New Approach Methodologies Research Articles

A critical review to identify data gaps and improve risk assessment of bisphenol A alternatives for human health.

Bisphenol A (BPA), a synthetic chemical widely used in the production of polycarbonate plastic and epoxy resins, has been associated with a variety of adverse effects in humans including metabolic, immunological, reproductive, and neurodevelopmental effects, raising concern about its health impact. In the EU, it has been classified as toxic to reproduction and as an endocrine disruptor and was thus included in the candidate list of substances of very high concern (SVHC). On this basis, its use has been banned or restricted in some products. As a consequence, industries turned to bisphenol alternatives, such as bisphenol S (BPS) and bisphenol F (BPF), which are now found in various consumer products, as well as in human matrices at a global scale. However, due to their toxicity, these two bisphenols are in the process of being regulated. Other BPA alternatives, whose potential toxicity remains largely unknown due to a knowledge gap, have also started to be used in manufacturing processes. The gradual restriction of the use of BPA underscores the importance of understanding the potential risks associated with its alternatives to avoid regrettable substitutions. This review aims to summarize the current knowledge on the potential hazards related to BPA alternatives prioritized by European Regulatory Agencies based on their regulatory relevance and selected to be studied under the European Partnership for the Assessment of Risks from Chemicals (PARC): BPE, BPAP, BPP, BPZ, BPS-MAE, and TCBPA. The focus is on data related to toxicokinetic, endocrine disruption, immunotoxicity, developmental neurotoxicity, and genotoxicity/carcinogenicity, which were considered the most relevant endpoints to assess the hazard related to those substances. The goal here is to identify the data gaps in BPA alternatives toxicology and hence formulate the future directions that will be taken in the frame of the PARC project, which seeks also to enhance chemical risk assessment methodologies using new approach methodologies (NAMs).

New approach methodologies (NAMs) for the in vitro assessment of cleaning products for respiratory irritation: workshop report.

The use of in vitro new approach methodologies (NAMs) to assess respiratory irritation depends on several factors, including the specifics of exposure methods and cell/tissue-based test systems. This topic was examined in the context of human health risk assessment for cleaning products at a 1-day public workshop held on 2 March 2023, organized by the American Cleaning Institute® (ACI). The goals of this workshop were to (1) review in vitro NAMs for evaluation of respiratory irritation, (2) examine different perspectives on current challenges and suggested solutions, and (3) publish a manuscript of the proceedings. Targeted sessions focused on exposure methods, in vitro cell/tissue test systems, and application to human health risk assessment. The importance of characterization of assays and development of reporting standards was noted throughout the workshop. The exposure methods session emphasized that the appropriate exposure system design depends on the purpose of the assessment. This is particularly important given the many dosimetry and technical considerations affecting relevance and translation of results to human exposure scenarios. Discussion in the in vitro cell/tissue test systems session focused on the wide variety of cell systems with varying suitability for evaluating key mechanistic steps, such as molecular initiating events (MIEs) and key events (KEs) likely present in any putative respiratory irritation adverse outcome pathway (AOP). This suggests the opportunity to further develop guidance around in vitro cell/tissue test system endpoint selection, assay design, characterization and validation, and analytics that provide information about a given assay's utility. The session on applications for human health protection emphasized using mechanistic understanding to inform the choice of test systems and integration of NAMs-derived data with other data sources (e.g., physicochemical properties, exposure information, and existing in vivo data) as the basis for in vitro to in vivo extrapolation. In addition, this group noted a need to develop procedures to align NAMs-based points of departure (PODs) and uncertainty factor selection with current human health risk assessment methods, together with consideration of elements unique to in vitro data. Current approaches are described and priorities for future characterization of in vitro NAMs to assess respiratory irritation are noted.

Animal-free safety assessment of chemicals: an innovation system perspective.

This perspective paper, which is the result of a collaborative effort between toxicologists and scholars in innovation and transition studies, presents a heuristic framework based on innovation system literature for understanding and appraising mission achievement to animal-free chemical safety assessment using New Approach Methodologies (NAMs). While scientific and technical challenges in this area are relatively well known, the recent establishment of missions and roadmaps to accelerate the acceptance and effective use of NAMs for chemical safety assessment raises new questions about how we can grasp the systemic nature of all changes needed in this transition. This includes recognising broader societal, institutional, and regulatory shifts necessary for NAM acceptance and uptake. Our paper discusses how the innovation system approach offers insights into key processes and associated activities that include as well as transcend the technical and scientific realm, and can help to accelerate acceptance and uptake of NAMs. Based on these insights, we present a comprehensive framework that, next to scientific and technological developments, recognises the need for coordinated efforts in areas like education, training, funding, policy-making, and public engagement to promote the acceptance and uptake of NAMs. Our framework can be used to perform structural and functional analyses of the innovation system of NAMs and animal-free safety assessment and as such provides handholds to track progress and organise collective efforts of actors to make sure we are moving in the right direction.

Standardization and optimization of the hiPSC-based PluriLum assay for detection of embryonic and developmental toxicants.

New approach methodologies (NAMs) for predicting embryotoxicity and developmental toxicity are urgently needed for generating human relevant data, while reducing turnover time and costs, and alleviating ethical concerns related to the use of animal models. We have previously developed the PluriLum assay, a NKX2.5-reporter gene 3D model using human-induced pluripotent stem cells (hiPSCs) that are genetically modified to enable the assessment of adverse effects of chemicals on the early-stage embryo. Aiming at improving the predictive value of the PluriLum assay for future screening purposes, we sought to introduce standardization steps to the protocol, improving the overall robustness of the PluriLum assay, as well as a shortening of the assay protocol. First, we showed that the initial size of embryoid bodies (EBs) is crucial for a proper differentiation into cardiomyocytes and overall reproducibility of the assay. When the starting diameter of the EBs exceeds 500 µm, robust differentiation can be anticipated. In terms of reproducibility, exposure to the fungicide epoxiconazole at smaller initial diameters resulted in a larger variation of the derived data, compared to more reliable concentration-response curves obtained using spheroids with larger initialdiameters. We further investigated the ideal length of the differentiation protocol, resulting in a shortening of the PluriLum assay by 24 h to 7 days. Following exposure to the teratogens all-trans and 13-cis retinoic acid, both cardiomyocyte contraction and measurement of NKX2.5-derived luminescence were recorded with a similar or increased sensitivity after 6 days of differentiation when compared to the original 7 days. Finally, we have introduced an efficient step for enzymatic dissociation of the EBs at assay termination. This allows for an even splitting of the individual EBs and testing of additional endpoints other than the NKX2.5-luciferase reporter, which was demonstrated in this work by the simultaneous assessment of ATP levels. In conclusion, we have introduced standardizations and streamlined the PluriLum assay protocol to improve its suitability as a NAM for screening of a large number of chemicals for developmental toxicity testing.

In silico models for the screening of human transthyretin disruptors

The use of New Approach Methodologies (NAMs), such as Quantitative Structure-Activity Relationship (QSAR) models, is highly recommended by international regulations to speed up hazard and risk assessment of Endocrine Disruptors, which are known to be linked to a wide spectrum of severe diseases on humans and wildlife. A very sensitive target for these chemicals is the thyroid hormone system, which plays a key role in regulating metabolic and cognitive functions. Several chemicals have been demonstrated to compete with the thyroid hormone thyroxine (T4) for binding to human thyroid hormone distributor protein transthyretin (hTTR). In this work, we generated three new datasets composed by T4-hTTR competing potencies of more than 200 heterogeneous chemicals measured by three different in vitro assays. These datasets were used for the development of new regression QSAR models. The best models were thoroughly validated by internal and external validation procedures. The mechanistic interpretation of the selected molecular descriptors provided information on structural features which are relevant to characterise hTTR binders, such as the presence of hydroxylated and halogenated aromatic rings. PCA analysis was used to rank the studied chemicals according to their increasing T4-hTTR competing potency. Hydroxylated and halogenated bicyclic aromatic compounds are ranked as the strongest hTTR binders. The new QSARs are useful to screen potential Thyroid Hormone System-Disrupting Chemicals (THSDCs), and to support the identification of sustainable alternatives to hazardous chemicals.

A proof-of-concept multi-tiered Bayesian approach for the integration of physiochemical properties and toxicokinetic time-course data for Daphnia magna

The use of in silico and in vitro methods, commonly referred to as New Approach Methodologies (NAMs), has been proposed to support environmental (and human) chemical safety decisions, ensuring enhanced environmental protection. Toxicokinetic models developed for environmentally relevant species are fundamental to the deployment of a NAMs-based safety strategy, enabling the conversion between external and internal chemical concentrations, although they require historical toxicokinetic data and robust physical models to be considered a viable solution. Daphnia magna is a key model organism in ecotoxicology albeit with limited and scattered quantitative toxicokinetic data, as for most invertebrates, resulting in a lack of robust toxicokinetic models. Moreover, current D. magna models are chemical specific, which restricts their applicability domain. One aim of this study was to address the current data availability limitations by collecting toxicokinetic time-course data for D. magna covering a broad chemical space and assessing the dataset's uniqueness. The collated toxicokinetic dataset included 48 time-courses for 30 chemicals from 17 studies, which was developed into an R package named AquaTK, with 11 studies unique to our work when compared to existing databases. Subsequently, a proof-of-concept Bayesian analysis was developed to estimate the steady-state concentration ratio (internal concentration / external concentration) from the data at three different levels of precision given three different data availability scenarios for environmental risk assessment. Specifically, an atrazine case study illustrates the multi-level modelling approach providing improvements (uncertainty reductions) in predictions of ratios for increasing amounts of data availability. Our work provides a consistent and self-contained Bayesian framework that irrespective of the hierarchy or resolution of individual experiments, can utilise the available information to generate optimal predictions of steady-state concentration ratios in D. magna. This approach is paramount to supporting the implementation of a NAMs based environmental safety paradigm shift in environmental risk assessment.

An industry perspective on the FDA modernization act 2.0/3.0: Potential next steps for sponsors to reduce animal use in drug development

Abstract Pharmaceutical developers are encouraged to adopt the best practices of being purposefully thoughtful about the use of animals, seeking alternatives wherever possible. They should engage with health authorities to increase their familiarity with the methods, study designs, data outputs and the context of use for new approach methodologies (NAMs). Although current state of technology does not yet provide adequate models to fully replace in vivo studies, many models are sufficiently good for an augmented approach that will enhance our understanding of in vitro to in vivo correlations and advance the long-term goal of reducing animal use through innovative NAMs. The goal of future nonclinical safety packages is to advance the utilization of such enabling technologies towards appropriate human risk characterization. Establishing confidence in NAMs is a critical first step. For example, sponsors may include both “traditional” and NAM-based nonclinical safety data in regulatory submissions to establish confidence with health authorities. In addition, regulators should create a “safe-harbor” for hybrid nonclinical data packages to facilitate iterative learning, refinement, and implementation of NAM-based safety assessment strategies. Sponsors are urged to contribute to NAMs evolution through consortia participation, peer-reviewed publications, and documenting animal reduction in studies/programs, accelerating the eventual elimination of animal use in pharmaceutical development, as envisioned in the FDA Modernization Act 3.0.

Differentially Induced Autophagy by Engineered Nanomaterial Treatment Has an Impact on Cellular Homeostasis and Cytotoxicity.

Considering the increasing production of engineered nanomaterials (ENMs), new approach methodologies (NAMs) are essential for safe-by-design approaches and risk assessment. Our aim was to enhance screening strategies with a focus on reactivity-triggered toxicities. We applied in vitro tests to 10 selected benchmark ENMs in two cell models, lung epithelial A549 and differentiated THP-1 macrophage-like cells. Previously, we categorized ENMs based on surface reactivity. Here we elucidated their reactivity-triggered cytotoxicity and mode of action using the WST-1 assay (metabolic activity), LDH assay (cell membrane integrity), autophagosome detection, and proteomics. Nonreactive SiO2 NM-200 showed no significant impact on cell viability. Conversely, highly reactive CuO and ZnO (NM-110 and NM-111) disrupted cell homeostasis. Interestingly, moderately reactive TiO2 (NM-101 and NM-105) and CeO2 (NM-211 and NM-212), apparently without an adverse effect, induced autophagosome formation, evidencing autophagy as a defensive mechanism. Our improved in vitro testing strategy, combined with state-of-the-art reactivity information, screens ENMs for potential reactivity-triggered toxicity.

Increasing Accessibility of Bayesian Network-Based Defined Approaches for Skin Sensitisation Potency Assessment.

Skin sensitisation is a critical adverse effect assessed to ensure the safety of compounds and materials exposed to the skin. Alongside the development of new approach methodologies (NAMs), defined approaches (DAs) have been established to promote skin sensitisation potency assessment by adopting and integrating standardised in vitro, in chemico, and in silico methods with specified data analysis procedures to achieve reliable and reproducible predictions. The incorporation of additional NAMs could help increase accessibility and flexibility. Using superior algorithms may help improve the accuracy of hazard and potency assessment and build confidence in the results. Here, we introduce two new DA models, with the aim to build DAs on freely available software and the newly developed kDPRA for covalent binding of a chemical to skin peptides and proteins. The new DA models are built on an existing Bayesian network (BN) modelling approach and expand on it. The new DA models include kDPRA data as one of the in vitro parameters and utilise in silico inputs from open-source QSAR models. Both approaches perform at least on par with the existing BN DA and show 63% and 68% accuracy when predicting four LLNA potency classes, respectively. We demonstrate the value of the Bayesian network's confidence indications for predictions, as they provide a measure for differentiating between highly accurate and reliable predictions (accuracies up to 87%) in contrast to low-reliability predictions associated with inaccurate predictions.

Leveraging new approach methodologies: ecotoxicological modelling of endocrine disrupting chemicals to Danio rerio through machine learning and toxicity studies

New approach methodologies (NAMs) offer information tailored to the intended application while reducing the use of animals. NAMs aim to develop quantitative structure-activity relationship (QSAR) and quantitive-Read-Across structure-activity relationship (q-RASAR) models to predict and categorize the acute toxicity of known and unknown endocrine-disrupting chemicals (EDCs) against zebrafish. EDCs are a diverse group of toxic substances that disrupt the endocrine system of humans and animals. The q-RASAR model was constructed and verified using validation metrics (R 2 = 0.886 and Q 2 = 0.814) which found to be more reliable model compare to QSAR model. The substructure fingerprint was well-fitted for the classification model and it was validated using 10-fold average accuracy (Q = 86.88%), specificity (Sp = 88.89%), Matthew’s correlation curve (MCC = 0.621) and receiver operating characteristics (ROC = 0.828). The dataset of unknown substances revealed that phenolphthalein (Php) exhibited a significant level of toxicity based on q-RASAR model. The docking and simulation study indicated that the computationally derived important features successfully bound to the target zebrafish sex hormone binding globulin (zfSHBG). The experimental LC50 value of 0.790 mg L−1 was very close to the predicted value of 0.763 mg L−1, which provides high confidence to the developed model.

Food for thought — Paving the way for a UK roadmap towards optimum consumer safety: Development, Endorsement and Regulatory acceptance of New Approach Methodologies (NAMs) in Chemical Risk Assessment and Beyond

Advances in biosciences, chemistry, technology, and computer sciences have resulted in the unparalleled development of candidate New Approach Methodologies over the last few years. Many of these are potentially invaluable in the safety assessment of chemicals, but very few have been adopted for regulatory decision making. There is an immediate opportunity to use NAMs in safety assessment where the vision is to be able to predict risk more rapidly, accurately, and efficiently to further assure consumer safety.In order to achieve this, the UK Food Standards Agency (FSA) and the Committee on Toxicity of Chemicals in Food, Consumer Products and the Environment (COT) have developed a roadmap towards acceptance and integration of these new approach methodologies into safety and risk assessments for regulatory decision making. The roadmap provides a UK blueprint for the transition of NAMs from the research laboratory to their use in regulatory decision making. This will require close collaboration across disciplines (chemists, toxicologists, informaticians, risk assessors and others), and across chemical sectors, to develop, verify and utilise appropriate models. Linking up internationally, and harmonization will be fundamental.

Unmasking metabolic disruptors: The NEMESIS project's quest for Novel Biomarkers, Evidence on Adverse Effects, and Efficient Methodologies

Metabolism disrupting chemicals (MDCs) elicit negative effects on metabolically active organs such as the liver and the pancreas, altering normal metabolic processes. Chemicals that are known, or suspected MDCs include compounds found in everyday consumer products and food, making low-dose, continuous exposure inevitable for humans. Through the discovery of chemically induced metabolic disruption, a concern has surfaced whether and how MDCs impact human health and the development of metabolic diseases. This has accelerated research around the topic, and it has been found that exposure to MDCs is linked to increased incidence of metabolic diseases including obesity and liver steatosis. Effective regulatory action is hindered by the lack of accurate methods to identify MDCs. The NEMESIS project addresses this regulatory gap by investigating the mechanisms through which MDCs cause metabolic disruption. The project aims at identifying novel biomarkers of exposure and link exposure to disease outcomes. As chemical toxicity testing is rapidly moving towards new approach methodologies (NAMs), NEMESIS promotes non-animal methodologies by employing state-of-the-art in vitro methods, epidemiological data, systems biology approaches, and seeks to replace mammalian in vivo experiments with alternative models. By understanding mechanisms of MDC-induced metabolic health effects, and through the development of reliable effect biomarkers and testing strategies, the NEMESIS project aims to facilitate more effective regulatory measures to improve and protect the health and well-being of EU citizens. The project is particularly focused on maximizing its impact through effective dissemination and communication efforts, to ensure that the project’s message and results reach a broad audience and are tailored to different population groups. These actions will improve the risk assessment of MDCs and ensure that the EU citizens are informed and protected from the harmful effects of MDCs and can adapt their consumer patterns and behaviors to prevent exposure.

VivoBodySeg: Machine learning-based analysis of C. elegans immobilized in vivoChip for automated developmental toxicity testing.

Developmental toxicity (DevTox) tests evaluate the adverse effects of chemical exposures on an organism's development. While large animal tests are currently heavily relied on, the development of new approach methodologies (NAMs) is encouraging industries and regulatory agencies to evaluate these novel assays. Several practical advantages have made C. elegans a useful model for rapid toxicity testing and studying developmental biology. Although the potential to study DevTox is promising, current low-resolution and labor-intensive methodologies prohibit the use of C. elegans for sub-lethal DevTox studies at high throughputs. With the recent availability of a large-scale microfluidic device, vivoChip, we can now rapidly collect 3D high-resolution images of ~ 1,000 C. elegans from 24 different populations. In this paper, we demonstrate DevTox studies using a 2.5D U-Net architecture (vivoBodySeg) that can precisely segment C. elegans in images obtained from vivoChip devices, achieving an average Dice score of 97.80. The fully automated platform can analyze 36 GB data from each device to phenotype multiple body parameters within 35 min on a desktop PC at speeds ~ 140× faster than the manual analysis. Highly reproducible DevTox parameters (4-8% CV) and additional autofluorescence-based phenotypes allow us to assess the toxicity of chemicals with high statistical power.

Proposal for a qualification system for New Approach Methodologies (NAMs) in the food and feed sector: example of implementation for nanomaterial risk assessment

Abstract Plenty of new approach methodologies (NAMs) for risk assessment have been developed but only some are included in OECD Test Guidelines (TGs) for regulatory implementation. Nevertheless, NAMs are increasingly applied, e.g. for nanomaterial (NM) risk assessments. The EFSA Guidance on NM risk assessment suggests that NAM‐derived data concerning degradation/dissolution (in relevant biofluids), intestinal uptake/crossing, genotoxicity, cytotoxicity, oxidative stress, (pro‐)inflammatory potential and barrier integrity, for many of which no OECD TGs exist, have to be evaluated first. Consequently, NM risk assessments involve data from non‐guideline studies, requiring time‐consuming and challenging case‐by‐case evaluations. Establishing an OECD TG is a formal process aiming for international use according to the Mutual Acceptance of Data (MAD). However, not every promising NAM can be prioritised for OECD TGs. A qualification, based on an expert opinion, may enable an efficient use of adequate NAMs for a specific context‐of‐use. Furthermore, it supports the optimisation of promising NAMs for regulatory applications. Existing qualification systems operate in the context of e.g., drug development tools (FDA) and research and development into pharmaceuticals (EMA). The NAMS4NANO consortium was tasked to propose a generic framework for a qualification system for chemical risk assessment in the food and feed sector to speed up the regulatory use of NAMs. Here we describe our proposal including the process and evaluation criteria. A detailed test method description, preferably as standard operating procedures (SOPs), describing the set‐up of the NAM including its application and evaluation phase is crucial. Furthermore, the scientific validity, i.e. its reliability and relevance for the context‐of‐use, needs to be demonstrated, for which we suggest a less rigorous process compared to OECD TGs. We propose to initially establish a qualification system for NM risk assessment, aligned with the EFSA framework. This document is an interim version to stipulate a broader discussion among experts and stakeholders.

Community-Engaged Research and the Use of Open Access ToxVal/ToxRef In Vivo Databases and New Approach Methodologies (NAM) to Address Human Health Risks From Environmental Contaminants.

The paper analyzes opportunities for integrating Open access resources (Abstract Sifter, US EPA and NTP Toxicity Value and Toxicity Reference [ToxVal/ToxRefDB]) and New Approach Methodologies (NAM) integration into Community Engaged Research (CEnR). CompTox Chemicals Dashboard and Integrated Chemical Environment with in vivo ToxVal/ToxRef and NAMs (in vitro) databases are presented in three case studies to show how these resources could be used in Pilot Projects involving Community Engaged Research (CEnR) from the University of California, Davis, Environmental Health Sciences Center. Case #1 developed a novel assay methodology for testing pesticide toxicity. Case #2 involved detection of water contaminants from wildfire ash and Case #3 involved contaminants on Tribal Lands. Abstract Sifter/ToxVal/ToxRefDB regulatory data and NAMs could be used to screen/prioritize risks from exposure to metals, PAHs and PFAS from wildfire ash leached into water and to investigate activities of environmental toxins (e.g., pesticides) on Tribal lands. Open access NAMs and computational tools can apply to detection of sensitive biological activities in potential or known adverse outcome pathways to predict points of departure (POD) for comparison with regulatory values for hazard identification. Open access Systematic Empirical Evaluation of Models or biomonitoring exposures are available for human subpopulations and can be used to determine bioactivity (POD) to exposure ratio to facilitate mitigation. These resources help prioritize chemical toxicity and facilitate regulatory decisions and health protective policies that can aid stakeholders in deciding on needed research. Insights into exposure risks can aid environmental justice and health equity advocates.

S10-02 New Approach Methodologies (NAMs): a quantitative in vitro to in vivo extrapolation case study with perfluorinated compounds

S10-02 New Approach Methodologies (NAMs): a quantitative in vitro to in vivo extrapolation case study with perfluorinated compounds

P19-63 Use of New Approach Methodologies (NAMs) to assess the safety of prostaglandins for use in cosmetics

P19-63 Use of New Approach Methodologies (NAMs) to assess the safety of prostaglandins for use in cosmetics

OS03-04 Integration of New Approach Methodologies (NAMs) data into hazard assessment of chemicals: a case study on three Azole Fungicides- Tebuconazole, Propiconazole, and Cyproconazole regulated under K-BPR

OS03-04 Integration of New Approach Methodologies (NAMs) data into hazard assessment of chemicals: a case study on three Azole Fungicides- Tebuconazole, Propiconazole, and Cyproconazole regulated under K-BPR

S19-02 Global initiatives to gain scientific confidence in New Approach Methodologies (NAMs)

S19-02 Global initiatives to gain scientific confidence in New Approach Methodologies (NAMs)

P19-32 Advancing the application of New Approach Methodologies (NAMs) in systemic toxicity assessment of cosmetic ingredients: insights from cosmetics Europe long range science strategy (2016–2022) case studies

P19-32 Advancing the application of New Approach Methodologies (NAMs) in systemic toxicity assessment of cosmetic ingredients: insights from cosmetics Europe long range science strategy (2016–2022) case studies