decrease in overlying C_diss expected for any chemical, C_free,over of highly hydrophobic chemicals was kept relatively constant following desorption from DOC, a mechanism comparable to passive dosing. Our mechanistic analyses emphasize that exposure will depend on the chemical's hydrophobicity, the test organism habitat and uptake of bound chemicals, and the properties of sediment components, including DOC. The model can help to re-evaluate existing toxicity data, optimize experimental setups, and extrapolate laboratory toxicity data to field exposure.

New insights into the mechanisms underlying 5-fluorouracil-induced intestinal toxicity based on transcriptomic and metabolomic responses in human intestinal organoids

5-Fluorouracil (5-FU) is a widely used chemotherapeutical that induces acute toxicity in the small and large intestine of patients. Symptoms can be severe and lead to the interruption of cancer treatments. However, there is limited understanding of the molecular mechanisms underlying 5-FU-induced intestinal toxicity. In this study, well-established 3D organoid models of human colon and small intestine (SI) were used to characterize 5-FU transcriptomic and metabolomic responses. Clinically relevant 5-FU concentrations for in vitro testing in organoids were established using physiologically based pharmacokinetic simulation of dosing regimens recommended for cancer patients, resulting in exposures to 10, 100 and 1000 µM. After treatment, different measurements were performed: cell viability and apoptosis; image analysis of cell morphological changes; RNA sequencing; and metabolome analysis of supernatant from organoids cultures. Based on analysis of the differentially expressed genes, the most prominent molecular pathways affected by 5-FU included cell cycle, p53 signalling, mitochondrial ATP synthesis and apoptosis. Short time-series expression miner demonstrated tissue-specific mechanisms affected by 5-FU, namely biosynthesis and transport of small molecules, and mRNA translation for colon; cell signalling mediated by Rho GTPases and fork-head box transcription factors for SI. Metabolomic analysis showed that in addition to the effects on TCA cycle and oxidative stress in both organoids, tissue-specific metabolic alterations were also induced by 5-FU. Multi-omics integration identified transcription factor E2F1, a regulator of cell cycle and apoptosis, as the best key node across all samples. These results provide new insights into 5-FU toxicity mechanisms and underline the relevance of human organoid models in the safety assessment in drug development.

Establishment of an in vitro method of rabbit embryo toxicity with toxicokinetics study

This report introduces a novel method, rabbit whole embryo culture (WEC) combined with toxicokinetics (TK), for toxicity testing. Rodent WEC has been extensively used for in vitro screening of developmental toxicity. To improve the reliability of in vitro data, it is important to consider TK and species specificity. To test the utility and effectiveness of this method, we investigated the toxic effect of thalidomide on rabbit embryos and its behavior in test systems both in vitro and in vivo under the same experimental condition. The data showed that thalidomide induced embryo malformations such as embryonic brain hypoplasia, short limb buds, and declined embryonic growth both in vitro and in vivo. The toxic effect increased with the increasing exposure of the embryo to thalidomide. In addition, we observed similar toxic effects and exposure-effect relationships in vivo and in vitro. Therefore, we preliminarily conclude that this new method can effectively predict and explain thalidomide toxicity. Furthermore, we investigated the behavior of test compounds in the WEC system for the first time, and this method is expected to be an important technique for in vitro toxicity study after extensive verification.

Gaining acceptance in next generation PBK modelling approaches for regulatory assessments - An OECD international effort

Physiologically Based Kinetic (PBK) models are valuable tools to help define safe external levels of chemicals based on internal doses at target organs in experimental animals, humans and organisms used in environmental risk assessment. As the toxicity testing paradigm shifts to alternative testing approaches, PBK model development has started to rely (mostly or entirely) on model parameters quantified using in vitro or in silico methods. Recently, the Organisation for Economic Cooperation and Development (OECD) published a guidance document (GD) describing a scientific workflow for characterising and validating PBK models developed using in vitro and in silico data. The GD provides an assessment framework for evaluating these models, with emphasis on the major uncertainties underlying model inputs and outputs. To help end-users submit or evaluate a PBK model for regulatory purposes, the GD also includes a template for documenting the model characteristics, and a checklist for evaluating the quality of a model. This commentary highlights the principles, criteria and tools laid out in the OECD PBK model GD, with the aim of facilitating the dialogue between model developers and risk assessors.

Quantitative In Vitro-to-In Vivo Extrapolation: Nominal versus Freely Dissolved Concentration

Discussions are ongoing on which dose metric should be used for quantitative in vitro-to-in vivo extrapolation (QIVIVE) of in vitro bioassay data. The nominal concentration of the test chemicals is most commonly used and easily accessible, while the concentration freely dissolved in the assay medium is considered to better reflect the bioavailable concentration but is tedious to measure. The aim of this study was to elucidate how much QIVIVE results will differ when using either nominal or freely dissolved concentrations. QIVIVE_nom and QIVIVE_free ratios, that is, the ratios of plasma concentrations divided by in vitro effect concentrations, were calculated for 10 pharmaceuticals using previously published nominal and freely dissolved effect concentrations for the activation of the peroxisome proliferator-activated receptor gamma (PPARγ) and the activation of oxidative stress response. The QIVIVE_nom ratios were higher than QIVIVE_free ratios by up to a factor of 60. The risk of in vivo effects was classified as being high or low for four chemicals using the QIVIVE_nom and for three chemicals using QIVIVE_free ratios. Unambiguous classification was possible for nine chemicals by combining the QIVIVE_nom or QIVIVE_free ratios with the respective specificity ratios (SR_nom or SR_free) of the in vitro effect data, which helps to identify whether the specific effect was influenced by cytotoxicity. QIVIVE_free models should be preferred as they account for differences in bioavailability between in vitro and in vivo, but QIVIVE_nom may still be useful for screening the effects of large numbers of chemicals because it is generally more conservative. The use of SR of the in vitro effect data as a second classification factor is recommended for QIVIVE_nom and QIVIVE_free models because a clearer picture can be obtained with respect to the likelihood that a biological effect will occur and that it is not caused by nonspecific cytotoxicity.

Development of a Web-Based Toolbox to Support Quantitative In-Vitro-to-In-Vivo Extrapolations (QIVIVE) within Nonanimal Testing Strategies

The goal of the present study was to develop an online web-based toolbox that contains generic physiologically based kinetic (PBK) models for rats and humans, including underlying calculation tools to predict plasma protein binding and tissue:plasma distribution, to be used for quantitative in-vitro-to-in-vivo extrapolations (QIVIVE). The PBK models within the toolbox allow first estimations of internal plasma and tissue concentrations of chemicals to be made, based on the logP and pKa of the chemicals and values for intestinal uptake and intrinsic hepatic clearance. As a case study, the toolbox was used to predict oral equivalent doses of in vitro ToxCast bioactivity data for the food additives methylparaben, propyl gallate, octyl gallate, and dodecyl gallate. These oral equivalent doses were subsequently compared with human exposure estimates, as a low tier assessment allowing prioritization for further assessment. The results revealed that daily intake levels of especially propyl gallate can lead to internal plasma concentrations that are close to in vitro biological effect concentrations, particularly with respect to the inhibition of human thyroid peroxidase (TPO). Estrogenic effects were not considered likely to be induced by the food additives, as daily exposure levels of the different compounds remained 2 orders of magnitude below the oral equivalent doses for in vitro estrogen receptor activation. Overall, the results of the study show how the toolbox, which is freely accessible through www.qivivetools.wur.nl, can be used to obtain initial internal dose estimates of chemicals and to prioritize chemicals for further assessment, based on the comparison of oral equivalent doses of in vitro biological activity data with human exposure levels.

Integrating biokinetics and in vitro studies to evaluate developmental neurotoxicity induced by chlorpyrifos in human iPSC-derived neural stem cells undergoing differentiation towards neuronal and glial cells

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Human iPSC-derived NSCs undergoing differentiation possess some metabolic competence.

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CPF entered the cells and was biotrasformed into its two main metabolites (CPFO and TCP).

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After repeated exposure, very limited bioaccumulation of CPF was observed.

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Treatment with CPF decreased neurite outgrowth, synapse number and electrical activity.

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Treatment with CPF increased BDNF levels and the percentage of astrocytes.

For some complex toxicological endpoints, chemical safety assessment has conventionally relied on animal testing. Apart from the ethical issues, also scientific considerations have been raised concerning the traditional approach, highlighting the importance for considering real life exposure scenario. Implementation of flexible testing strategies, integrating multiple sources of information, including in vitro reliable test methods and in vitro biokinetics, would enhance the relevance of the obtained results. Such an approach could be pivotal in the evaluation of developmental neurotoxicity (DNT), especially when applied to human cell-based models, mimicking key neurodevelopmental processes, relevant to human brain development.

Here, we integrated the kinetic behaviour with the toxicodynamic alterations of chlorpyrifos (CPF), such as in vitro endpoints specific for DNT evaluation, after repeated exposure during differentiation of human neural stem cells into a mixed culture of neurons and astrocytes. The upregulation of some cytochrome P450 and glutathione S-transferase genes during neuronal differentiation and the formation of the two major CPF metabolites (due to bioactivation and detoxification) supported the metabolic competence of the used in vitro model. The alterations in the number of synapses, neurite outgrowth, brain derived neurotrophic factor, the proportion of neurons and astrocytes, as well as spontaneous electrical activity correlated well with the CPF ability to enter the cells and be bioactivated to CPF-oxon. Overall, our results confirm that combining in vitro biokinetics and assays to evaluate effects on neurodevelopmental endpoints in human cells should be regarded as a key strategy for a quantitative characterization of DNT effects.

Setting the stage for next-generation risk assessment with non-animal approaches: the EU-ToxRisk project experience

In 2016, the European Commission launched the EU-ToxRisk research project to develop and promote animal-free approaches in toxicology. The 36 partners of this consortium used in vitro and in silico methods in the context of case studies (CSs). These CSs included both compounds with a highly defined target (e.g. mitochondrial respiratory chain inhibitors) as well as compounds with poorly defined molecular initiation events (e.g. short-chain branched carboxylic acids). The initial project focus was on developing a science-based strategy for read-across (RAx) as an animal-free approach in chemical risk assessment. Moreover, seamless incorporation of new approach method (NAM) data into this process (= NAM-enhanced RAx) was explored. Here, the EU-ToxRisk consortium has collated its scientific and regulatory learnings from this particular project objective. For all CSs, a mechanistic hypothesis (in the form of an adverse outcome pathway) guided the safety evaluation. ADME data were generated from NAMs and used for comprehensive physiological-based kinetic modelling. Quality assurance and data management were optimized in parallel. Scientific and Regulatory Advisory Boards played a vital role in assessing the practical applicability of the new approaches. In a next step, external stakeholders evaluated the usefulness of NAMs in the context of RAx CSs for regulatory acceptance. For instance, the CSs were included in the OECD CS portfolio for the Integrated Approach to Testing and Assessment project. Feedback from regulators and other stakeholders was collected at several stages. Future chemical safety science projects can draw from this experience to implement systems toxicology-guided, animal-free next-generation risk assessment.

Temperature effect on perfluorooctane sulfonate toxicokinetics in rainbow trout (Oncorhynchus mykiss): Exploration via a physiologically based toxicokinetic model

Salmonids are poikilotherms, which means that their internal temperature varies with that of water. Water temperature thus controls many of their lifecycle processes and physiological functions, which could influence the mechanisms of absorption, distribution, metabolism and excretion (ADME) of many substances, including perfluorinated alkyl acids (PFAAs). However, the processes governing the fate of PFAAs are still poorly understood in fish. Here we developed a physiologically-based toxicokinetic (PBTK) model for rainbow trout (Oncorhynchus mykiss) to study changes in physiological functions and PFAA ADME at different temperatures. The model was calibrated using experimental data from dietary exposure to perfluorooctane sulfonate at 7 °C and 19 °C. Predictions of PFOS concentrations were globally satisfactory at both temperatures, when accounting for the influence of temperature on growth, ventilation rate, cardiac output, clearances, and absorption rates. Accounting for the influence of temperature on tissue-plasma partition coefficients significantly improved predicted in-organ PFOS concentrations.

The EU-ToxRisk method documentation, data processing and chemical testing pipeline for the regulatory use of new approach methods

Hazard assessment, based on new approach methods (NAM), requires the use of batteries of assays, where individual tests may be contributed by different laboratories. A unified strategy for such collaborative testing is presented. It details all procedures required to allow test information to be usable for integrated hazard assessment, strategic project decisions and/or for regulatory purposes. The EU-ToxRisk project developed a strategy to provide regulatorily valid data, and exemplified this using a panel of > 20 assays (with > 50 individual endpoints), each exposed to 19 well-known test compounds (e.g. rotenone, colchicine, mercury, paracetamol, rifampicine, paraquat, taxol). Examples of strategy implementation are provided for all aspects required to ensure data validity: (i) documentation of test methods in a publicly accessible database; (ii) deposition of standard operating procedures (SOP) at the European Union DB-ALM repository; (iii) test readiness scoring accoding to defined criteria; (iv) disclosure of the pipeline for data processing; (v) link of uncertainty measures and metadata to the data; (vi) definition of test chemicals, their handling and their behavior in test media; (vii) specification of the test purpose and overall evaluation plans. Moreover, data generation was exemplified by providing results from 25 reporter assays. A complete evaluation of the entire test battery will be described elsewhere. A major learning from the retrospective analysis of this large testing project was the need for thorough definitions of the above strategy aspects, ideally in form of a study pre-registration, to allow adequate interpretation of the data and to ensure overall scientific/toxicological validity.

Development of a generic zebrafish embryo PBPK model and application to the developmental toxicity assessment of valproic acid analogs

In order to better explain, predict, or extrapolate to humans the developmental toxicity effects of chemicals to zebrafish (Danio rerio) embryos, we developed a physiologically-based pharmacokinetic (PBPK) model designed to predict organ concentrations of neutral or ionizable chemicals, up to 120 h post-fertilization. Chemicals' distribution is modeled in the cells, lysosomes, and mitochondria of ten organs of the embryo. The model's partition coefficients are calculated with sub-models using physicochemical properties of the chemicals of interest. The model accounts for organ growth and changes in metabolic clearance with time. We compared ab initio model predictions to data obtained on culture medium and embryo concentrations of valproic acid (VPA) and nine analogs during continuous dosing under the OECD test guideline 236. We further improved the predictions by estimating metabolic clearance and partition coefficients from the data by Bayesian calibration. We also assessed the performance of the model at reproducing data published by Brox et al. (2016) on VPA and 16 other chemicals. We finally compared dose-response relationships calculated for mortality and malformations on the basis of predicted whole embryo concentrations versus those based on nominal water concentrations. The use of target organ concentrations substantially shifted the magnitude of dose-response parameters and the relative toxicity ranking of chemicals studied.

Experimental Validation of Mass Balance Models for in Vitro Cell-Based Bioassays

The freely dissolved concentration in the assay medium (C_free) and the total cellular concentration (C_cell) are essential input parameters for quantitative in vitro-to-in vivo extrapolations (QIVIVE), but available prediction tools for C_free and C_cell have not been sufficiently validated with experimental data. In this study, medium-water distribution ratios (D_FBS/w) and cell-water distribution ratios (D_cell/w) for four different cells lines were determined experimentally for 12 neutral and five ionizable chemicals. Literature data for seven organic acids were added to the dataset, leading to 24 chemicals in total. A mass balance model based on bovine serum albumin-water (D_BSA/w) and liposome-water distribution ratios (D_lip/w) of the chemicals was used to calculate D_FBS/w and D_cell/w. For all neutral and basic test chemicals, the mass balance model predicted D_FBS/w and D_cell/w within a factor of 3 and 3.4, respectively, indicating that existing models can reliably predict C_free and C_cell for these chemicals. For organic acids, a further refinement of the model will be required as large deviations between modeled and measured binding to assay medium and cells of up to a factor of 370 were found. Furthermore, saturation of medium proteins should be further explored for organic acids and neutral chemicals with moderate hydrophobicity.