Use of New Approach Methodologies (NAMs) in regulatory decisions for chemical safety: Report from an EPAA Deep Dive Workshop.

New Approach Methodologies (NAMs) are considered to include any in vitro, in silico or chemistry-based method, as well as the strategies to implement them, that may provide information that could inform chemical safety assessment. Current chemical legislation in the European Union is limited in its acceptance of the widespread use of NAMs. The European Partnership for Alternative Approaches to Animal Testing (EPAA) therefore convened a 'Deep Dive Workshop' to explore the use of NAMs in chemical safety assessment, the aim of which was to support regulatory decisions, whilst intending to protect human health. The workshop recognised that NAMs are currently used in many industrial sectors, with some considered as fit for regulatory purpose. Moreover, the workshop identified key discussion points that can be addressed to increase the use and regulatory acceptance of NAMs. These are based on the changes needed in frameworks for regulatory requirements and the essential needs in education, training and greater stakeholder engagement as well the gaps in the scientific basis of NAMs.

Knowledge-Driven Approaches to Create the MTox700+ Metabolite Panel for Predicting Toxicity.

Endogenous metabolite levels describe the molecular phenotype that is most downstream from chemical exposure. Consequently, quantitative changes in metabolite levels have the potential to predict mode-of-action and adversity, with regulatory toxicology predicated on the latter. However, toxicity-related metabolic biomarker resources remain highly fragmented and incomplete. Although development of the S1500+ gene biomarker panel has accelerated the application of transcriptomics to toxicology, a similar initiative for metabolic biomarkers is lacking. Our aim was to define a publicly available metabolic biomarker panel, equivalent to S1500+, capable of predicting pathway perturbations and/or adverse outcomes. We conducted a systematic review of multiple toxicological resources, yielding 189 proposed metabolic biomarkers from existing assays (BASF, Bowes-44, and Tox21), 342 biomarkers from databases (Adverse Outcome Pathway Wiki, Comparative Toxicogenomics Database, QIAGEN Ingenuity Pathway Analysis, and Toxin and Toxin-Target Database), and 435 biomarkers from the literature. Evidence mapping across all 8 resources generated a panel of 722 metabolic biomarkers for toxicology (MTox700+), of which 462 (64%) are associated with molecular pathways and 575 (80%) with adverse outcomes. Comparing MTox700+ and S1500+ revealed that 418 (58%) metabolic biomarkers associate with pathways shared across both panels, with further metabolites mapping to unique pathways. Metabolite reference standards are commercially available for 646 (90%) of the panel metabolites, and assays exist for 578 (80%) of these biomarkers. This study has generated a publicly available metabolic biomarker panel for toxicology, which through its future laboratory deployment, is intended to help build foundational knowledge to support the generation of molecular mechanistic data for chemical hazard assessment.

Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology.

Omics methodologies are widely used in toxicological research to understand modes and mechanisms of toxicity. Increasingly, these methodologies are being applied to questions of regulatory interest such as molecular point-of-departure derivation and chemical grouping/read-across. Despite its value, widespread regulatory acceptance of omics data has not yet occurred. Barriers to the routine application of omics data in regulatory decision making have been: 1) lack of transparency for data processing methods used to convert raw data into an interpretable list of observations; and 2) lack of standardization in reporting to ensure that omics data, associated metadata and the methodologies used to generate results are available for review by stakeholders, including regulators. Thus, in 2017, the Organisation for Economic Co-operation and Development (OECD) Extended Advisory Group on Molecular Screening and Toxicogenomics (EAGMST) launched a project to develop guidance for the reporting of omics data aimed at fostering further regulatory use. Here, we report on the ongoing development of the first formal reporting framework describing the processing and analysis of both transcriptomic and metabolomic data for regulatory toxicology. We introduce the modular structure, content, harmonization and strategy for trialling this reporting framework prior to its publication by the OECD.

Utility of In Vitro Bioactivity as a Lower Bound Estimate of In Vivo Adverse Effect Levels and in Risk-Based Prioritization.

Use of high-throughput, in vitro bioactivity data in setting a point-of-departure (POD) has the potential to accelerate the pace of human health safety evaluation by informing screening-level assessments. The primary objective of this work was to compare PODs based on high-throughput predictions of bioactivity, exposure predictions, and traditional hazard information for 448 chemicals. PODs derived from new approach methodologies (NAMs) were obtained for this comparison using the 50th (PODNAM, 50) and the 95th (PODNAM, 95) percentile credible interval estimates for the steady-state plasma concentration used in in vitro to in vivo extrapolation of administered equivalent doses. Of the 448 substances, 89% had a PODNAM, 95 that was less than the traditional POD (PODtraditional) value. For the 48 substances for which PODtraditional < PODNAM, 95, the PODNAM and PODtraditional were typically within a factor of 10 of each other, and there was an enrichment of chemical structural features associated with organophosphate and carbamate insecticides. When PODtraditional < PODNAM, 95, it did not appear to result from an enrichment of PODtraditional based on a particular study type (eg, developmental, reproductive, and chronic studies). Bioactivity:exposure ratios, useful for identification of substances with potential priority, demonstrated that high-throughput exposure predictions were greater than the PODNAM, 95 for 11 substances. When compared with threshold of toxicological concern (TTC) values, the PODNAM, 95 was greater than the corresponding TTC value 90% of the time. This work demonstrates the feasibility, and continuing challenges, of using in vitro bioactivity as a protective estimate of POD in screening-level assessments via a case study.

The implementation of RAAF in the OECD QSAR Toolbox.

The Read-Across Assessment Framework (RAAF) was developed by the European Chemicals Agency (ECHA) as an internal tool providing a framework for a consistent, structured and transparent assessment of grouping of chemicals and read-across. Following a RAAF-based evaluation, also developers and users of read-across predictions outside ECHA can judge whether their read-across rationale is sufficiently robust from a regulatory perspective. The aim of this paper is to describe the implementation of RAAF functionalities in the OECD QSAR Toolbox report. These can be activated in the prediction report after performing a readacross prediction. Once the user manually selects the appropriate scenario, the RAAF assessment elements appear and are automatically aligned with the suitable category elements of the Toolbox report. Subsequently, these are evaluated as part of the category consistency assessment functionality. The implementation of the RAAF functionality is illustrated in practice with two examples.

(Q)SARs as Adaptations to REACH Information Requirements.

REACH is a regulation of the European Union adopted to improve the safe use of chemicals with regard to human health and the environment. The safe use of chemicals can be achieved only if the hazard and the exposure of the substances are well characterized. Testing on animals has been traditionally the main tool for hazard assessment. For ethical and economic reasons, alternative ways of testing that do not use laboratory animals have been developed by different parties (regulatory agencies, researchers, industry) over the recent decades, and their proper use in hazard assessment is encouraged under REACH. In this chapter, we describe how (Q)SAR models and predictions are included into REACH and their adequate use promoted by the European Chemicals Agency (ECHA).

How Adverse Outcome Pathways Can Aid the Development and Use of Computational Prediction Models for Regulatory Toxicology.

Efforts are underway to transform regulatory toxicology and chemical safety assessment from a largely empirical science based on direct observation of apical toxicity outcomes in whole organism toxicity tests to a predictive one in which outcomes and risk are inferred from accumulated mechanistic understanding. The adverse outcome pathway (AOP) framework provides a systematic approach for organizing knowledge that may support such inference. Likewise, computational models of biological systems at various scales provide another means and platform to integrate current biological understanding to facilitate inference and extrapolation. We argue that the systematic organization of knowledge into AOP frameworks can inform and help direct the design and development of computational prediction models that can further enhance the utility of mechanistic and in silico data for chemical safety assessment. This concept was explored as part of a workshop on AOP-Informed Predictive Modeling Approaches for Regulatory Toxicology held September 24-25, 2015. Examples of AOP-informed model development and its application to the assessment of chemicals for skin sensitization and multiple modes of endocrine disruption are provided. The role of problem formulation, not only as a critical phase of risk assessment, but also as guide for both AOP and complementary model development is described. Finally, a proposal for actively engaging the modeling community in AOP-informed computational model development is made. The contents serve as a vision for how AOPs can be leveraged to facilitate development of computational prediction models needed to support the next generation of chemical safety assessment.

Analysis of the ecotoxicity data submitted within the framework of the REACH Regulation. Part 2. Experimental aquatic toxicity assays.

This paper summarises the aquatic ecotoxicity data submitted in the REACH(1) registration dossiers and disseminated by the European Chemicals Agency (ECHA(2)). The analysis describes both the guidelines and the species mostly used by registrants. Non-OECD guidelines have been extensively used, in particular in covering of fish and aquatic invertebrate studies, but the main concern is that in 22-36% of the cases, depending on the endpoint, no information on the methodological approach and potential equivalences to test guidelines has been provided. As expected, most studies were conducted with those species typically used in laboratory ecotoxicity testing; nevertheless, the database provides a broad range of available species, covering the most relevant taxonomic groups for both freshwater and marine systems, although most are just occasionally used. This species diversity is essential for higher tier testing strategies, including the use of Species Sensitivity Distribution approaches. The assessment suggests that collecting available information has been the main approach used by registrants to fulfil their REACH information requirements for this first REACH registration deadline. Many studies are disclosed for the first time, and all are available through searchable web tools.

Analysis of the ecotoxicity data submitted within the framework of the REACH Regulation. Part 1. General overview and data availability for the first registration deadline.

REACH(1) entered into force in June 2007 and has hence been operational for six years. With the first registration deadline in November 2010, the European Chemicals Agency (ECHA(2)) has received a large amount of scientific and administrative information related to chemical substances. In order to understand what type of data on ecotoxicity endpoints was submitted under the REACH framework a detailed analysis of the availability and content of relevant information was performed. To avoid unnecessary testing, the REACH Regulation provides registrants with the possibility to build testing strategies and to adopt the standard information requirements based on the specific conditions listed in the regulation. The types of information submitted by registrants to fulfil data requirements for aquatic, sediment and terrestrial toxicity endpoints were analysed. The REACH database analysis confirms large differences in the availability of experimental aquatic versus sediment and soil ecotoxicity data. Information requirements on aquatic organisms are mainly covered by experimental data, while those for sediment and soil are mostly waived.

Analysis of the ecotoxicity data submitted within the framework of the REACH Regulation: part 4. Experimental terrestrial toxicity assays.

This paper summarises the terrestrial ecotoxicity data submitted in the REACH registration dossiers and disseminated by ECHA. The analysis describes both the guidelines and the test species mostly used by registrants. REACH information requirements in relation to the effects on terrestrial organisms encompass three trophic levels; invertebrates, plants and micro-organisms, and the study of both long and short-term exposure. The results observed for soil invertebrates showed that on one hand there was a clear prevalence for testing on the species recommended by the standard test guidelines. On the other, the reporting included a large variety of species from very different families, demonstrating the feasibility for conducting toxicity tests on a number of relevant groups e.g. for species sensitivity distribution approaches. Standard toxicity testing with terrestrial plants under REACH follows a different approach and requires simultaneous testing on several species, using the same test conditions, adapted to each species, if needed. The test methods used to conduct the studies were only reported for 30% of cases. The most extensively reported test guidelines for terrestrial plants were OECD 208, ISO 11269-1 and ISO 11269-1. Information requirements for soil micro-organisms under REACH are related to the analysis of functional endpoints instead of on species or taxa. As recommended in REACH, OECD 216 and OECD 217 were the most often used test methods for soil micro-organisms. But overall, the test method was reported for only about 40% of the experimental studies. Moreover, it is noted that information on potential effects on soil micro-organisms is available for a limited number of REACH registered substances. The assessment suggests that providing waiving justifications and collecting available information, which in many cases might be well used for covering standard REACH data requirements, have been the main approaches used by registrants for the first REACH registration deadline.

Analysis of the ecotoxicity data submitted within the framework of the REACH Regulation. Part 3. Experimental sediment toxicity assays.

For the first REACH registration deadline, companies have submitted registrations with relevant hazard and exposure information for substances at the highest tonnage level (above 1000 tonnes per year). At this tonnage level, information on the long-term toxicity of a substance to sediment organisms is required. There are a number of available test guidelines developed and accepted by various national/international organisations, which can be used to investigate long-term toxicity to sediment organisms. However instead of testing, registrants may also use other options to address toxicity to sediment organisms, e.g. weight of evidence approach, grouping of substances and read-across approaches, as well as substance-tailored exposure-driven testing. The current analysis of the data provided in ECHA database focuses on the test methods applied and the test organisms used in the experimental studies to assess long-term toxicity to sediment organisms. The main guidelines used for the testing of substances registered under REACH are the OECD guidelines and OSPAR Protocols on Methods for the Testing of Chemicals used in the Offshore Oil Industry: "Part A: A Sediment Bioassay using an Amphipod Corophium sp." explaining why one of the mostly used test organisms is the marine amphipod Corophium sp. In total, testing results with at least 40 species from seven phyla are provided in the database. However, it can be concluded that the ECHA database does not contain a high enough number of available experimental data on toxicity to sediment organisms for it to be used extensively by the scientific community (e.g. for development of non-testing methods to predict hazards to sediment organisms).

Development of micro-electrode array based tests for neurotoxicity: assessment of interlaboratory reproducibility with neuroactive chemicals.

Neuronal assemblies within the nervous system produce electrical activity that can be recorded in terms of action potential patterns. Such patterns provide a sensitive endpoint to detect effects of a variety of chemical and physical perturbations. They are a function of synaptic changes and do not necessarily involve structural alterations. In vitro neuronal networks (NNs) grown on micro-electrode arrays (MEAs) respond to neuroactive substances as well as the in vivo brain. As such, they constitute a valuable tool for investigating changes in the electrophysiological activity of the neurons in response to chemical exposures. However, the reproducibility of NN responses to chemical exposure has not been systematically documented. To this purpose six independent laboratories (in Europe and in USA) evaluated the response to the same pharmacological compounds (Fluoxetine, Muscimol, and Verapamil) in primary neuronal cultures. Common standardization principles and acceptance criteria for the quality of the cultures have been established to compare the obtained results. These studies involved more than 100 experiments before the final conclusions have been drawn that MEA technology has a potential for standard in vitro neurotoxicity/neuropharmacology evaluation. The obtained results show good intra- and inter-laboratory reproducibility of the responses. The consistent inhibitory effects of the compounds were observed in all the laboratories with the 50% Inhibiting Concentrations (IC(50)s) ranging from: (mean ± SEM, in µM) 1.53 ± 0.17 to 5.4 ± 0.7 (n = 35) for Fluoxetine, 0.16 ± 0.03 to 0.38 ± 0.16 µM (n = 35) for Muscimol, and 2.68 ± 0.32 to 5.23 ± 1.7 (n = 32) for Verapamil. The outcome of this study indicates that the MEA approach is a robust tool leading to reproducible results. The future direction will be to extend the set of testing compounds and to propose the MEA approach as a standard screen for identification and prioritization of chemicals with neurotoxicity potential.

Application of micro-electrode arrays (MEAs) as an emerging technology for developmental neurotoxicity: evaluation of domoic acid-induced effects in primary cultures of rat cortical neurons.

Due to lack of knowledge only a few industrial chemicals have been identified as developmental neurotoxicants. Current developmental neurotoxicity (DNT) guidelines (OECD and EPA) are based entirely on in vivo studies that are both time consuming and costly. Consequently, there is a high demand to develop alternative in vitro methods for initial screening to prioritize chemicals for further DNT testing. One of the most promising tools for neurotoxicity assessment is the measurement of neuronal electrical activity using micro-electrode arrays (MEAs) that provides a functional and neuronal specific endpoint that until now has been used mainly to detect acute neurotoxicity. Here, electrical activity measurements were evaluated to be a suitable endpoint for the detection of potential developmental neurotoxicants. Initially, primary cortical neurons grown on MEA chips were characterized for different cell markers over time, using immunocytochemistry. Our results show that primary cortical neurons could be a promising in vitro model for DNT testing since some of the most critical neurodevelopment processes such as progenitor cell commitment, proliferation and differentiation of astrocytes and maturation of neurons are present. To evaluate if electrical activity could be a suitable endpoint to detect chemicals with DNT effects, our model was exposed to domoic acid (DomA), a potential developmental neurotoxicant for up to 4 weeks. Long-term exposure to a low concentration (50nM) of DomA increased the basal spontaneous electrical activity as measured by spike and burst rates. Moreover, the effect induced by the GABA(A) receptor antagonist bicuculline was significantly lower in the DomA treated cultures than in the untreated ones. The MEA measurements indicate that chronic exposure to DomA changed the spontaneous electrical activity leading to the possible neuronal mal functioning. The obtained results suggest that the MEAs could be a useful tool to identify compounds with DNT potential.

Generation of functional neural artificial tissue from human umbilical cord blood stem cells.

Stem cell-based regenerative neurology is an emerging concept for treatment of diseases of central nervous system. Among variety of proposed procedures, one of the most promising is refilling of cystic cavities of injured brain parenchyma with artificial neural tissue. Recent studies revealed that after allogenic transplantation in rodents these tissue-engineered entities were shown efficient in repair of hypoxic/ischemic brain injury. Human umbilical cord blood (HUCB) was recognized to be an efficient and noncontroversial source of neural stem cells (NSC). The main purpose of this study was to generate HUCB-derived neural artificial tissue and investigate their functional properties. Neural organoids formed on human-originated biodegradable scaffolds within 3 weeks and resembled niche structure where immature stem cells (Oct4+ and Sox2+) and proliferating neuroblasts (Nestin+, GFAP+, and Ki67+) were present. Such aggregates were placed on multi-electrode chips and differentiated toward mature neurons (TUJ1+ and MAP2+). These three-dimensional aggregates in contrast to two-dimensional cultures formed functional circuits and generated spontaneous field/action potentials. Our results indicate that three-dimensional environment facilitates maturation of HUCB-derived NSC what should be considered regarding regenerative medicine application.

Micro-stamped surfaces for the patterned growth of neural stem cells.

We present a method for patterning neural stem cells based on pre-patterning polypeptides on a cell-repellent surface (poly(ethylene) oxide-like, PEO-like, plasma-deposited films). The method ensures cell attachment and stability for several weeks, as well as it allows cell migration and differentiation. Various patterns of approximately 1 nm thick cell adhesive poly-L-lysine (PLL) have been created on a cell-repellent PEO-like matrix by microcontact printing using different array configurations and printing conditions. The cell-repellent property of PEO-like film determined the confinement of the cells on the printed patterns. Optimization of the printing method showed that the most homogeneous patterns over large areas were obtained using PLL diluted in carbonate buffer (100mM) at pH 8.4. Neural stem cells cultured on the PLL patterns in low serum and in differentiating medium over 20 days exhibited a good confinement to the polypeptide domains. The number of cells attached increased linearly with the micro-stamped PLL area. The cells were able to extend random axon-like projections to the outside of the patterns and presented high amount of ramifications when cultured in differentiating medium. Migration and axon-like outgrowth have been successfully guided by means of an interconnected squares configuration. The surfaces are suitable for controlling the patterning of stem cells and provide a platform for the assessment of the way how different cell arrangements and culture conditions influence cell interactions and cell developmental processes.

Digital movie analysis for quantification of beating frequencies, chronotropic effects, and beating areas in cardiomyocyte cultures.

Software, named Cardio Analyser, was developed for digital movie analysis of beating frequencies, drug-induced chronotropic effects, and quantification of beating areas of contracting cardiomyocyte cultures. A major novelty of the software is the introduction of automated noise filtering and automated movie analysis of beating frequencies and areas of contracting cardiomyocyte cultures. The software was based on the observation that the intensity of light transmitted through a contractive tissue changes periodically in a way that correlates with the contractions. We provided proof of principle for the method by derivation of relevant data from movies of multicellular cardiomyocyte cultures derived from embryonic stem cells. Moreover, we compared the data to equivalent results obtained by extracellular electric field potential recordings. The comparison demonstrated higher sensitivity to chronotropic effects of the beta-adrenoceptor agonist isoprenaline, and hence implied that more embryonic stem cells underwent differentiation into beta-adrenoceptor-responding cardiomyocytes, in the experimental setup applied for movie analysis than in the setup used for extracellular electric field potential recordings. Our study indicates that the movie analysis method may have potential to be optimized for screening in early drug discovery, aiming to identify cardiac drug candidates or to alert for adverse effects on heart functionality or embryonic heart development.

Electrophysiological recording of re-aggregating brain cell cultures on multi-electrode arrays to detect acute neurotoxic effects.

Neurotoxicity aims to understand how xenobiotics interfere with the function of the nervous system and to unravel their mechanisms of action. Neuronal activity is the primary functional output of the nervous system and deviations from its resting level may indicate toxicity. Consequently, the monitoring of electrophysiological activity in complex cell culture systems appears particularly promising for neurotoxicity assessment. To detect acute neurotoxic effects of chemicals we developed a test system based on the electrophysiological recordings from neural networks in re-aggregating brain cell cultures using multi-electrode arrays. We characterised the electrophysiological properties of the cultures and, using known neurotoxicants, evaluated their usefulness to predict neurotoxic effects. Aggregates displayed evoked field potentials and spontaneous neural activity involving glutamatergic and GABAergic synaptic transmission. Paired pulse inhibition indicated the presence of short-term synaptic plasticity via functional inhibitory networks. Cultures were treated with 0.1-100 microM of trimethyltin chloride (TMT), methyl mercury chloride (MeHgCl), parathion or paraoxon, and with 0.1-100mM of ethanol for up to 100 min. TMT (10 microM), MeHgCl (1 microM) and ethanol (100mM) all decreased the amplitude of evoked field potential. The effect of ethanol was reversible. In contrast paraoxon (10 microM) increased the amplitudes of evoked field potentials while parathion showed no significant effects. The effects of TMT and ethanol on the frequency of spontaneous activity were consistent with those obtained for evoked field potentials. All effects occurred at levels at which cytotoxic injuries were not detectable. Taken together our system expressed electrophysiological properties similar to those of established slice culture preparations. It detected known neurotoxicants at subcytotoxic levels and therefore appears suitable for the assessment of toxic insults specifically interfering with nervous system function, e.g. neuronal activity, synaptic transmission and short-term plasticity. If incorporated into testing strategies, it might represent a valuable tool for the mechanistic assessment of neurotoxic effects.