Adverse outcome pathway networks I: Development and applications

Interpretation of thyroid-relevant bioactivity data for comparison to in vivo exposures: A prioritization approach for putative chemical inhibitors of in vitro deiodinase activity

Many ToxCast assay endpoints can be mapped to molecular initiating events (MIEs) within the thyroid adverse outcome pathway (AOP) network. Herein, we provide a framework for interpretation of thyroid-relevant bioactivity data across MIEs. As a proof-of-concept, we used ToxCast data on the inhibition of deiodinase (DIO) enzymes, which convert thyroid hormones between active and inactive forms, and identified substances most likely to inhibit DIO enzymes. Data from 4 relevant cell-free in vitro assays are available for >2000 chemicals in single concentration screening and 327 chemicals in multi-concentration screening. We filtered to identify chemicals that demonstrated inhibition for each DIO enzyme less likely to be confounded by assay interference, refining the list of putatively active chemicals from 523 to 135. In vitro bioactivity data were then used to estimate administered equivalent doses (AEDs) using a novel high-throughput toxicokinetic (HTTK) model for in vitro to in vivo extrapolation (IVIVE) of dose. To consider potential thyroid-disrupting activity in an appropriate life-stage and dose context, we extended an existing human maternal-fetal HTTK model to allow for simulations involving the first trimester of pregnancy. For many chemicals, using modeled fetal tissue concentrations produced lower AED estimates than using modeled maternal plasma concentrations alone, at least partially due to conservative assumptions in our HTTK model of complete gestation. This extensible approach for MIE groups of thyroid-related bioactivity data from ToxCast may inform further screening or analyses for potential adverse outcomes during pregnancy and development.

Exploring the neurodegenerative potential of per- and polyfluoroalkyl substances through an adverse outcome pathway network

While emerging evidence links per- and polyfluoroalkyl substances (PFAS) to neurotoxicity, their potential role in neurodegeneration remains poorly understood. Moreover, existing neurodegeneration-related adverse outcome pathways (AOPs) available on AOP-Wiki have not yet been integrated into a unified network. To address these gaps, this study aims to develop the first neurodegeneration-related AOP network and utilize it to explore the possible contributions of long-chain legacy PFAS to neurodegeneration, specifically concerning Alzheimer's and Parkinson's diseases. A total of 74 AOPs were screened from AOP-Wiki, of which 13 neurodegeneration-related AOPs met the eligibility criteria and were incorporated into a network. We analyzed the resulting AOP network using topological parameters such as in-degree, out-degree, eccentricity, and betweenness centrality. To elucidate the mechanistic contributions of PFAS exposure to neurodegenerative pathways, we integrated evidence linking PFAS exposure to key events (KEs) within the network. The results highlighted increased intracellular calcium as the network hub with the highest connectivity followed by critical KEs such as neurodegeneration, neuronal apoptosis, oxidative stress, N-methyl-d-aspartate receptor (NMDA-R) overactivation, and mitochondrial dysfunction. Consistent with toxicological evidence, the pathways highlighted by the AOP network indicate that PFAS may adversely affect neurotransmitter systems, particularly through NMDA-R overactivation, leading to excitotoxicity. This may result in calcium dyshomeostasis, mitochondrial dysfunction, inflammatory-oxidative cascades, neuroinflammation, and neuronal cell death. By providing a mechanistic basis for understanding the neurodegenerative potential of PFAS, this study offers a crucial framework for assessing the risks associated with these chemicals which may inform future regulatory measures and public health strategies. Further experimental validation is needed to confirm the mechanistic contributions of PFAS exposure in neurodegeneration, particularly in animal models or human populations.

Cyclosporin A toxicity on endothelial cells differentiated from induced pluripotent stem cells: Assembling an adverse outcome pathway

Cyclosporin A (CSA) is a potent immunosuppressive agent in pharmacologic studies. However, there is evidence for side effects, specifically regarding vascular dysfunction. Its mode of action inducing endothelial cell toxicity is partially unclear, and a connection with an adverse outcome pathway (AOP) is not established yet. Therefore, we designed this study to get deeper insights into the mechanistic toxicology of CSA on angiogenesis. Stem cells, especially induced pluripotent stem cells (iPSCs) with the ability of differentiation to all organs of the body, are considered a promising in vitro model to reduce animal experimentation. In this study, we differentiated iPSCs to endothelial cells (ECs) as one cell type that in other studies would allow to generate multi-cell type organoids from single donors. Flow cytometry and immunostaining confirmed our scalable differentiation protocol. Then dose and time course experiments assessing CSA cytotoxicity on iPS derived endothelial cells were performed. Transcriptomic data suggested CSA dependent induction of reactive oxygen species (ROS), mitochondrial dysfunction, and impaired angiogenesis via ROS induction which was confirmed by in vitro experiments. In order to put these data into a potential adverse outcome pathway (AOP) context, we performed a literature review for CSA-mediated endothelial cell toxicity and combined our experimental data with the publicly available knowledge. Such an AOP will help to design in vitro test batteries and to model events observed in human toxicity studies, as well in predictive toxicology.

Using transcriptomics data and Adverse Outcome Pathway networks to explore endocrine disrupting properties of Cadmium and PCB-126

Omics-technologies such as transcriptomics offer valuable insights into toxicity mechanisms. However, integrating this type of data into regulatory frameworks remains challenging due to uncertainties regarding toxicological relevance and links to adverse outcomes. Furthermore, current assessments of endocrine disruptors (EDs) relevant to human health require substantial amounts of data, and primarily rely on standardized animal studies. Identifying EDs is a high priority in the EU, but so are efforts to replace and reduce animal testing. Alternative methods to investigate EDs are needed, and so are health risk assessment methods that support uptake of novel mechanistic information. This study aims to utilize Adverse Outcome Pathways (AOPs) to integrate transcriptomics data for identifying EDs, by establishing a link between molecular data and adverse outcomes. Cadmium (Cd) and 3,3',4,4',5-pentachlorobiphenyl (PCB126) were used as model compounds due to their observed effects on the endocrine system. An AOP network for the estrogen, androgen, thyroid, and steroidogenesis (EATS)-modalities was constructed. RNA sequencing (RNA-Seq) was conducted on zebrafish (Danio rerio) embryos exposed to Cd or PCB126 for 4 days. RNA-Seq data were then linked to the AOP network via Gene Ontology (GO) terms. Enrichment Maps in Cytoscape and the QIAGEN Ingenuity Pathway Analysis (IPA) software were also used to identify potential ED properties and to support the assessment. Potentially EATS-related GO Biological Process (BP) terms were identified for both compounds. A lack of accurate standardized terms in KEs of the AOP network hindered a data-driven mapping approach. Instead, manual mapping of GO BP terms onto the AOP network revealed more connections, underscoring the need for harmonizing AOP development for regulatory use. Both the Enrichment Maps and the IPA results further supported potentially EATS-related effects of both compounds. While AOP networks show promise in integrating RNA-Seq data, several challenges remain.

AOP-networkFinder-a versatile tool for the reconstruction and visualization of Adverse Outcome Pathway networks from AOP-Wiki

Motivation

The Adverse Outcome Pathways (AOP)-Wiki, a knowledge database for AOPs, requires an efficient way to present an overview of its content for the reconstruction of networks by experts in a given domain. We have developed the AOP-networkFinder, a user-friendly tool that retrieves AOPs of interest, allows network generation and cleaning, and finally visualizes networks built around the retrieved AOPs. Our tool constructs AOP networks by connecting AOPs that use the same Key Events (KEs) in a versatile but controlled manner. Genes related to these KEs are also displayed. The constructed networks can then be exported as images or to Cytoscape for further fine-tuning and statistical analysis.

Results

The AOP-networkFinder allows users to comprehensively identify relationships between KEs and visualize the overall structure of an AOP both quickly and easily. This is immensely beneficial to researchers who need to understand the complex interplay between different KEs and the overall pathway they are studying and helps them to build further networks of interest while logging relevant information about changes within the network. These efforts are in line with the Findable, Accessible, Interoperable, and Reusable principles, which are crucial attributes for any developed databases and tools for optimizing (re)use in a dynamically changing landscape of AOP-Wiki.

Availability and implementation

The AOP-networkFinder is an open-source application and is available online at aop-networkfinder.no, in the 'Computational Toxicology at Norwegian Institute of Public Health' Zenodo community at DOI 10.5281/zenodo.11068434, in the GitHub repository at github.com/folkehelseinstituttet/AOPnetworkFinder_v1, as well as in a Docker image at hub.docker.com/r/nurre123/aop_network_finder. The software is available under the GNU Affero General Public License (AGPL), v3.0. The tool uses the AOP-Wiki SPARQL endpoint to retrieve AOP data.

Burnt Plastic (Pyroplastic) from the M/V X-Press Pearl Ship Fire and Plastic Spill Contain Compounds That Activate Endocrine and Metabolism-Related Human and Fish Transcription Factors

In May 2021, the M/V X-Press Pearl ship fire disaster led to the largest maritime spill of resin pellets (nurdles) and burnt plastic (pyroplastic). Field samples collected from beaches in Sri Lanka nearest to the ship comprised nurdles and pieces of pyroplastic. Three years later, the toxicity of the spilled material remains unresolved. To begin understanding its potential toxicity, solvent extracts of the nurdles and pyroplastic were screened for their bioactivity by several Attagene FACTORIAL bioassays (TF, NR, and AquaTox), which measured the activity of a combined 70 human transcription factor response elements and nuclear receptors and 6 to 7 nuclear receptors for each of three phylogenetically distinct fish species. Extracts of the pyroplastics robustly activated end points for the human aryl hydrocarbon receptor (AhR), estrogen receptor (ER), pregnane X receptor (PXR), peroxisome proliferator-activated receptor (PPAR), retinoid X receptor (RXR), and oxidative stress (NRF2) and had the potential for activation of several others. The bioactivity profile of the pyroplastics was most similar (similarity score = 0.96) to that of probable human carcinogens benzo[b]fluoranthene and benzo[k]fluoranthene despite the extracts being a complex mixture of thousands of compounds. The activity diminished only slightly for extracts of pyroplastic collected eight months after the spill. The AquaTox FACTORIAL bioassay measured the activation of ERα, ERβ, androgen receptor (AR), PPARα, PPARγ, and RXRβ for human, zebrafish (Danio rerio), Japanese medaka (Oryzias latipes), and rainbow trout (Oncorhynchus mykiss), revealing species-specific sensitivities to the chemicals associated with the pyroplastics. These findings provide needed information to guide long-term monitoring efforts, make hazard assessments of the spilled material, and direct further research on pyroplastic, an emerging global contaminant.

Discovery of phloridzin as a new antagonist for Di(2-ethylhexyl) phthalate-induced male reproductive toxicity based on the adverse outcome pathway network and drug-target gene set enrichment analysis

Di(2-ethylhexyl) phthalate (DEHP) is a widespread ubiquitous phthalate environmental contaminant. The male reproductive toxicity (MRT) from exposure to DEHP and its main metabolite, mono(2-ethylhexyl) phthalate (MEHP), has been well documented. Fully elucidating its toxic mechanism and discovering effective antagonists are desirable means to reduce the health risks of DEHP. In this study, 552 genes related to MRT induced by DEHP/MEHP were screened out from the Comparative Toxicogenomics Database (CTD) and DisGeNET database. Next, we developed a global adverse outcome pathway (AOP) network based on the existed AOP-wiki. After functional enrichment analyses and mapping to the global AOP network, we found that the increased ROS level, cell cycle arrest, and increased apoptosis are key events (KEs) involved in DEHP-mediated MRT, which was validated in TM3 Leydig cell model. Among them, cellular apoptosis is the core KE in DEHP-induced MRT via network topological analysis. Eventually, we developed a novel in silico antagonist screening platform (http://43.136.69.224:3838/wlab/) based on drug-target gene set enrichment analysis (dtGSEA version 2.0). Several potential candidates that mitigate DEHP-mediated cellular apoptosis have been screened out, including quercetin, taurine, methionine, and phloridzin. Further experimental results demonstrated that phloridzin provided the most effective protection against MEHP-induced apoptosis in TM3 cells probably through the p53 and MAPK signaling pathways. Molecular docking and molecular dynamics simulations suggest that STAT3 and RUNX1 may be important targets for phloridzin to antagonize MEHP-induced MRT. Our study provides a new approach to discover the antagonists for the toxicity of environmental contaminants based on AOP network and dtGSEA methods.

Adverse Outcome Pathways Mechanistically Describing Hepatotoxicity

Adverse outcome pathways (AOPs) describe toxicological processes from a dynamic perspective by linking a molecular initiating event to a specific adverse outcome via a series of key events and key event relationships. In the field of computational toxicology, AOPs can potentially facilitate the design and development of in silico prediction models for hazard identification. Various AOPs have been introduced for several types of hepatotoxicity, such as steatosis, cholestasis, fibrosis, and liver cancer. This chapter provides an overview of AOPs on hepatotoxicity, including their development, assessment, and applications in toxicology.

Ecotoxicology dilemmas: issues with dose, causality, response, mixtures, and modifying factors

Ecotoxicology has model assumptions that are the basis of the discipline's scientific validity and regulatory utility. Using testing data to advance knowledge and practical applications is contingent on assumption validation of underlying models, an uncommon practice. Fundamental components-dose, causality, response-are confounded, as test metrics are each accumulations of a multiplicity of factors. Consequently, ecotoxicology test interpretation of both legacy and new approach methodologies is plagued by unaddressed issues related to interactions of within and between dose, causation, response, and modifying factors-each component is effectively a mixture-such that established relationships are more correlative than causal. Limited knowledge about the multiplicity of modifying factors influencing dose, causality, and response at each level of biological organization and the challenge of establishing dose metrics in upper ecological levels, where the paradigm is stressor-causality-response, further confounds the formidable task of in vitro to in vivo, laboratory-to-field, and toxicity-to-ecology translation. Although available aquatic ecotoxicity data and information have been successfully fitted to explanatory frameworks in past and present regulatory policies, environmental protection successes are more attributable to good policy than to scientific knowledge. Unresolved issues in the simple model frameworks and regulatory policies that initially advanced environmental protection are now impeding development of newer policies and procedures due to inadequate consideration of basic model assumptions. Resolution of the problem will begin when the problem definition of the tasks is refined to reflect the reality of the challenge. This is a necessary step towards achieving the objective of advancing the efficiency, effectiveness, and sophistication of environmental effects assessment and management in regulatory ecotoxicology.

Conceptual basis for the development of guidance for the use of biomarkers of effect in regulatory risk assessment of chemicals

This Scientific Report was carried out in the context of the self-task mandate (M-2023-00097) of the EFSA's Scientific Committee on 'Guidance on the use of biomarkers of effect in regulatory risk assessment of chemicals'. In the first phase, the project on biomarkers of effect started with a feasibility study (EFSA-Q-2024-00128), with the intention to look closer at definitions and descriptions of biomarkers of effect, as well as to explore several concepts related to the context of application and other scientific principles to be further considered for its development. In addition, relevant activities, initiatives and knowledge in this area were collected and analysed within a complementary mapping study. The outcome of this phase aimed to create a structured basis for future guidance, to identify challenges and to recommend a way forward for its development. The recommendations refer especially to terminologies, the scope of the guidance and several scientific and technical aspects of the selection and interpretation of biomarkers of effect that need to be addressed in future guidance. Moreover, further recommendation refers to the collaborative process to be established with other regulatory organisations that should support the harmonisation and reduce divergencies in the application of methodologies across organisations or sectors.

Network-based investigation of petroleum hydrocarbons-induced ecotoxicological effects and their risk assessment

Petroleum hydrocarbons (PHs) are compounds composed mostly of carbon and hydrogen, originating from crude oil and its derivatives. PHs are primarily released into the environment through the diffusion of oils, resulting from anthropogenic activities like transportation and offshore drilling, and accidental incidents such as oil spills. Once released, these PHs can persist in different ecosystems and cause long-term detrimental ecological impacts. While the hazards associated with such PH contaminations are often assessed by the concentrations of total petroleum hydrocarbons in the environment, studies focusing on the risks associated with individual PHs are limited. In this study, different network-based frameworks were utilized to explore and understand the adverse ecological effects associated with PH exposure. First, a list of 320 PHs was systematically curated from published reports. Next, biological endpoint data from toxicological databases was systematically integrated, and a stressor-centric adverse outcome pathway (AOP) network, linking 75 PHs with 177 ecotoxicologically-relevant high confidence AOPs within AOP-Wiki, was constructed. Further, stressor-species networks, based on reported toxicity concentrations and bioconcentration factors data within ECOTOX, were constructed for 80 PHs and 28 PHs, respectively. It was found that crustaceans are documented to be affected by many of these PHs. Finally, the aquatic toxicity data within ECOTOX was used to construct species sensitivity distributions for PHs, and their corresponding hazard concentrations (HC05), that are harmful to 5% of species in the aquatic ecosystem, were derived. Further, the predicted no-effect concentrations (PNECs) and risk quotients for the US EPA priority polycyclic aromatic hydrocarbons (PAHs) were computed by using their environmental concentration data for Indian coastal and river waters. Overall, this study highlights the importance of using network-based approaches and risk assessment methods to understand the PH-induced toxicities effectively.

Microbial function matters: Microbiome-aware nano-ecotoxicology needs functional endpoints besides compositional data

The microbiome provides an active barrier to the external environment and aids in the metabolism of the host. Nanomaterials are known to interact with this microbiome host plane. Given the recent advances in techniques to study the microbiome, there has been a vast increase in studies trying to find causality in host response via the microbiome in nano-ecotoxicology. Our review integrates the latest advancements in understanding the microbiome's role in elucidating host health related to nanomaterial exposure, thereby explicitly emphasizing the gap between compositional and functional studies. Both the techniques used to interfere and the current understanding of microbiome-host relationships in nano-ecotoxicology are discussed. To further highlight the functional side of the microbiome, we performed an explorative meta-analysis to bridge the gap between top-down and bottom-up studies. This review gives a perspective on generalising microbiome-aware nano-ecotoxicology and discusses methodologies to enhance the interpretation of nanomaterial or chemical exposure to host-microbiome interactions. The current study discloses that correlations built on compositional data are not a good proxy for host outcome and more in-depth analysis coupled with functional analysis should be explored more in microbiome-aware nano-ecotoxicology.

Combining transcriptomics and metabolomics to assess neurodevelopmental alteration caused by in utero exposure of mice to three putative thyroid hormone system disruptors

Gestating mice were exposed to three chemicals, tetrabromo-bisphenol A (TBBPA; 2 mg/kg/day), amitrole (25 and 50 mg/kg/day) and pyraclostrobin (0.4 and 2 mg/kg/day) to assess their capacity to act as thyroid hormone disruptors and compromise neurodevelopment. Propyl-thio-uracyl, a known pharmacological inhibitor of thyroid gland secretion, was used at both high and low dose as a reference thyroid hormone system disruptor (1 ppm, 1500 ppm). A combination of plasma metabolomics and striatum transcriptomics revealed the induced change in pups at the postnatal stages. Although the underlying mechanism is unlikely to involve thyroid hormone disruption, these chemicals had a detectable effect on pups' neurodevelopment.

Leveraging integrative toxicogenomic approach towards development of stressor-centric adverse outcome pathway networks for plastic additives

Plastics are widespread pollutants found in atmospheric, terrestrial and aquatic ecosystems due to their extensive usage and environmental persistence. Plastic additives, that are intentionally added to achieve specific functionality in plastics, leach into the environment upon plastic degradation and pose considerable risk to ecological and human health. Limited knowledge concerning the presence of plastic additives throughout plastic life cycle has hindered their effective regulation, thereby posing risks to product safety. In this study, we leveraged the adverse outcome pathway (AOP) framework to understand the mechanisms underlying plastic additives-induced toxicities. We first identified an exhaustive list of 6470 plastic additives from chemicals documented in plastics. Next, we leveraged heterogenous toxicogenomics and biological endpoints data from five exposome-relevant resources, and identified associations between 1287 plastic additives and 322 complete and high quality AOPs within AOP-Wiki. Based on these plastic additive-AOP associations, we constructed a stressor-centric AOP network, wherein the stressors are categorized into ten priority use sectors and AOPs are linked to 27 disease categories. We visualized the plastic additives-AOP network for each of the 1287 plastic additives and made them available in a dedicated website: https://cb.imsc.res.in/saopadditives/ . Finally, we showed the utility of the constructed plastic additives-AOP network by identifying highly relevant AOPs associated with benzo[a]pyrene (B[a]P), bisphenol A (BPA), and bis(2-ethylhexyl) phthalate (DEHP) and thereafter, explored the associated toxicity pathways in humans and aquatic species. Overall, the constructed plastic additives-AOP network will assist regulatory risk assessment of plastic additives, thereby contributing towards a toxic-free circular economy for plastics.

Investigation of parenteral nutrition-induced hepatotoxicity using human liver spheroid co-cultures

Parenteral nutrition (PN) is typically administered to individuals with gastrointestinal dysfunction, a contraindication for enteral feeding, and a need for nutritional therapy. When PN is the only energy source in patients, it is defined as total parenteral nutrition (TPN). TPN is a life-saving approach for different patient populations, both in infants and adults. However, despite numerous benefits, TPN can cause adverse effects, including metabolic disorders and liver injury. TPN-associated liver injury, known as intestinal failure-associated liver disease (IFALD), represents a significant problem affecting up to 90% of individuals receiving TPN. IFALD pathogenesis is complex, depending on the TPN components as well as on the patient's medical conditions. Despite numerous animal studies and clinical observations, the molecular mechanisms driving IFALD remain largely unknown. The present study was set up to elucidate the mechanisms underlying IFALD. For this purpose, human liver spheroid co-cultures were treated with a TPN mixture, followed by RNA sequencing analysis. Subsequently, following exposure to TPN and its single nutritional components, several key events of liver injury, including mitochondrial dysfunction, endoplasmic reticulum stress, oxidative stress, apoptosis, and lipid accumulation (steatosis), were studied using various techniques. It was found that prolonged exposure to TPN substantially changes the transcriptome profile of liver spheroids and affects multiple metabolic and signaling pathways contributing to liver injury. Moreover, TPN and its main components, especially lipid emulsion, induce changes in all key events measured and trigger steatosis.

Endocrine disruption assessment in aquatic vertebrates - Identification of substance-induced thyroid-mediated effect patterns

According to the World Health Organisation and European Commission definitions, substances shall be considered as having endocrine disrupting properties if they show adverse effects, have endocrine activity and the adverse effects are a consequence of the endocrine activity (using a weight-of-evidence approach based on biological plausibility), unless the adverse effects are not relevant to humans or non-target organisms at the (sub)population level. To date, there is no decision logic on how to establish endocrine disruption via the thyroid modality in non-mammalian vertebrates. This paper describes an evidence-based decision logic compliant with the integrated approach to testing and assessment (IATA) concept, to identify thyroid-mediated effect patterns in aquatic vertebrates using amphibians as relevant models for thyroid disruption assessment. The decision logic includes existing test guidelines and methods and proposes detailed considerations on how to select relevant assays and interpret the findings. If the mammalian dataset used as the starting point indicates no thyroid concern, the Xenopus Eleutheroembryonic Thyroid Assay allows checking out thyroid-mediated activity in non-mammalian vertebrates, whereas the Amphibian Metamorphosis Assay or its extended, fixed termination stage variant inform on both thyroid-mediated activity and potentially population-relevant adversity. In evaluating findings, the response patterns of all assay endpoints are considered, including the direction of changes. Thyroid-mediated effect patterns identified at the individual level in the amphibian tests are followed by mode-of-action and population relevance assessments. Finally, all data are considered in an overarching weight-of-evidence evaluation. The logic has been designed generically and can be adapted, e.g. to accommodate fish tests once available for thyroid disruption assessments. It also ensures that all scientifically relevant information is considered, and that animal testing is minimised. The proposed decision logic can be included in regulatory assessments to facilitate the conclusion on whether substances meet the endocrine disruptor definition for the thyroid modality in non-mammalian vertebrates.

Evaluation of the ecological risk of pesticide residues from the European LUCAS Soil monitoring 2018 survey

The 2018 LUCAS (Land Use and Coverage Area frame Survey) Soil Pesticides survey provides a European Union (EU)-scale assessment of 118 pesticide residues in more than 3473 soil sites. This study responds to the policy need to develop risk-based indicators for pesticides in the environment. Two mixture risk indicators are presented for soil based, respectively, on the lowest and the median of available No Observed Effect Concentration (NOECsoil,min and NOECsoil,50) from publicly available toxicity datasets. Two further indicators were developed based on the corresponding equilibrium concentration in the aqueous phase and aquatic toxicity data, which are available as species sensitivity distributions. Pesticides were quantified in 74.5% of the sites. The mixture risk indicator based on the NOECsoil,min exceeds 1 in 14% of the sites and 0.1 in 23%. The insecticides imidacloprid and chlorpyrifos and the fungicide epoxiconazole are the largest contributors to the overall risk. At each site, one or a few substances drive mixture risk. Modes of actions most likely associated with mixture effects include modulation of acetylcholine metabolism (neonicotinoids and organophosphate substances) and sterol biosynthesis inhibition (triazole fungicides). Several pesticides driving the risk have been phased out since 2018. Following LUCAS surveys will determine the effectiveness of substance-specific risk management and the overall progress toward risk reduction targets established by EU and UN policies. Newly generated data and knowledge will stimulate needed future research on pesticides, soil health, and biodiversity protection. Integr Environ Assess Manag 2024;20:1639-1653. © 2024 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

A Network Toxicology Approach for Mechanistic Modelling of Nanomaterial Hazard and Adverse Outcomes

Hazard assessment is the first step in evaluating the potential adverse effects of chemicals. Traditionally, toxicological assessment has focused on the exposure, overlooking the impact of the exposed system on the observed toxicity. However, systems toxicology emphasizes how system properties significantly contribute to the observed response. Hence, systems theory states that interactions store more information than individual elements, leading to the adoption of network based models to represent complex systems in many fields of life sciences. Here, they develop a network-based approach to characterize toxicological responses in the context of a biological system, inferring biological system specific networks. They directly link molecular alterations to the adverse outcome pathway (AOP) framework, establishing direct connections between omics data and toxicologically relevant phenotypic events. They apply this framework to a dataset including 31 engineered nanomaterials with different physicochemical properties in two different in vitro and one in vivo models and demonstrate how the biological system is the driving force of the observed response. This work highlights the potential of network-based methods to significantly improve their understanding of toxicological mechanisms from a systems biology perspective and provides relevant considerations and future data-driven approaches for the hazard assessment of nanomaterials and other advanced materials.

Transcriptome-centric approach to the derivation of adverse outcome pathway networks of vascular dysfunction after long-term low-level exposure of human endothelial cells to dibutyl phthalate

Dibutyl phthalate (DBP) is an endocrine disruptor that adversely affects reproduction; however, evidence suggests it can also impact other systems, including vascular function. The mechanisms underlying DBP-induced vascular dysfunction, particularly after long-term low-level exposure of endothelial cells to this phthalate, remain largely unknown. To address this gap, we used experimentally derived data on differentially expressed genes (DEGs) obtained after 12 weeks of exposure of human vascular endothelial cells EA.hy926 to the concentrations of DBP to which humans are routinely exposed (10-9 M, 10-8 M, and 10-7 M) and various computational tools and manual data curation to build the first adverse outcome pathway (AOP) network relevant to DBP-induced vascular toxicity. DEGs were used to infer transcription factors (molecular initiating events) and molecular functions and biological processes (key events, KEs) using the Enrichr database. The AOP-helpFinder 2.0, an artificial intelligence-based web tool, was used to link genes and KEs and assign confidence scores to co-occurred terms. We constructed the AOP networks using Cytoscape and then manually arranged KEs to depict the flow of mechanistic information across different levels of network organization. An AOP network was created for each DBP concentration, revealing several distinct high-confidence subnetworks that could be involved in DBP-induced vascular toxicity: the insulin-like growth factor subnetwork for 10-7 M DBP, the CXCL8-dependent chemokine subnetwork for 10-8 M DBP, and the fatty acid subnetwork for 10-9 M DBP. We also developed an AOP network providing a mechanistic insight into the dose-dependent effects of DBP in endothelial cells leading to vascular dysfunction. In summary, we present novel putative AOP networks describing the mechanistic flow of information involved in DBP-induced vascular dysfunction in a long-term low-level exposure scenario.

Zooplankton-based adverse outcome pathways: A tool for assessing endocrine disrupting compounds in aquatic environments

Endocrine disrupting compounds (EDCs) pose a significant ecological risk, particularly in aquatic ecosystems. EDCs have become a focal point in ecotoxicology, and their identification and regulation have become a priority. Zooplankton have gained global recognition as bioindicators, benefiting from rigorous standardization and regulatory validation processes. This review aims to provide a comprehensive summary of zooplankton-based adverse outcome pathways (AOPs) with a focus on EDCs as toxicants and the utilisation of freshwater zooplankton as bioindicators in ecotoxicological assessments. This review presents case studies in which zooplankton have been used in the development of AOPs, emphasizing the identification of molecular initiating events (MIEs) and key events (KEs) specific to zooplankton exposed to EDCs. Zooplankton-based AOPs may become an important resource for understanding the intricate processes by which EDCs impair the endocrine system. Furthermore, the data sources, experimental approaches, advantages, and challenges associated with zooplankton-based AOPs are discussed. Zooplankton-based AOPs framework can provide vital tools for consolidating toxicological knowledge into a structured toxicity pathway of EDCs, offering a transformative platform for facilitating enhanced risk assessment and chemical regulation.

Building an Adverse Outcome Pathway network for COVID-19

The COVID-19 pandemic generated large amounts of data on the disease pathogenesis leading to a need for organizing the vast knowledge in a succinct manner. Between April 2020 and February 2023, the CIAO consortium exploited the Adverse Outcome Pathway (AOP) framework to comprehensively gather and systematically organize published scientific literature on COVID-19 pathology. The project considered 24 pathways relevant for COVID-19 by identifying essential key events (KEs) leading to 19 adverse outcomes observed in patients. While an individual AOP defines causally linked perturbed KEs towards an outcome, building an AOP network visually reflect the interrelatedness of the various pathways and outcomes. In this study, 17 of those COVID-19 AOPs were selected based on quality criteria to computationally derive an AOP network. This primary network highlighted the need to consider tissue specificity and helped to identify missing or redundant elements which were then manually implemented in the final network. Such a network enabled visualization of the complex interactions of the KEs leading to the various outcomes of the multifaceted COVID-19 and confirmed the central role of the inflammatory response in the disease. In addition, this study disclosed the importance of terminology harmonization and of tissue/organ specificity for network building. Furthermore the unequal completeness and quality of information contained in the AOPs highlighted the need for tighter implementation of the FAIR principles to improve AOP findability, accessibility, interoperability and re-usability. Finally, the study underlined that describing KEs specific to SARS-CoV-2 replication and discriminating physiological from pathological inflammation is necessary but requires adaptations to the framework. Hence, based on the challenges encountered, we proposed recommendations relevant for ongoing and future AOP-aligned consortia aiming to build computationally biologically meaningful AOP networks in the context of, but not limited to, viral diseases.

Development of the integrated fish endocrine disruptor test-Part B: Implementation of thyroid-related endpoints

Given the vital role of thyroid hormones (THs) in vertebrate development, it is essential to identify chemicals that interfere with the TH system. Whereas, among nonmammalian laboratory animals, fish are the most frequently utilized test species in endocrine disruptor research, for example, in guidelines for the detection of effects on the sex hormone system, there is no test guideline (TG) using fish as models for thyroid-related effects; rather, amphibians are used. Therefore, the objective of the present project was to integrate thyroid-related endpoints for fish into a test protocol combining OECD TGs 229 (Fish Short-Term Reproduction Assay) and 234 (Fish Sexual Development Test). The resulting integrated Fish Endocrine Disruption Test (iFEDT) was designed as a comprehensive approach to covering sexual differentiation, early development, and reproduction and to identifying disruption not only of the sexual and/or reproductive system but also the TH system. Two 85-day exposure tests were performed using different well-studied endocrine disruptors: 6-propyl-2-thiouracil (PTU) and 17α-ethinylestradiol (EE2). Whereas the companion Part A of this study presents the findings on effects by PTU and EE2 on endpoints established in existing TGs, the present Part B discusses effects on novel thyroid-related endpoints such as TH levels, thyroid follicle histopathology, and eye development. 6-Propyl-2-thiouracil induced a massive proliferation of thyroid follicles in any life stage, and histopathological changes in the eyes proved to be highly sensitive for TH system disruption especially in younger life stages. For measurement of THs, further methodological development is required. 17-α-Ethinylestradiol demonstrated not only the well-known disruption of the hypothalamic-pituitary-gonadal axis, but also induced effects on thyroid follicles in adult zebrafish (Danio rerio) exposed to higher EE2 concentrations, suggesting crosstalk between endocrine axes. The novel iFEDT has thus proven capable of simultaneously capturing endocrine disruption of both the steroid and thyroid endocrine systems. Integr Environ Assess Manag 2024;20:830-845. © 2023 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Single-cell and multi-omics analyses highlight cancer-associated fibroblasts-induced immune evasion and epithelial mesenchymal transition for smoking bladder cancer

Tobacco carcinogens are recognized as critical hazard factors for bladder tumorigenesis, affecting the prognosis of patients through aromatic amines components. However, the specific function of tobacco carcinogens and systematic assessment models in the prognosis of bladder cancer remains poorly elucidated. We retrieved bladder cancer specific tobacco carcinogens-related genes from Comparative Toxicogenomic Database, our Nanjing Bladder Cancer cohort and TCGA database. Gene×Gene interaction method was utilized to establish a prognostic signature. Integrative assessment of immunogenomics, tumor microenvironments and single-cell RNA-sequencing were performed to illustrate the internal relations of key events from different levels. Finally, we comprehensively identified 33 essential tobacco carcinogens-related genes to construct a novel prognostic signature, and found that high-risk patients were characterized by significantly worse overall survival (HR=2.25; Plog-rank < 0.01). Single-cell RNA-sequencing and multi-omics analysis demonstrated that cancer-associated fibroblasts mediated the crosstalk between epithelial-mesenchymal transition progression and immune evasion. Moreover, an adverse outcome pathway framework was established to facilitate our understanding to the tobacco carcinogens-triggered bladder tumorigenesis. Our study systematically provided immune microenvironmental alternations for smoking-induced adverse survival outcomes in bladder cancer. These findings facilitated the integrative multi-omics insights into risk assessment and toxic mechanisms of tobacco carcinogens.

Parental exposure to antidepressants has lasting effects on offspring? A case study with zebrafish

Fish have common neurotransmitter pathways with humans, exhibiting a significant degree of conservation and homology. Thus, exposure to fluoxetine makes fish potentially susceptible to biochemical and physiological changes, similarly to what is observed in humans. Over the years, several studies demonstrated the potential effects of fluoxetine on different fish species and at different levels of biological organization. However, the effects of parental exposure to unexposed offspring remain largely unknown. The consequences of 15-day parental exposure to relevant concentrations of fluoxetine (100 and 1000 ng/L) were assessed on offspring using zebrafish as a model organism. Parental exposure resulted in offspring early hatching, non-inflation of the swimming bladder, increased malformation frequency, decreased heart rate and blood flow, and reduced growth. Additionally, a significant behavioral impairment was also found (reduced startle response, basal locomotor activity, and altered non-associative learning during early stages and a negative geotaxis and scototaxis, reduced thigmotaxis, and anti-social behavior at later life stages). These behavior alterations are consistent with decreased anxiety, a significant increase in the expression of the monoaminergic genes slc6a4a (sert), slc6a3 (dat), slc18a2 (vmat2), mao, tph1a, and th2, and altered levels of monoaminergic neurotransmitters. Alterations in behavior, expression of monoaminergic genes, and neurotransmitter levels persisted until offspring adulthood. Given the high conservation of neuronal pathways between fish and humans, data show the possibility of potential transgenerational and multigenerational effects of pharmaceuticals' exposure. These results reinforce the need for transgenerational and multigenerational studies in fish, under realistic scenarios, to provide realistic insights into the impact of these pharmaceuticals.

An integrative data-centric approach to derivation and characterization of an adverse outcome pathway network for cadmium-induced toxicity

Cadmium is a prominent toxic heavy metal that contaminates both terrestrial and aquatic environments. Owing to its high biological half-life and low excretion rates, cadmium causes a variety of adverse biological outcomes. Adverse outcome pathway (AOP) networks were envisioned to systematically capture toxicological information to enable risk assessment and chemical regulation. Here, we leveraged AOP-Wiki and integrated heterogeneous data from four other exposome-relevant resources to build the first AOP network relevant for inorganic cadmium-induced toxicity. From AOP-Wiki, we filtered 309 high confidence AOPs, identified 312 key events (KEs) associated with inorganic cadmium from five exposome-relevant databases using a data-centric approach, and thereafter, curated 30 cadmium relevant AOPs (cadmium-AOPs). By constructing the undirected AOP network, we identified a large connected component of 18 cadmium-AOPs. Further, we analyzed the directed network of 59 KEs and 82 key event relationships (KERs) in the largest component using graph-theoretic approaches. Subsequently, we mined published literature using artificial intelligence-based tools to provide auxiliary evidence of cadmium association for all KEs in the largest component. Finally, we performed case studies to verify the rationality of cadmium-induced toxicity in humans and aquatic species. Overall, cadmium-AOP network constructed in this study will aid ongoing research in systems toxicology and chemical exposome.

Chemical-induced liver cancer: an adverse outcome pathway perspective

INTRODUCTION

The evaluation of the potential carcinogenicity is a key consideration in the risk assessment of chemicals. Predictive toxicology is currently switching toward non-animal approaches that rely on the mechanistic understanding of toxicity.

AREAS COVERED

Adverse outcome pathways (AOPs) present toxicological processes, including chemical-induced carcinogenicity, in a visual and comprehensive manner, which serve as the conceptual backbone for the development of non-animal approaches eligible for hazard identification. The current review provides an overview of the available AOPs leading to liver cancer and discusses their use in advanced testing of liver carcinogenic chemicals. Moreover, the challenges related to their use in risk assessment are outlined, including the exploitation of available data, the need for semantic ontologies, and the development of quantitative AOPs.

EXPERT OPINION

To exploit the potential of liver cancer AOPs in the field of risk assessment, 3 immediate prerequisites need to be fulfilled. These include developing human relevant AOPs for chemical-induced liver cancer, increasing the number of AOPs integrating quantitative toxicodynamic and toxicokinetic data, and developing a liver cancer AOP network. As AOPs and other areas in the field continue to evolve, liver cancer AOPs will progress into a reliable and robust tool serving future risk assessment and management.

Building an adverse outcome pathway network for estrogen-, androgen- and steroidogenesis-mediated reproductive toxicity

Introduction: Adverse Outcome Pathways (AOPs) can support both testing and assessment of endocrine disruptors (EDs). There is, however, a need for further development of the AOP framework to improve its applicability in a regulatory context. Here we have inventoried the AOP-wiki to identify all existing AOPs related to mammalian reproductive toxicity arising from disruption to the estrogen, androgen, and steroidogenesis modalities. Core key events (KEs) shared between relevant AOPs were also identified to aid in further AOP network (AOPN) development. Methods: A systematic approach using two different methods was applied to screen and search the entire AOP-wiki library. An AOPN was visualized using Cytoscape. Manual refinement was performed to remove AOPS devoid of any KEs and/or KERs. Results: Fifty-eight AOPs relevant for mammalian reproductive toxicity were originally identified, with 42 AOPs included in the final AOPN. Several of the KEs and KE relationships (KERs) described similar events and were thus merged to optimize AOPN construction. Sixteen sub-networks related to effects on hormone levels or hormone activity, cancer outcomes, male and female reproductive systems, and overall effects on fertility and reproduction were identified within the AOPN. Twenty-six KEs and 11 KERs were identified as core blocks of knowledge in the AOPN, of which 19 core KEs are already included as parameters in current OECD and US EPA test guidelines. Discussion: The AOPN highlights knowledge gaps that can be targeted for further development of a more complete AOPN that can support the identification and assessment of EDs.

Causal diagramming for assessing human system risk in spaceflight

For over a decade, the National Aeronautics and Space Administration (NASA) has tracked and configuration-managed approximately 30 risks that affect astronaut health and performance before, during and after spaceflight. The Human System Risk Board (HSRB) at NASA Johnson Space Center is responsible for setting the official risk posture for each of the human system risks and determining-based on evaluation of the available evidence-when that risk posture changes. The ultimate purpose of tracking and researching these risks is to find ways to reduce spaceflight-induced risk to astronauts. The adverse effects of spaceflight begin at launch and continue throughout the duration of the mission, and in some cases, across the lifetime of the astronaut. Historically, research has been conducted in individual risk "silos" to characterize risk, however, astronauts are exposed to all risks simultaneously. In January of 2020, the HSRB at NASA began assessing the potential value of causal diagramming as a tool to facilitate understanding of the complex causes and effects that contribute to spaceflight-induced human system risk. Causal diagrams in the form of directed acyclic graphs (DAGs) are used to provide HSRB stakeholders with a shared mental model of the causal flow of risk. While primarily improving communication among those stakeholders, DAGs also allow a composite risk network to be created that can be tracked and configuration managed. This paper outlines the HSRB's pilot process for this effort, the lessons learned, and future goals for data-driven risk management approaches.

Comprehensive mapping of the AOP-Wiki database: identifying biological and disease gaps

Introduction: The Adverse Outcome Pathway (AOP) concept facilitates rapid hazard assessment for human health risks. AOPs are constantly evolving, their number is growing, and they are referenced in the AOP-Wiki database, which is supported by the OECD. Here, we present a study that aims at identifying well-defined biological areas, as well as gaps within the AOP-Wiki for future research needs. It does not intend to provide a systematic and comprehensive summary of the available literature on AOPs but summarizes and maps biological knowledge and diseases represented by the already developed AOPs (with OECD endorsed status or under validation). Methods: Knowledge from the AOP-Wiki database were extracted and prepared for analysis using a multi-step procedure. An automatic mapping of the existing information on AOPs (i.e., genes/proteins and diseases) was performed using bioinformatics tools (i.e., overrepresentation analysis using Gene Ontology and DisGeNET), allowing both the classification of AOPs and the development of AOP networks (AOPN). Results: AOPs related to diseases of the genitourinary system, neoplasms and developmental anomalies are the most frequently investigated on the AOP-Wiki. An evaluation of the three priority cases (i.e., immunotoxicity and non-genotoxic carcinogenesis, endocrine and metabolic disruption, and developmental and adult neurotoxicity) of the EU-funded PARC project (Partnership for the Risk Assessment of Chemicals) are presented. These were used to highlight under- and over-represented adverse outcomes and to identify and prioritize gaps for further research. Discussion: These results contribute to a more comprehensive understanding of the adverse effects associated with the molecular events in AOPs, and aid in refining risk assessment for stressors and mitigation strategies. Moreover, the FAIRness (i.e., data which meets principles of findability, accessibility, interoperability, and reusability (FAIR)) of the AOPs appears to be an important consideration for further development.

Development of an adverse outcome pathway network for nephrotoxicity

Adverse outcome pathways (AOPs) were introduced in modern toxicology to provide evidence-based representations of the events and processes involved in the progression of toxicological effects across varying levels of the biological organisation to better facilitate the safety assessment of chemicals. AOPs offer an opportunity to address knowledge gaps and help to identify novel therapeutic targets. They also aid in the selection and development of existing and new in vitro and in silico test methods for hazard identification and risk assessment of chemical compounds. However, many toxicological processes are too intricate to be captured in a single, linear AOP. As a result, AOP networks have been developed to aid in the comprehension and placement of associated events underlying the emergence of related forms of toxicity-where complex exposure scenarios and interactions may influence the ultimate adverse outcome. This study utilised established criteria to develop an AOP network that connects thirteen individual AOPs associated with nephrotoxicity (as sourced from the AOP-Wiki) to identify several key events (KEs) linked to various adverse outcomes, including kidney failure and chronic kidney disease. Analysis of the modelled AOP network and its topological features determined mitochondrial dysfunction, oxidative stress, and tubular necrosis to be the most connected and central KEs. These KEs can provide a logical foundation for guiding the selection and creation of in vitro assays and in silico tools to substitute for animal-based in vivo experiments in the prediction and assessment of chemical-induced nephrotoxicity in human health.

Evaluating the effects of climate change and chemical, physical, and biological stressors on nearshore coral reefs: A case study in the Great Barrier Reef, Australia

An understanding of the combined effects of climate change (CC) and other anthropogenic stressors, such as chemical exposures, is essential for improving ecological risk assessments of vulnerable ecosystems. In the Great Barrier Reef, coral reefs are under increasingly severe duress from increasing ocean temperatures, acidification, and cyclone intensities associated with CC. In addition to these stressors, inshore reef systems, such as the Mackay-Whitsunday coastal zone, are being impacted by other anthropogenic stressors, including chemical, nutrient, and sediment exposures related to more intense rainfall events that increase the catchment runoff of contaminated waters. To illustrate an approach for incorporating CC into ecological risk assessment frameworks, we developed an adverse outcome pathway network to conceptually delineate the effects of climate variables and photosystem II herbicide (diuron) exposures on scleractinian corals. This informed the development of a Bayesian network (BN) to quantitatively compare the effects of historical (1975-2005) and future projected climate on inshore hard coral bleaching, mortality, and cover. This BN demonstrated how risk may be predicted for multiple physical and biological stressors, including temperature, ocean acidification, cyclones, sediments, macroalgae competition, and crown of thorns starfish predation, as well as chemical stressors such as nitrogen and herbicides. Climate scenarios included an ensemble of 16 downscaled models encompassing current and future conditions based on multiple emission scenarios for two 30-year periods. It was found that both climate-related and catchment-related stressors pose a risk to these inshore reef systems, with projected increases in coral bleaching and coral mortality under all future climate scenarios. This modeling exercise can support the identification of risk drivers for the prioritization of management interventions to build future resilient reefs. Integr Environ Assess Manag 2024;20:401-418. © 2023 Norwegian Institute for Water Research and The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC). This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Specific effects on the thyroid relevant for performing a dietary cumulative risk assessment of pesticide residues: 2024 update

EFSA updated its previous work on the establishment of specific effects that are considered relevant for grouping pesticide residues targeting the thyroid and for performing the retrospective assessment of dietary cumulative risk (CRA). The two specific effects already selected in 2019 leading to the two cumulative assessment groups (CAGs) 'hypothyroidism' and 'C-cell hypertrophy, hyperplasia and neoplasia' were reconfirmed. Compared to 2019, the list of indicators that can be used to identify these specific effects was refined to only include histopathological changes. In a second phase of the work, data will be extracted on indicators of the specific effects from the dossiers on active substances (a.s.) used as plant protection products. The criteria for including a.s. into CAGs were also updated, together with the hazard characterisation methodology and the lines of evidence for assessing CAG-membership probabilities. The tasks related to the data extraction and the establishment of the CAGs on hypothyroidism and on C-cell hypertrophy, hyperplasia and neoplasia are beyond the scope of this report. This part of the CRA process has been outsourced and will be the subject of a separate report.

Predicting the Metal Mixture Toxicity with a Toxicokinetic-Toxicodynamic Model Considering the Time-Dependent Adverse Outcome Pathways

Chemicals mainly exist in ecosystems as mixtures, and understanding and predicting their effects are major challenges in ecotoxicology. While the adverse outcome pathway (AOP) and toxicokinetic-toxicodynamic (TK-TD) models show promise as mechanistic approaches in chemical risk assessment, there is still a lack of methodology to incorporate the AOP into a TK-TD model. Here, we describe a novel approach that integrates the AOP and TK-TD models to predict mixture toxicity using metal mixtures (specifically Cd-Cu) as a case study. We preliminarily constructed an AOP of the metal mixture through temporal transcriptome analysis together with confirmatory bioassays. The AOP revealed that prolonged exposure time activated more key events and adverse outcomes, indicating different modes of action over time. We selected a potential key event as a proxy for damage and used it as a measurable parameter to replace the theoretical parameter (scaled damage) in the TK-TD model. This refined model, which connects molecular responses to organism outcomes, effectively predicts Cd-Cu mixture toxicity over time and can be extended to other metal mixtures and even multicomponent mixtures. Overall, our results contribute to a better understanding of metal mixture toxicity and provide insights for integrating the AOP and TK-TD models to improve risk assessment for chemical mixtures.

Microplastics as carriers of toxic pollutants: Source, transport, and toxicological effects

Microplastic pollution has emerged as a new environmental concern due to our reliance on plastic. Recent years have seen an upward trend in scholarly interest in the topic of microplastics carrying contaminants; however, the available review studies have largely focused on specific aspects of this issue, such as sorption, transport, and toxicological effects. Consequently, this review synthesizes the state-of-the-art knowledge on these topics by presenting key findings to guide better policy action toward microplastic management. Microplastics have been reported to absorb pollutants such as persistent organic pollutants, heavy metals, and antibiotics, leading to their bioaccumulation in marine and terrestrial ecosystems. Hydrophobic interactions are found to be the predominant sorption mechanism, especially for organic pollutants, although electrostatic forces, van der Waals forces, hydrogen bonding, and pi-pi interactions are also noteworthy. This review reveals that physicochemical properties of microplastics, such as size, structure, and functional groups, and environmental compartment properties, such as pH, temperature, and salinity, influence the sorption of pollutants by microplastic. It has been found that microplastics influence the growth and metabolism of organisms. Inadequate methods for collection and analysis of environmental samples, lack of replication of real-world settings in laboratories, and a lack of understanding of the sorption mechanism and toxicity of microplastics impede current microplastic research. Therefore, future research should focus on filling in these knowledge gaps.

Blurred lines: Crossing the boundaries between the chemical exposome and the metabolome

The aetiology of every human disease lies in a combination of genetic and environmental factors, each contributing in varying proportions. While genomics investigates the former, a comparable holistic paradigm was proposed for environmental exposures in 2005, marking the onset of exposome research. Since then, the exposome definition has broadened to include a wide array of physical, chemical, and psychosocial factors that interact with the human body and potentially alter the epigenome, the transcriptome, the proteome, and the metabolome. The chemical exposome, deeply intertwined with the metabolome, includes all small molecules originating from diet as well as pharmaceuticals, personal care and consumer products, or pollutants in air and water. The set of techniques to interrogate these exposures, primarily mass spectrometry and nuclear magnetic resonance spectroscopy, are also extensively used in metabolomics. Recent advances in untargeted metabolomics using high resolution mass spectrometry have paved the way for the development of methods able to provide in depth characterisation of both the internal chemical exposome and the endogenous metabolome simultaneously. Herein we review the available tools, databases, and workflows currently available for such work, and discuss how these can bridge the gap between the study of the metabolome and the exposome.

In utero exposure to ionizing radiation and metabolic regulation: perspectives for future multi- and trans-generation effects studies

PURPOSE

The radiation protection community has been particularly attentive to the risks of delayed effects on offspring from low dose or low dose-rate exposures to ionizing radiation. Despite this, the current epidemiologic studies and scientific data are still insufficient to provide the necessary evidence for improving risk assessment guidelines. This literature review aims to inform future studies on multigenerational and transgenerational effects. It primarily focuses on animal studies involving in utero exposure and discusses crucial elements for interpreting the results. These elements include in utero exposure scenarios relative to the developmental stages of the embryo/fetus, and the primary biological mechanisms responsible for transmitting heritable or hereditary effects to future generations. The review addresses several issues within the contexts of both multigenerational and transgenerational effects, with a focus on hereditary perspectives.

CONCLUSIONS

Knowledge consolidation in the field of Developmental Origins of Health and Disease (DOHaD) has led us to propose a new study strategy. This strategy aims to address the transgenerational effects of in utero exposure to low dose and low dose-rate radiation. Within this concept, there is a possibility that disruption of epigenetic programming in embryonic and fetal cells may occur. This disruption could lead to metabolic dysfunction, which in turn may cause abnormal responses to future environmental challenges, consequently increasing disease risk. Lastly, we discuss methodological limitations in our studies. These limitations are related to cohort size, follow-up time, model radiosensitivity, and analytical techniques. We propose scientific and analytical strategies for future research in this field.

Deriving aquatic PNECs of endocrine disruption effects for PFOS and PFOA by combining species sensitivity weighted distributions and adverse outcome pathway networks

Perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA), as emerging endocrine-disrupting chemicals (EDCs), pose adverse effects on aquatic organisms. Conventional ecological risk assessment (ERA) not fully considering the mode of toxicity action of PFOS and PFOA, may result in an underestimation of risks and confuse decision-makers. In the study, we developed species sensitivity weighted distribution (SSWD) models based on adverse outcome pathway (AOP) networks for deriving predicted no-effect concentrations (PNECs). Three kinds of weighting criteria (intraspecies variation, trophic level abundance, and data quality) and weighted log-normal distribution methods were adopted. The developed models considered the inter/intraspecies variation and integrated nontraditional endpoints of endocrine-disrupting effects. The PNECs of endocrine disruption effects were derived as 2.52 μg/L (95% confidence intervals 0.667-9.85 μg/L) for PFOS and 18.7 μg/L (5.40-71.0 μg/L) for PFOA, which were more conservative than those derived from the SSD method and were comparable with the values in the literature based on the chronic toxicity data. For PFOS, the effect of growth and development was the most sensitive; however, for PFOA, the effect of reproduction was the most sensitive in the effects of growth and development, reproduction, biochemistry and genetics, and survival. The endocrine-disrupting effects of PFOS and PFOA are significant and need to be fully recognized in the ERA. This study provided an ERA framework that can improve the ecological relevance and reduce the uncertainty of PNECs of EDCs.

The adverse outcome pathway for breast cancer: a knowledge management framework bridging biomedicine and toxicology

Breast cancer is the most common cancer worldwide, with an estimated 2.3 million new cases diagnosed every year. Effective measures for cancer prevention and cancer therapy require a detailed understanding of the individual key disease mechanisms involved and their interactions at the molecular, cellular, tissue, organ, and organism level. In that regard, the rapid progress of biomedical and toxicological research in recent years now allows the pursuit of new approaches based on non-animal methods that provide greater mechanistic insight than traditional animal models and therefore facilitate the development of Adverse Outcome Pathways (AOPs) for human diseases. We performed a systematic review of the current state of published knowledge with regard to breast cancer to identify relevant key mechanisms for inclusion into breast cancer AOPs, i.e. decreased cell stiffness and decreased cell adhesion, and to concurrently map non-animal methods addressing these key events. We conclude that the broader sharing of expertise and methods between biomedical research and toxicology enabled by the AOP knowledge management framework can help to coordinate global research efforts and accelerate the transition to advanced non-animal methods, which, when combined into powerful method batteries, closely mimic human physiology and disease states without the need for animal testing.

Advancing Computational Toxicology by Interpretable Machine Learning

Chemical toxicity evaluations for drugs, consumer products, and environmental chemicals have a critical impact on human health. Traditional animal models to evaluate chemical toxicity are expensive, time-consuming, and often fail to detect toxicants in humans. Computational toxicology is a promising alternative approach that utilizes machine learning (ML) and deep learning (DL) techniques to predict the toxicity potentials of chemicals. Although the applications of ML- and DL-based computational models in chemical toxicity predictions are attractive, many toxicity models are "black boxes" in nature and difficult to interpret by toxicologists, which hampers the chemical risk assessments using these models. The recent progress of interpretable ML (IML) in the computer science field meets this urgent need to unveil the underlying toxicity mechanisms and elucidate the domain knowledge of toxicity models. In this review, we focused on the applications of IML in computational toxicology, including toxicity feature data, model interpretation methods, use of knowledge base frameworks in IML development, and recent applications. The challenges and future directions of IML modeling in toxicology are also discussed. We hope this review can encourage efforts in developing interpretable models with new IML algorithms that can assist new chemical assessments by illustrating toxicity mechanisms in humans.

Advancing food safety risk assessment in China: development of new approach methodologies (NAMs)

Novel techniques and methodologies are being developed to advance food safety risk assessment into the next-generation. Considering the shortcomings of traditional animal testing, new approach methodologies (NAMs) will be the main tools for the next-generation risk assessment (NGRA), using non-animal methodologies such as in vitro and in silico approaches. The United States Environmental Protection Agency and the European Food Safety Authority have established work plans to encourage the development and application of NAMs in NGRA. Currently, NAMs are more commonly used in research than in regulatory risk assessment. China is also developing NAMs for NGRA but without a comprehensive review of the current work. This review summarizes major NAM-related research articles from China and highlights the China National Center for Food Safety Risk Assessment (CFSA) as the primary institution leading the implementation of NAMs in NGRA in China. The projects of CFSA on NAMs such as the Food Toxicology Program and the strategies for implementing NAMs in NGRA are outlined. Key issues and recommendations, such as discipline development and team building, are also presented to promote NAMs development in China and worldwide.

AOP Report: Aryl Hydrocarbon Receptor Activation Leads to Early-Life Stage Mortality via Sox9 Repression-Induced Craniofacial and Cardiac Malformations

The aryl hydrocarbon receptors (Ahrs) are evolutionarily conserved ligand-dependent transcription factors that are activated by structurally diverse endogenous compounds as well as environmental chemicals such as polycyclic aromatic hydrocarbons and halogenated aromatic hydrocarbons. Activation of the Ahr leads to several transcriptional changes that can cause developmental toxicity resulting in mortality. Evidence was assembled and evaluated for two novel adverse outcome pathways (AOPs) which describe how Ahr activation (molecular initiating event) can lead to early-life stage mortality (adverse outcome), via either SOX9-mediated craniofacial malformations (AOP 455) or cardiovascular toxicity (AOP 456). Using a key event relationship (KER)-by-KER approach, we collected evidence using both a narrative search and a systematic review based on detailed search terms. Weight of evidence for each KER was assessed to inform overall confidence of the AOPs. The AOPs link to previous descriptions of Ahr activation and connect them to two novel key events (KEs), increase in slincR expression, a newly characterized long noncoding RNA with regulatory functions, and suppression of SOX9, a critical transcription factor implicated in chondrogenesis and cardiac development. In general, confidence levels for KERs ranged between medium and strong, with few inconsistencies, as well as several opportunities for future research identified. While the majority of KEs have only been demonstrated in zebrafish with 2,3,7,8-tetrachlorodibenzo-p-dioxin as an Ahr activator, evidence suggests that the two AOPs likely apply to most vertebrates and many Ahr-activating chemicals. Addition of the AOPs into the AOP-Wiki (https://aopwiki.org/) helps expand the growing Ahr-related AOP network to 19 individual AOPs, of which six are endorsed or in progress and the remaining 13 relatively underdeveloped. Environ Toxicol Chem 2023;42:2063-2077. © 2023 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Connecting Suborganismal Data to Bioenergetic Processes: Killifish Embryos Exposed to a Dioxin-Like Compound

A core challenge for ecological risk assessment is to integrate molecular responses into a chain of causality to organismal or population-level outcomes. Bioenergetic theory may be a useful approach for integrating suborganismal responses to predict organismal responses that influence population dynamics. We describe a novel application of dynamic energy budget (DEB) theory in the context of a toxicity framework (adverse outcome pathways [AOPs]) to make quantitative predictions of chemical exposures to individuals, starting from suborganismal data. We use early-life stage exposure of Fundulus heteroclitus to dioxin-like chemicals (DLCs) and connect AOP key events to DEB processes through "damage" that is produced at a rate proportional to the internal toxicant concentration. We use transcriptomic data of fish embryos exposed to DLCs to translate molecular indicators of damage into changes in DEB parameters (damage increases somatic maintenance costs) and DEB models to predict sublethal and lethal effects on young fish. By changing a small subset of model parameters, we predict the evolved tolerance to DLCs in some wild F. heteroclitus populations, a data set not used in model parameterization. The differences in model parameters point to reduced sensitivity and altered damage repair dynamics as contributing to this evolved resistance. Our methodology has potential extrapolation to untested chemicals of ecological concern. Environ Toxicol Chem 2023;42:2040-2053. © 2023 Oak Ridge National Laboratory and The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

A framework for prioritizing contaminants in retrospective ecological assessments: Application in the Milwaukee Estuary (Milwaukee, WI)

Watersheds are subjected to diverse anthropogenic inputs, exposing aquatic biota to a wide range of chemicals. Detection of multiple, different chemicals can challenge natural resource managers who often have to determine where to allocate potentially limited resources. Here, we describe a weight-of-evidence framework for retrospectively prioritizing aquatic contaminants. To demonstrate framework utility, we used data from 96-h caged fish studies to prioritize chemicals detected in the Milwaukee Estuary (WI, USA; 2017-2018). Across study years, 77/178 targeted chemicals were detected. Chemicals were assigned prioritization scores based on spatial and temporal detection frequency, environmental distribution, environmental fate, ecotoxicological potential, and effect prediction. Chemicals were sorted into priority bins based on the intersection of prioritization score and data availability. Data-limited chemicals represented those that did not have sufficient data to adequately evaluate ecotoxicological potential or environmental fate. Seven compounds (fluoranthene, benzo[a]pyrene, pyrene, atrazine, metolachlor, phenanthrene, and DEET) were identified as high or medium priority and data sufficient and flagged as candidates for further effects-based monitoring studies. Twenty-one compounds were identified as high or medium priority and data limited and flagged as candidates for further ecotoxicological research. Fifteen chemicals were flagged as the lowest priority in the watershed. One of these chemicals (2-methylnaphthalene) displayed no data limitations and was flagged as a definitively low-priority chemical. The remaining chemicals displayed some data limitations and were considered lower-priority compounds (contingent on further ecotoxicological and environmental fate assessments). The remaining 34 compounds were flagged as low or medium priority. Altogether, this prioritization provided a screening-level (non-definitive) assessment that could be used to focus further resource management and risk assessment activities in the Milwaukee Estuary. Furthermore, by providing detailed methodology and a practical example with real experimental data, we demonstrated that the proposed framework represents a transparent and adaptable approach for prioritizing contaminants in freshwater environments. Integr Environ Assess Manag 2023;19:1276-1296. © 2022 SETAC.

Optimization of an adverse outcome pathway network on chemical-induced cholestasis using an artificial intelligence-assisted data collection and confidence level quantification approach

BACKGROUND

Adverse outcome pathway (AOP) networks are versatile tools in toxicology and risk assessment that capture and visualize mechanisms driving toxicity originating from various data sources. They share a common structure consisting of a set of molecular initiating events and key events, connected by key event relationships, leading to the actual adverse outcome. AOP networks are to be considered living documents that should be frequently updated by feeding in new data. Such iterative optimization exercises are typically done manually, which not only is a time-consuming effort, but also bears the risk of overlooking critical data. The present study introduces a novel approach for AOP network optimization of a previously published AOP network on chemical-induced cholestasis using artificial intelligence to facilitate automated data collection followed by subsequent quantitative confidence assessment of molecular initiating events, key events, and key event relationships.

METHODS

Artificial intelligence-assisted data collection was performed by means of the free web platform Sysrev. Confidence levels of the tailored Bradford-Hill criteria were quantified for the purpose of weight-of-evidence assessment of the optimized AOP network. Scores were calculated for biological plausibility, empirical evidence, and essentiality, and were integrated into a total key event relationship confidence value. The optimized AOP network was visualized using Cytoscape with the node size representing the incidence of the key event and the edge size indicating the total confidence in the key event relationship.

RESULTS

This resulted in the identification of 38 and 135 unique key events and key event relationships, respectively. Transporter changes was the key event with the highest incidence, and formed the most confident key event relationship with the adverse outcome, cholestasis. Other important key events present in the AOP network include: nuclear receptor changes, intracellular bile acid accumulation, bile acid synthesis changes, oxidative stress, inflammation and apoptosis.

CONCLUSIONS

This process led to the creation of an extensively informative AOP network focused on chemical-induced cholestasis. This optimized AOP network may serve as a mechanistic compass for the development of a battery of in vitro assays to reliably predict chemical-induced cholestatic injury.

Cross-species applicability of an adverse outcome pathway network for thyroid hormone system disruption

Thyroid hormone system disrupting compounds are considered potential threats for human and environmental health. Multiple adverse outcome pathways (AOPs) for thyroid hormone system disruption (THSD) are being developed in different taxa. Combining these AOPs results in a cross-species AOP network for THSD which may provide an evidence-based foundation for extrapolating THSD data across vertebrate species and bridging the gap between human and environmental health. This review aimed to advance the description of the taxonomic domain of applicability (tDOA) in the network to improve its utility for cross-species extrapolation. We focused on the molecular initiating events (MIEs) and adverse outcomes (AOs) and evaluated both their plausible domain of applicability (taxa they are likely applicable to) and empirical domain of applicability (where evidence for applicability to various taxa exists) in a THSD context. The evaluation showed that all MIEs in the AOP network are applicable to mammals. With some exceptions, there was evidence of structural conservation across vertebrate taxa and especially for fish and amphibians, and to a lesser extent for birds, empirical evidence was found. Current evidence supports the applicability of impaired neurodevelopment, neurosensory development (eg, vision) and reproduction across vertebrate taxa. The results of this tDOA evaluation are summarized in a conceptual AOP network that helps prioritize (parts of) AOPs for a more detailed evaluation. In conclusion, this review advances the tDOA description of an existing THSD AOP network and serves as a catalog summarizing plausible and empirical evidence on which future cross-species AOP development and tDOA assessment could build.

Expanding adverse outcome pathways towards one health models for nanosafety

The ever-growing production of nano-enabled products has generated the need for dedicated risk assessment strategies that ensure safety for humans and the environment. Transdisciplinary approaches are needed to support the development of new technologies while respecting environmental limits, as also highlighted by the EU Green Deal Chemicals Strategy for Sustainability and its safe and sustainable by design (SSbD) framework. The One Health concept offers a holistic multiscale approach for the assessment of nanosafety. However, toxicology is not yet capable of explaining the interaction between chemicals and biological systems at the multiscale level and in the context of the One Health framework. Furthermore, there is a disconnect between chemical safety assessment, epidemiology, and other fields of biology that, if unified, would enable the adoption of the One Health model. The development of mechanistic toxicology and the generation of omics data has provided important biological knowledge of the response of individual biological systems to nanomaterials (NMs). On the other hand, epigenetic data have the potential to inform on interspecies mechanisms of adaptation. These data types, however, need to be linked to concepts that support their intuitive interpretation. Adverse Outcome Pathways (AOPs) represent an evolving framework to anchor existing knowledge to chemical risk assessment. In this perspective, we discuss the possibility of integrating multi-level toxicogenomics data, including toxicoepigenetic insights, into the AOP framework. We anticipate that this new direction of toxicogenomics can support the development of One Health models applicable to groups of chemicals and to multiple species in the tree of life.

Towards a science-based testing strategy to identify maternal thyroid hormone imbalance and neurodevelopmental effects in the progeny - Part IV: the ECETOC and CLE Proposal for a Thyroid Function-Related Neurodevelopmental Toxicity Testing and Assessment Scheme (Thyroid-NDT-TAS)

Following the European Commission Endocrine Disruptor Criteria, substances shall be considered as having endocrine disrupting properties if they (a) elicit adverse effects, (b) have endocrine activity, and (c) the two are linked by an endocrine mode-of-action (MoA) unless the MoA is not relevant for humans. A comprehensive, structured approach to assess whether substances meet the Endocrine Disruptor Criteria for the thyroid modality (EDC-T) is currently unavailable. Here, the European Centre for Ecotoxicology and Toxicology of Chemicals Thyroxine Task Force and CropLife Europe propose a Thyroid Function-Related Neurodevelopmental Toxicity Testing and Assessment Scheme (Thyroid-NDT-TAS). In Tier 0, before entering the Thyroid-NDT-TAS, all available in vivo, in vitro and in silico data are submitted to weight-of-evidence (WoE) evaluations to determine whether the substance of interest poses a concern for thyroid disruption. If so, Tier 1 of the Thyroid-NDT-TAS includes an initial MoA and human relevance assessment (structured by the key events of possibly relevant adverse outcome pathways) and the generation of supportive in vitro/in silico data, if relevant. Only if Tier 1 is inconclusive, Tier 2 involves higher-tier testing to generate further thyroid- and/or neurodevelopment-related data. Tier 3 includes the final MoA and human relevance assessment and an overarching WoE evaluation to draw a conclusion on whether, or not, the substance meets the EDC-T. The Thyroid-NDT-TAS is based on the state-of-the-science, and it has been developed to minimise animal testing. To make human safety assessments more accurate, it is recommended to apply the Thyroid-NDT-TAS during future regulatory assessments.

A curated gene and biological system annotation of adverse outcome pathways related to human health

Adverse outcome pathways (AOPs) are emerging as a central framework in modern toxicology and other fields in biomedicine. They serve as an extension of pathway-based concepts by depicting biological mechanisms as causally linked sequences of key events (KEs) from a molecular initiating event (MIE) to an adverse outcome. AOPs guide the use and development of new approach methodologies (NAMs) aimed at reducing animal experimentation. While AOPs model the systemic mechanisms at various levels of biological organisation, toxicogenomics provides the means to study the molecular mechanisms of chemical exposures. Systematic integration of these two concepts would improve the application of AOP-based knowledge while also supporting the interpretation of complex omics data. Hence, we established this link through rigorous curation of molecular annotations for the KEs of human relevant AOPs. We further expanded and consolidated the annotations of the biological context of KEs. These curated annotations pave the way to embed AOPs in molecular data interpretation, facilitating the emergence of new knowledge in biomedicine.

Reversibility of Thyroid Hormone System-Disrupting Effects on Eye and Thyroid Follicle Development in Zebrafish (Danio rerio) Embryos

Early vertebrate development is partially regulated by thyroid hormones (THs). Environmental pollutants that interact with the TH system (TH system-disrupting chemicals [THSDCs]) can have massively disrupting effects on this essential phase. Eye development of fish is directly regulated by THs and can, therefore, be used as a thyroid-related endpoint in endocrine disruptor testing. To evaluate the effects of THSDC-induced eye malformations during early development, zebrafish (Danio rerio) embryos were exposed for 5 days postfertilization (dpf) to either propylthiouracil, a TH synthesis inhibitor, or tetrabromobisphenol A, which interacts with TH receptors. Subsequently, one half of the embryos were exposed further to the THSDCs until 8 dpf, while the other half of the embryos were raised in clean water for 3 days to check for reversibility of effects. Continued THSDC exposure altered eye size and pigmentation and induced changes in the cellular structure of the retina. This correlated with morphological alterations of thyroid follicles as revealed by use of a transgenic zebrafish line. Interestingly, effects were partly reversible after a recovery period as short as 3 days. Results are consistent with changes in TH levels measured in different tissues of the embryos, for example, in the eyes. The results show that eye development in zebrafish embryos is very sensitive to THSDC treatment but able to recover quickly from early exposure by effective repair mechanisms. Environ Toxicol Chem 2023;42:1276-1292. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

New approach methods to improve human health risk assessment of thyroid hormone system disruption-a PARC project

Current test strategies to identify thyroid hormone (TH) system disruptors are inadequate for conducting robust chemical risk assessment required for regulation. The tests rely heavily on histopathological changes in rodent thyroid glands or measuring changes in systemic TH levels, but they lack specific new approach methodologies (NAMs) that can adequately detect TH-mediated effects. Such alternative test methods are needed to infer a causal relationship between molecular initiating events and adverse outcomes such as perturbed brain development. Although some NAMs that are relevant for TH system disruption are available-and are currently in the process of regulatory validation-there is still a need to develop more extensive alternative test batteries to cover the range of potential key events along the causal pathway between initial chemical disruption and adverse outcomes in humans. This project, funded under the Partnership for the Assessment of Risk from Chemicals (PARC) initiative, aims to facilitate the development of NAMs that are specific for TH system disruption by characterizing in vivo mechanisms of action that can be targeted by in embryo/in vitro/in silico/in chemico testing strategies. We will develop and improve human-relevant in vitro test systems to capture effects on important areas of the TH system. Furthermore, we will elaborate on important species differences in TH system disruption by incorporating non-mammalian vertebrate test species alongside classical laboratory rat species and human-derived in vitro assays.