An adverse outcome pathway on the disruption of retinoic acid metabolism leading to developmental craniofacial defects

A pragmatic workflow for human relevance assessment of toxicological pathways and associated new approach methodologies

Currently, safety assessments of chemical substances are predominantly based on animal data. Multiple considerations call for the use of alternative testing strategies that are based on new approach methodologies (NAMs). However, the human relevance of these testing strategies is usually uncertain. This necessitates a harmonized and accepted workflow for assessing their applicability for regulatory purposes. This report proposes such a workflow, applicable for assessing the human relevance of a toxicological pathway and the relevance of NAMs related to the different components of the pathway. The workflow starts with an established toxicological pathway, of which the adverse outcome is relevant for human health risk assessment and that has sufficient weight of evidence. Human relevance is assessed through three main questions, related to the different components (steps) of the pathway, the pathology of human syndromes that have a similar adverse outcome, and quantitative aspects. The latter comprise both interspecies differences and in vitro - in vivo differences. The combined evidence is scored as 'strong', 'moderate' or 'weak' support of human relevance, based on expert judgement. The workflow developed was tested in a case study, through application to an AOP describing craniofacial malformations after in utero exposure to triazoles. Based on evidence collected for two of the three main questions, the case study provided moderate to strong support for human relevance of both the various components of the AOP and its associated NAMs. Furthermore, it demonstrated that the workflow is a promising approach that allows for a more transparent scientific evaluation of human relevance of toxicological pathways and associated NAMs. Therefore, despite some areas for improvement, we consider the workflow an important step forward for application of AOPs and related NAMs in human health risk assessment.

Critical appraisal of the expert knowledge elicitation (EKE) methodology to identify uncertainties in building cumulative assessment groups for craniofacial alterations

The European Food Safety Authority (EFSA) conducted a retrospective cumulative dietary risk assessment (CRA) on active substances (AS) and metabolites included in the plant protection products registered in Europe which could provoke craniofacial alterations. Two Cumulative Assessment groups (CAGs) were established: one for alterations due to abnormal skeletal development (CAG-DAC) and one for head soft tissue alterations and brain neural tube defects (CAG-DAH). The probability that each substance is correctly assigned to the specific CAGs (CAG-membership probability) was assessed using weight of evidence and expert knowledge elicitation (EKE) techniques conducted for the six substances identified as risk drivers in each CAG. Four out of the six substances allocated to the CAG-DAC or to the CAG-DAH presented a large interval of uncertainty, with probability of belonging to the attributed CAG between 10 % and 70 % or 33-90 %, which makes it difficult to determine if the substances truly belong to the CAG. In the present work the probability ranges of each risk driver were reassigned according to the approximate probability scale recommended in the EFSA guidance on uncertainty analysis. It is proposed that AS with a high probability are to be included in the CAG and those with a low probability removed from the CAG. For compounds with very large probability ranges, uncertainty assessments would have to be redone to reach narrower probability ranges. Finally, whenever recent decisions on reproduction toxicity classifications made by the European Chemical Agency (ECHA) are available, these should be used to conclude on CAG memberships.

Cumulative risk assessment methodology applied to non-dietary exposures: developmental alterations in professional agricultural settings

The safety assessment of combined exposure to xenobiotics has been an emerging topic for several years. Methodologies and approaches for cumulative risk assessment (CRA) are being developed primarily for the dietary risk assessment of pesticides, thus focusing only on consumer exposure. However, as highlighted in recent years, non-dietary exposures, such as those encountered by professionals in agricultural settings, may pose a significant risk due to their higher levels compared to dietary exposure. Despite this, existing methodologies for cumulative risk assessment (CRA) have not adequately addressed this critical aspect. In the EU, even if several legislations highlight the need to address the non-dietary CRA, no legal requirements are in place yet, therefore, there are no harmonized methodologies and approaches currently available. In a first step to fill this gap, this study is aimed at exploring CRA methodology applied to non-dietary exposure to pesticide in agricultural settings, specifically targeting operators, re-entry workers, and bystanders. The primary objective of the study was to verify the feasibility of an electronic register of plant protection treatments as data source for identifying and characterizing in field mixtures and consequently estimating cumulative non-dietary systemic exposure in real life. The relevant active substances selected for this investigation were those listed in foetal craniofacial alterations cumulative assessment groups (CAGs), established by the European Food Safety Authority (EFSA) for dietary CRA. Exposures to pesticides were estimated using European Union agreed mathematical models. The preliminary findings of this investigation effectively revealed the value of the register of treatments in assessing real-life plant protection products (PPP) usage in professional agricultural settings. In conclusion, the study provides encouraging insights into using the pesticide dietary CRA approach for non-dietary risk assessment in agricultural settings, underlining the necessity for further research and investigation of its feasibility for the evaluation of other acute effects but also for long-term effects related CAGs.

Assessing molecular changes underlying isopropylated phenyl phosphate (IPP)-induced larval sensorimotor response deficits in zebrafish

Isopropylated phenyl phosphates (IPP) are an additive organophosphate flame retardant (OPFR) that has been extensively used in furniture, electronics, automobiles, plastics, and children's products to slow down the spread of fire but its continued leaching leads to toxicity concerns. Toxicological information on this important legacy contaminant is limiting. Using zebrafish, our prior whole embryonic RNA-seq data revealed disruption of gene sets enriched for DNA methylation, neurotransmitter synthesis, retinoic acid signaling and eye development. Within this study, we used zebrafish embryos to systemically study these biological targets. Our initial range-finding experiments revealed significant morphological impacts like pericardial edema, yolk sac edema and spinal curvature, coupled with a significant increase in the levels of dopamine and 3-methoxytyramine. We then conducted an in vitro retinoic acid receptor (RAR) assay and showed that IPP inhibits RARα, but not RARβ and RARγ. Following this, our larval behavioral (photomotor and acoustic response assays) at environmentally relevant, sub-μM concentrations showed significant hypoactivity, indicating sensorimotor deficits within exposed embryo. We then assessed global DNA methylation using a combination of whole-mount immunohistochemistry and ELISA for 5-methylcytosine (5-mC) and showed significant IPP-induced hypermethylation within whole embryo in situ. Finally, we focused on eye and brains as targets. We dissected eyes and brains from IPP-exposed larvae and conducted 5-mC assessments and mRNA-sequencing. Interestingly, neither of the organs showed differences in 5-mC levels and the brains also did not show substantial transcriptomic effects. However, for eyes, mRNA sequencing showed 135 differentially expressed genes and these were enriched for several nervous system-associated pathways, including voltage gated ion channel activity, synaptic transmission and neurotransmitter signaling. Collectively, our data shows that IPP exposures can disrupt a battery of biological pathways spanning neurometabolomic, genetic, epigenetic as well as organ-level targets. Notably, these impacts occur at concentrations within environmental relevance where overt toxic morphological phenotypes are not recorded. Future work will focus on understanding the contribution of these molecular targets to behavioral phenotypes.

An adverse outcome pathway approach linking retinoid signaling disruption to teratogenicity and population-level outcomes

Recent research efforts in endocrine disruption have focused on evaluating non-EATS (estrogen, androgen, thyroid, and steroidogenesis) pathways. Retinoid signaling disruption is noteworthy because of its teratogenic effects and environmental relevance. However, current environmental risk assessments are limited in their ability to evaluate impacts on individuals and populations. This study characterizes an Adverse Outcome Pathway (AOP) network linking retinoid signaling disruption to teratogenicity and survival in zebrafish. We identified Retinoic Acid Receptor (RAR) overactivation as the molecular initiating event leading to key events including craniofacial (CFM) and tail (TM) malformations, posterior swim bladder (SB) non-inflation, impaired swimming performance, and reduced feeding, ultimately resulting in decreased survival. Our study (1) determines critical sensitivity windows for CFM, posterior SB non-inflation, and TM, (2) provides quantitative measurements for CFM and TM, and (3) defines impacts on higher biological levels including food ingestion, swimming, and survival. Results show that all-trans retinoic acid (ATRA) induces strong teratogenic effects with sensitivity windows between 4 and 48 h post fertilization (hpf) for CFM, TM, and posterior SB non-inflation. TM is the most sensitive indicator, with EC50 of 0.2 - 0.26 µg/L across exposure windows 4-48, 4-72, 4-96, and 4-120 hpf. Besides inducing known malformations, ATRA impaired posterior SB inflation with EC50 of 1 - 1.21 µg/L across the same exposure windows. ATRA exposure (1 µg/L) resulted in 50 % food ingestion inhibition at 7 days post fertilization (dpf) and 10 % survival at 14 dpf. This study provides a regulatory-relevant framework linking developmental effects to population outcomes, highlighting ecological risks and needs for improved risk assessments.

Developmental exposure to pesticides that disrupt retinoic acid signaling causes persistent retinoid and behavioral dysfunction in zebrafish

Early developmental exposure to environmental toxicants may play a role in the risk for developing autism. A variety of pesticides have direct effects on retinoic acid (RA) signaling and as RA signaling has important roles in neurodevelopment, such compounds may cause developmental neurotoxicity through an overlapping adverse outcome pathway. It is hypothesized that a pesticide's embryonic effects on retinoid function may correspond with neurobehavioral disruption later in development. In the current studies, we determined the effects of RA-acting pesticides on neurobehavioral development in zebrafish. Buprofezin and imazalil caused generalized hypoactivity in the larval motility test, whereas chlorothalonil and endosulfan I led to selective hypoactivity and hyperactivity, respectively. With buprofezin, chlorothalonil, and imazalil, hypoactivity and/or novel anxiety-like behaviors persisted in adulthood and buprofezin additionally decreased social attraction responses in adulthood. Endosulfan I did not produce significant adult behavioral effects. Using qPCR analyses of adult brain tissue, we observed treatment-induced alterations in RA synthesis or catabolic genes, indicating persistent changes in RA homeostasis. These changes were compound-specific, with respect to expression directionality, and potential patterns of homeostatic disruption. Results suggest the likely persistence of disruptions in RA signaling well into adulthood and may represent compensatory mechanisms following early life stage exposures. This study demonstrates that early developmental exposure to environmental toxicants that interfere with RA signaling causes short as well as long-term behavioral disruption in a well-established zebrafish behavioral model and expand upon the meaning of the RA adverse outcome pathway, indicating that observed effects likely correspond with the nature of underlying homeostatic effects.

Thallium - poisoner's poison: An overview and review of current knowledge on the toxicological effects and mechanisms

Thallium (Tl) is one of the most toxic metals and its historic use in homicides has led it to be known as "the poisoner's poison." This review summarizes the methods for identifying Tl and determining its concentrations in biological samples in recently reported poisoning cases, as well as the toxicokinetics, toxicological effects, toxicity mechanisms, and detoxication methods of Tl. Recent findings regarding Tl neurotoxicological pathways and toxicological effects of Tl during pregnancy are also presented. Confirmation of elevated Tl concentrations in blood, urine, or hair is indispensable for diagnosing Tl poisoning. The kidneys show the highest Tl concentration within 24 h after ingestion, while the brain shows the highest concentration thereafter. Tl has a very slow excretion rate due to its large distribution volume. Following acute exposure, gastrointestinal symptoms are observed at an early stage, and neurological dysfunction is observed later: Tl causes the most severe damage in the central nervous system. Alopecia and Mees' lines in the nails are observed within 1 month after Tl poisoning. The toxicological mechanism of Tl is considered to be interference of vital potassium-dependent processes with Tl+ because its ionic radius is similar to that of K+, as well as inhibition of enzyme reactions by the binding of Tl to -SH groups, which disturbs vital metabolic processes. Tl toxicity is also related to reactive oxygen species generation and mitochondrial dysfunction. Prussian blue is the most effective antidote, and metallothionein alone or in combination with Prussian blue was recently reported to have cytoprotective effects after Tl exposure. Because Tl poisoning cases are still reported, early determination of Tl in biological samples and treatment with an antidote are essential.

The First Steps on AOPs' Concepts, Development, and Applications in Teratology

An Adverse Outcome Pathway (AOP) is an analytical model that describes, through a graphical representation, a linear sequence of biologically connected events at different levels of biological organization, causally leading to an adverse effect on human health or the environment. In general, AOPs are constructed based on five central principles: systematic development and review, chemical-agnostic, modular, networks, and living documents. Furthermore, AOPs have the potential to be used, for example, to investigate certain molecular targets; relate the regulation of specific genes or proteins among AOPs; extrapolate biological processes, pathways, or diseases from one species to another; and even predict adverse effects in particular populations. AOPs also emerge as an alternative to animal experimentation in studies of developmental malformations. It's even possible now to develop a quantitative AOP to predict teratogenic effects for some substances. However, the construction of high-quality AOPs requires standardization in the way these models are developed and reviewed, ensuring an adequate degree of flexibility and guaranteeing efficiency. The development of AOPs should strictly be based on the guidance documents developed by the OECD. Nevertheless, an important step for those developing AOPs is the choice of an apical endpoint or an initiating molecular event in order to initiate the construction of the pathway. Another crucial step is a systematic literature review based on the random combination of the blocks of information. With these two fundamental steps completed, it only remains to follow the guidance documents on Developing and Assessing Adverse Outcome Pathways and AOP Developers' Handbook supplement provided by the OECD to organize and construct an AOP. This modern approach will bring radical changes in the field of toxicity testing, regarding the prediction of apical toxic effects using molecular-level effects.

Moderate alcohol consumption during pregnancy increases potency of two different drugs (the antifungal fluconazole and the antiepileptic valproate) in inducing craniofacial defects: prediction by the in vitro rat whole embryo culture

The prenatal exposure to ethanol (Eth), fluconazole (FLUCO) and sodium valproate (VPA) is related to effects on development, producing characteristic syndromic pictures. Among embryotoxic effects described for the three molecules, the alteration on craniofacial morphogenesis is a common feature in humans and animal models, including rodent embryos developed in vitro. The aim of the present work is to evaluate the developmental effects of low Eth serum concentration (17 mM, corresponding to the legal limit to drive in UK, USA, Canada, and many other countries) in mixture with increasing realistic concentrations of the antifungal drug FLUCO (62.5-500 µM) or with increasing realistic concentrations of the antiepileptic drug VPA (31.25-250 µM). Groups exposed to Eth alone (17-127.5 mM), FLUCO alone (62.5-500 µM) or VPA alone (31.25-750 µM) were also included. The chosen alternative animal model was the post-implantation rat whole embryo culture (WEC). E9.5 embryos were exposed in vitro to the test molecules during the whole test period (48 h, corresponding to the developmental stages characteristics of any vertebrate, for human embryos post-fertilization days 23-31). Data were statistically analyzed and processed for modelling applying the benchmark dose (BMD) and relative potency factor (RPF) approaches. Concentration-related effects on facial outcomes were observed in all experimental groups, with a significant enhancement in the groups co-exposed with Eth in comparison to the single exposures. Data obtained by the present work suggest an additional alert for the assumption of even low levels of alcohol in pregnant women during FLUCO or VPA therapy.

Retrospective cumulative dietary risk assessment of craniofacial alterations by residues of pesticides

EFSA established cumulative assessment groups and conducted retrospective cumulative risk assessments for two types of craniofacial alterations (alterations due to abnormal skeletal development, head soft tissue alterations and brain neural tube defects) for 14 European populations of women in childbearing age. Cumulative acute exposure calculations were performed by probabilistic modelling using monitoring data collected by Member States in 2017, 2018 and 2019. A rigorous uncertainty analysis was performed using expert knowledge elicitation. Considering all sources of uncertainty, their dependencies and differences between populations, it was concluded with varying degrees of certainty that the MOET resulting from cumulative exposure is above 100 for the two types of craniofacial alterations. The threshold for regulatory consideration established by risk managers is therefore not exceeded. Considering the severity of the effects under consideration, it was also assessed whether the MOET is above 500. This was the case with varying levels of certainty for the head soft tissue alterations and brain neural tube defects. However, for the alterations due to abnormal skeletal development, it was found about as likely as not that the MOET is above 500 in most populations. For two populations, it was even found more likely that the MOET is below 500. These results were discussed in the light of the conservatism of the methodological approach.

Predictive assays for craniofacial malformations: evaluation in Xenopus laevis embryos exposed to triadimefon

Craniofacial defects are one of the most frequent abnormalities at birth, but their experimental evaluation in animal models requires complex procedures. The aim of the present work is the comparison of different methodologies to identify dose- and stage-related craniofacial malformations in Xenopus laevis assay (R-FETAX, where the full cartilage evaluation, including flat mount technique, is the gold standard for skeletal defect detection). Different methods (external morphological evaluation of fresh samples, deglutition test, whole mount cartilage evaluation and Meckel-palatoquadrate angle measurements) were applied. Triadimefon (FON) was selected as the causative molecule as it is known to induce craniofacial defects in different animal models, including the amphibian X. laevis.FON exposure (0-31.25 μM) was scheduled to cover the whole 6-day test (from gastrula to free swimming tadpole stage) or each crucial developmental phases: gastrula, neurula, early morphogenesis, late morphogenesis, tadpole. Dose-dependent effects (fusions among craniofacial cartilages) were evident for groups exposed during the morphogenetic periods (neurula, early morphogenesis, late morphogenesis); gastrula was insensitive to the tested concentrations, tadpole group showed malformations only at 31.25 μM. The overall NOAEL was set at 3.9 μM. Results were evaluated applying benchmark dose (BMD) approach. The comparison of relative potencies from different methods showed deglutition as the only assay comparable with the gold standard (cartilage full evaluation).In conclusion, we suggest deglutition test as a reliable method for a rapid screening of craniofacial abnormalities in the alternative model X. laevis. This is a rapid, inexpensive and vital test allowing to preserve samples for the application of further morphological or molecular investigations.

Computational model for fetal skeletal defects potentially linked to disruption of retinoic acid signaling

All-trans retinoic acid (ATRA) gradients determine skeletal patterning morphogenesis and can be disrupted by diverse genetic or environmental factors during pregnancy, leading to fetal skeleton defects. Adverse Outcome Pathway (AOP) frameworks for ATRA metabolism, signaling, and homeostasis allow for the development of new approach methods (NAMs) for predictive toxicology with less reliance on animal testing. Here, a data-driven model was constructed to identify chemicals associated with both ATRA pathway bioactivity and prenatal skeletal defects. The phenotype data was culled from ToxRefDB prenatal developmental toxicity studies and produced a list of 363 ToxRefDB chemicals with altered skeletal observations. Defects were classified regionally as cranial, post-cranial axial, appendicular, and other (unspecified) features based on ToxRefDB descriptors. To build a multivariate statistical model, high-throughput screening bioactivity data from >8,070 chemicals in ToxCast/Tox21 across 10 in vitro assays relevant to the retinoid signaling system were evaluated and compared to literature-based candidate reference chemicals in the dataset. There were 48 chemicals identified for effects on both in vivo skeletal defects and in vitro ATRA pathway targets for computational modeling. The list included 28 chemicals with prior evidence of skeletal defects linked to retinoid toxicity and 20 chemicals without prior evidence. The combination of thoracic cage defects and DR5 (direct repeats of 5 nucleotides for RAR/RXR transactivation) disruption was the most frequently occurring phenotypic and target disturbance, respectively. This data model provides valuable AOP elucidation and validates current mechanistic understanding. These findings also shed light on potential avenues for new mechanistic discoveries related to ATRA pathway disruption and associated skeletal dysmorphogenesis due to environmental exposures.

Dose Addition in the Induction of Craniofacial Malformations in Zebrafish Embryos Exposed to a Complex Mixture of Food-Relevant Chemicals with Dissimilar Modes of Action

BACKGROUND

Humans are exposed to combinations of chemicals. In cumulative risk assessment (CRA), regulatory bodies such as the European Food Safety Authority consider dose addition as a default and sufficiently conservative approach. The principle of dose addition was confirmed previously for inducing craniofacial malformations in zebrafish embryos in binary mixtures of chemicals with either similar or dissimilar modes of action (MOAs).

OBJECTIVES

In this study, we explored a workflow to select and experimentally test multiple compounds as a complex mixture with each of the compounds at or below its no observed adverse effect level (NOAEL), in the same zebrafish embryo model.

METHODS

Selection of candidate compounds that potentially induce craniofacial malformations was done using in silico methods-structural similarity, molecular docking, and quantitative structure-activity relationships-applied to a database of chemicals relevant for oral exposure in humans via food (EuroMix inventory, n = 1,598 ). A final subselection was made manually to represent different regulatory fields (e.g., food additives, industrial chemicals, plant protection products), different chemical families, and different MOAs.

RESULTS

A final selection of eight compounds was examined in the zebrafish embryo model, and craniofacial malformations were observed in embryos exposed to each of the compounds, thus confirming the developmental toxicity as predicted by the in silico methods. When exposed to a mixture of the eight compounds, each at its NOAEL, substantial craniofacial malformations were observed; according to a dose-response analysis, even embryos exposed to a 7-fold dilution of this mixture still exhibited a slight abnormal phenotype. The cumulative effect of the compounds in the mixture was in accordance with dose addition (added doses of the individual compounds after adjustment for relative potencies), despite different MOAs of the compounds involved.

DISCUSSION

This case study of a complex mixture inducing craniofacial malformations in zebrafish embryos shows that dose addition can adequately predicted the cumulative effect of a mixture of multiple substances at low doses, irrespective of the (expected) MOA. The applied workflow may be useful as an approach for CRA in general. https://doi.org/10.1289/EHP9888.

A Deep Learning-Based Quantitative Structure-Activity Relationship System Construct Prediction Model of Agonist and Antagonist with High Performance

Molecular design and evaluation for drug development and chemical safety assessment have been advanced by quantitative structure–activity relationship (QSAR) using artificial intelligence techniques, such as deep learning (DL). Previously, we have reported the high performance of prediction models molecular initiation events (MIEs) on the adverse toxicological outcome using a DL-based QSAR method, called DeepSnap-DL. This method can extract feature values from images generated on a three-dimensional (3D)-chemical structure as a novel QSAR analytical system. However, there is room for improvement of this system’s time-consumption. Therefore, in this study, we constructed an improved DeepSnap-DL system by combining the processes of generating an image from a 3D-chemical structure, DL using the image as input data, and statistical calculation of prediction-performance. Consequently, we obtained that the three prediction models of agonists or antagonists of MIEs achieved high prediction-performance by optimizing the parameters of DeepSnap, such as the angle used in the depiction of the image of a 3D-chemical structure, data-split, and hyperparameters in DL. The improved DeepSnap-DL system will be a powerful tool for computer-aided molecular design as a novel QSAR system.