A mode-of-action ontology model for safety evaluation of chemicals: Outcome of a series of workshops on repeated dose toxicity

Empirical analysis of lead neurotoxicity mode of action and its application in health risk assessment

The mode of action (MOA) framework is proposed to inform a biological link between chemical exposures and adverse health effects. Despite a significant increase in knowledge and awareness, the application of MOA in human health risk assessment (RA) remains limited. This study aims to discuss the adoption of MOA for health RA within a regulatory context, taking our previously proposed but not yet validated MOA for lead neurotoxicity as an example. We first conducted a quantitative weight of evidence (qWOE) assessment, which revealed that the MOA has a moderate confidence. Then, targeted bioassays were performed within an in vitro blood-brain barrier (BBB) model to quantitatively validate the scientific validity of key events (KEs) in terms of essentiality and concordance of empirical support (dose/temporal concordance), which increases confidence in utilizing the MOA for RA. Building upon the quantitative validation data, we further conducted benchmark dose (BMD) analysis to map dose-response relationships for the critical toxicity pathways, and the lower limit of BMD at a 5% response (BMDL5) was identified as the point of departure (POD) value for adverse health effects. Notably, perturbation of the Aryl Hydrocarbon Receptor (AHR) signaling pathway exhibited the lowest POD value, measured at 0.0062 μM. Considering bioavailability, we further calculated a provisional health-based guidance value (HBGV) for children's lead intake, determining it to be 2.56 μg/day. Finally, the health risk associated with the HBGV was assessed using the hazard quotient (HQ) approach, which indicated that the HBGV established in this study is a relative safe reference value for lead intake. In summary, our study described the procedure for utilizing MOA in health RA and set an example for MOA-based human health risk regulation.

Zebrafish and nematodes as whole organism models to measure developmental neurotoxicity

Despite the growing epidemiological evidence of an association between toxin exposure and developmental neurotoxicity (DNT), systematic testing of DNT is not mandatory in international regulations for admission of pharmaceuticals or industrial chemicals. However, to date around 200 compounds, ranging from pesticides, pharmaceuticals and industrial chemicals, have been tested for DNT in the current OECD test guidelines (TG-443 or TG-426). There are calls for the development of new approach methodologies (NAMs) for DNT, which has resulted in a DNT testing battery using in vitro human cell-based assays. These assays provide a means to elucidate the molecular mechanisms of toxicity in humans which is lacking in animal-based toxicity tests. However, cell-based assays do not represent all steps of the complex process leading to DNT. Validated models with a multi-organ network of pathways that interact at the molecular, cellular and tissue level at very specific timepoints in a life cycle are currently missing. Consequently, whole model organisms are being developed to screen for, and causally link, new molecular targets of DNT compounds and how they affect whole brain development and neurobehavioral endpoints. Given the practical and ethical restraints associated with vertebrate testing, lower animal models that qualify as 3 R (reduce, refine and replace) models, including the nematode (Caenorhabditis elegans) and the zebrafish (Danio rerio) will prove particularly valuable for unravelling toxicity pathways leading to DNT. Although not as complex as the human brain, these 3 R-models develop a complete functioning brain with numerous neurodevelopmental processes overlapping with human brain development. Importantly, the main signalling pathways relating to (neuro)development, metabolism and growth are highly conserved in these models. We propose the use of whole model organisms specifically zebrafish and C. elegans for DNT relevant endpoints.

EU’s next generation risk assessment: hurdles and opportunities for new approach methodologies

The EU’s decision to ban animal testing for toxicity testing, has positively influenced the pace of developing New Approach Methodologies (NAMs). This development also supports replacing animal methods in other forms of risk assessment (RA), such as for oral-toxicity testing. This study aims to identify the hurdles and opportunities for validation and implementation of NAMs in the current EU’s chemical RA. Through conducting semi-structured interviews with 14 stakeholders, experiences and perspectives about the validation and implementation of NAMs in RA for orally ingested chemicals were analyzed. Stakeholders considered the use of NAMs for RA processes both a cultural and generational issue. Both were perceived as hurdles for reaching the next generation RA approach. The differing views on NAMs originated from experience and stakeholder positions, but communication and collaboration on developing future RA approaches could support overcoming this skepticism. Irrespectively of their background, all interviewees were generally optimistic that NAMs will support the development of more accurate and sustainable RA. This research highlights the need for the EU to adjust legislation and guidance documents to shift in testing requirements from the traditional overexposure approach to more predictive, mechanistic testing in RA, which will take time. This study, however, shows that—when all stakeholders engage in communication and confidence building—NAMs can already play an important role in reducing and refining animal testing.

Neuronal differentiation pathways and compound-induced developmental neurotoxicity in the human neural progenitor cell test (hNPT) revealed by RNA-seq

There is an increased awareness that the use of animals for compound-induced developmental neurotoxicity (DNT) testing has limitations. Animal-free innovations, especially the ones based on human stem cell-based models are pivotal in studying DNT since they can mimic processes relevant to human brain development. Here we present the human neural progenitor test (hNPT), a 10-day protocol in which neural progenitor cells differentiate into a neuron-astrocyte co-culture. The study aimed to characterise differentiation over time and to find neurodevelopmental processes sensitive to compound exposure using transcriptomics. 3992 genes regulated in unexposed control cultures (p ≤ 0.001, log2FC ≥ 1) showed Gene Ontology (GO-) term enrichment for neuronal and glial differentiation, neurite extension, synaptogenesis, and synaptic transmission. Exposure to known or suspected DNT compounds (acrylamide, chlorpyrifos, fluoxetine, methyl mercury, or valproic acid) at concentrations resulting in 95% cell viability each regulated unique combinations of GO-terms relating to neural progenitor proliferation, neuronal and glial differentiation, axon development, synaptogenesis, synaptic transmission, and apoptosis. Investigation of the GO-terms 'neuron apoptotic process' and 'axon development' revealed common genes that were responsive across compounds, and might be used as biomarkers for DNT. The GO-term 'synaptic signalling', on the contrary, whilst also responsive to all compounds tested, showed little overlap in gene expression regulation patterns between the conditions. This GO-term may articulate compound-specific effects that may be relevant for revealing differences in mechanism of toxicity. Given its focus on neural progenitor cell to mature multilineage neuronal cell maturation and its detailed molecular readout based on gene expression analysis, hNPT might have added value as a tool for neurodevelopmental toxicity testing in vitro. Further assessment of DNT-specific biomarkers that represent these processes needs further studies.

A State-of-the-Art Review on the Alternatives to Animal Testing for the Safety Assessment of Cosmetics

Almost a decade after the stipulated deadline in the 7th amendment to the EU Cosmetics Directive, which bans the marketing of animal-tested cosmetics in the EU from 2013, animal experimentation for cosmetic-related purposes remains a topic of animated debate. Cosmetic industry continues to be scrutinised for the practice, despite its leading role in funding and adopting innovation in this field. This paper aims to provide a state-of-the-art review of the field on alternative testing methods, also known as New Approach Methodologies (NAMs), with the focus on assessing the safety of cosmetic ingredients and products. It starts with innovation drivers and global regulatory responses, followed by an extensive, endpoint-specific overview of accepted/prospective NAMs. The overview covers main developments in acute toxicity, skin corrosion/irritation, serious eye damage/irritation, skin sensitisation, repeated dose toxicity, reproductive toxicity/endocrine disruption, mutagenicity/genotoxicity, carcinogenicity, photo-induced toxicity, and toxicokinetics. Specific attention was paid to the emerging in silico methodology. This paper also provides a brief overview of the studies on public perception of animal testing in cosmetics. It concludes with a view that educating consumers and inviting them to take part in advocacy could be an effective tool to achieve policy changes, regulatory acceptance, and investment in innovation.

Probabilistic risk assessment - the keystone for the future of toxicology

Safety sciences must cope with uncertainty of models and results as well as information gaps. Acknowledging this uncer-tainty necessitates embracing probabilities and accepting the remaining risk. Every toxicological tool delivers only probable results. Traditionally, this is taken into account by using uncertainty / assessment factors and worst-case / precautionary approaches and thresholds. Probabilistic methods and Bayesian approaches seek to characterize these uncertainties and promise to support better risk assessment and, thereby, improve risk management decisions. Actual assessments of uncertainty can be more realistic than worst-case scenarios and may allow less conservative safety margins. Most importantly, as soon as we agree on uncertainty, this defines room for improvement and allows a transition from traditional to new approach methods as an engineering exercise. The objective nature of these mathematical tools allows to assign each methodology its fair place in evidence integration, whether in the context of risk assessment, sys-tematic reviews, or in the definition of an integrated testing strategy (ITS) / defined approach (DA) / integrated approach to testing and assessment (IATA). This article gives an overview of methods for probabilistic risk assessment and their application for exposure assessment, physiologically-based kinetic modelling, probability of hazard assessment (based on quantitative and read-across based structure-activity relationships, and mechanistic alerts from in vitro studies), indi-vidual susceptibility assessment, and evidence integration. Additional aspects are opportunities for uncertainty analysis of adverse outcome pathways and their relation to thresholds of toxicological concern. In conclusion, probabilistic risk assessment will be key for constructing a new toxicology paradigm - probably!

An overview of current practices for regulatory risk assessment with lessons learnt from cosmetics in the European Union

Risk assessments of various types of chemical compounds are carried out in the European Union (EU) foremost to comply with legislation and to support regulatory decision-making with respect to their safety. Historically, risk assessment has relied heavily on animal experiments. However, the EU is committed to reduce animal experimentation and has implemented several legislative changes, which have triggered a paradigm shift towards human-relevant animal-free testing in the field of toxicology, in particular for risk assessment. For some specific endpoints, such as skin corrosion and irritation, validated alternatives are available whilst for other endpoints, including repeated dose systemic toxicity, the use of animal data is still central to meet the information requirements stipulated in the different legislations. The present review aims to provide an overview of established and more recently introduced methods for hazard assessment and risk characterisation for human health, in particular in the context of the EU Cosmetics Regulation (EC No 1223/2009) as well as the Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) Regulation (EC 1907/2006).

Safer chemicals using less animals: kick-off of the European ONTOX project

The 3Rs concept, calling for replacement, reduction and refinement of animal experimentation, is receiving increasing attention around the world, and has found its way to legislation, in particular in the European Union. This is aligned by continuing high-level efforts of the European Commission to support development and implementation of 3Rs methods. In this respect, the European project called "ONTOX: ontology-driven and artificial intelligence-based repeated dose toxicity testing of chemicals for next generation risk assessment" was recently initiated with the goal to provide a functional and sustainable solution for advancing human risk assessment of chemicals without the use of animals in line with the principles of 21^st century toxicity testing and next generation risk assessment. ONTOX will deliver a generic strategy to create new approach methodologies (NAMs) in order to predict systemic repeated dose toxicity effects that, upon combination with tailored exposure assessment, will enable human risk assessment. For proof-of-concept purposes, focus is put on NAMs addressing adversities in the liver, kidneys and developing brain induced by a variety of chemicals. The NAMs each consist of a computational system based on artificial intelligence and are fed by biological, toxicological, chemical and kinetic data. Data are consecutively integrated in physiological maps, quantitative adverse outcome pathway networks and ontology frameworks. Supported by artificial intelligence, data gaps are identified and are filled by targeted in vitro and in silico testing. ONTOX is anticipated to have a deep and long-lasting impact at many levels, in particular by consolidating Europe's world-leading position regarding the development, exploitation, regulation and application of animal-free methods for human risk assessment of chemicals.

A Robust, Mechanistically Based In Silico Structural Profiler for Hepatic Cholestasis

Owing to the primary role which it holds within metabolism of xenobiotics, the liver stands at heightened risk of exposure to, and injury from, potentially hazardous substances. A principal manifestation of liver dysfunction is cholestasis-the impairment of physiological bile circulation from its point of origin within the organ to the site of action in the small intestine. The capacity for early identification of compounds liable to exert cholestatic effects is of particular utility within the field of pharmaceutical development, where contribution toward candidate attrition is great. Shortcomings associated with the present in vitro methodologies forecasting cholestasis render their predictivity questionable, permitting scope for the adoption of computational toxicology techniques. As such, the intention of this study has been to construct an in silico profiler, founded upon clinical data, highlighting structural motifs most reliably associated with the end point. Drawing upon a list of >1500 small molecular drugs, compiled and annotated by Kotsampasakou, E. and Ecker, G. F. (J. Chem. Inf. Model. 2017, 57, 608-615), we have formulated a series of 15 structural alerts. These describe fragments intrinsic within distinct pharmaceutical classes including psychoactive tricyclics, β-lactam antimicrobials, and estrogenic/androgenic steroids. Description of the coverage and selectivity of each are provided, alongside consideration of the underlying reactive mechanisms and relevant structure-activity concerns. Provision of mechanistic anchoring ensures that potential exists for framing within the adverse outcome pathway paradigm-the chemistry conveyed through the alert, in particular enabling rationalization at the level of the molecular initiating event.

An ontology for developmental processes and toxicities of neural tube closure

In recent years, the development and implementation of animal-free approaches to chemical and pharmaceutical hazard and risk assessment has taken off. Alternative approaches are being developed starting from the perspective of human biology and physiology. Neural tube closure is a vital step that occurs early in human development. Correct closure of the neural tube depends on a complex interplay between proteins along a number of protein concentration gradients. The sensitivity of neural tube closure to chemical disturbance of signalling pathways such as the retinoid pathway, is well known. To map the pathways underlying neural tube closure, literature data on the molecular regulation of neural tube closure were collected. As the process of neural tube closure is highly conserved in vertebrates, the extensive literature available for the mouse was used whilst considering its relevance for humans. Thus, important cell compartments, regulatory pathways, and protein interactions essential for neural tube closure under physiological circumstances were identified and mapped. An understanding of aberrant processes leading to neural tube defects (NTDs) requires detailed maps of neural tube embryology, including the complex genetic signals and responses underlying critical cellular dynamical and biomechanical processes. The retinoid signaling pathway serves as a case study for this ontology because of well-defined crosstalk with the genetic control of neural tube patterning and morphogenesis. It is a known target for mechanistically-diverse chemical structures that disrupt neural tube closure The data presented in this manuscript will set the stage for constructing mathematical models and computer simulation of neural tube closure for human-relevant AOPs and predictive toxicology.

New ideas for non-animal approaches to predict repeated-dose systemic toxicity: Report from an EPAA Blue Sky Workshop

The European Partnership for Alternative Approaches to Animal Testing (EPAA) convened a 'Blue Sky Workshop' on new ideas for non-animal approaches to predict repeated-dose systemic toxicity. The aim of the Workshop was to formulate strategic ideas to improve and increase the applicability, implementation and acceptance of modern non-animal methods to determine systemic toxicity. The Workshop concluded that good progress is being made to assess repeated dose toxicity without animals taking advantage of existing knowledge in toxicology, thresholds of toxicological concern, adverse outcome pathways and read-across workflows. These approaches can be supported by New Approach Methodologies (NAMs) utilising modern molecular technologies and computational methods. Recommendations from the Workshop were based around the needs for better chemical safety assessment: how to strengthen the evidence base for decision making; to develop, standardise and harmonise NAMs for human toxicity; and the improvement in the applicability and acceptance of novel techniques. "Disruptive thinking" is required to reconsider chemical legislation, validation of NAMs and the opportunities to move away from reliance on animal tests. Case study practices and data sharing, ensuring reproducibility of NAMs, were viewed as crucial to the improvement of non-animal test approaches for systemic toxicity.

Dose addition in chemical mixtures inducing craniofacial malformations in zebrafish (Danio rerio) embryos

A challenge in cumulative risk assessment is to model hazard of mixtures. EFSA proposed to only combine chemicals linked to a defined endpoint, in so-called cumulative assessment groups, and use the dose-addition model as a default to predict combined effects. We investigated the effect of binary mixtures of compounds known to cause craniofacial malformations, by assessing the effect in the head skeleton (M-PQ angle) in 120hpf zebrafish embryos. We combined chemicals with similar mode of action (MOA), i.e. the triazoles cyproconazole, triadimefon and flusilazole; next, reference compounds cyproconazole or triadimefon were combined with dissimilar acting compounds, TCDD, thiram, VPA, prochloraz, fenpropimorph, PFOS, or endosulfan. These mixtures were designed as (near) equipotent combinations of the contributing compounds, in a range of cumulative concentrations. Dose-addition was assessed by evaluation of the overlap of responses of each of the 14 tested binary mixtures with those of the single compounds. All 10 test compounds induced an increase of the M-PQ angle, with varying potency and specificity. Mixture responses as predicted by dose-addition did not deviate from the observed responses, supporting dose-addition as a valid assumption for mixture risk assessment. Importantly, dose-addition was found irrespective of MOA of contributing chemicals.