Adverse outcome pathway development II: best practices

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.

TRPA1 nanovesicle-conjugated receptonics for rapid biocide screening

Although biocides are important materials in modern society and help protect human health and the environment, increasing exposure to combined biocides can cause severe side effects in the human body, such as lung fibrosis. In this study, we developed a receptonics system to screen for biocides in combined household chemical products based on biocides. The system contains transient receptor potential ankyrin 1 (TRPA1) nanovesicles (NVs) to sense biocides based on pain receptors and a side-gated field-effect transistor (SGFET) using a single-layer graphene (SLG) micropattern channel. The binding affinities between the TRPA1 receptor and the various biocides were estimated by performing biosimulation and using a calcium ion (Ca2+) assay, and the sensitivity of the system was compared with that of TRPA1 NV receptonics systems. Based on the results of the TRPA1 NV receptonics system, the antagonistic and potentiation effects of combined biocides and household chemical products depended on the concentration. Finally, the TRPA1 NV receptonics system was applied to screen for biocides in real products, and its performance was successful. Based on these results, the TRPA1 NV receptonics system can be utilized to perform risk evaluations and identify biocides in a simple and rapid manner.

Current Challenges to Align Inflammatory Key Events in Animals and Lung Cell Models In Vitro

With numerous novel and innovative in vitro models emerging every year to reduce or replace animal testing, there is an urgent need to align the design, harmonization, and validation of such systems using in vitro-in vivo extrapolation (IVIVE) approaches. In particular, in inhalation toxicology, there is a lack of predictive and prevalidated in vitro lung models that can be considered a valid alternative for animal testing. The predictive power of such models can be enhanced by applying the Adverse Outcome Pathways (AOP) framework, which casually links key events (KE) relevant to IVIVE. However, one of the difficulties identified is that the endpoint analysis and readouts of specific assays in in vitro and animal models for specific toxicants are currently not harmonized, making the alignment challenging. We summarize the current state of the art in endpoint analysis in the two systems, focusing on inflammatory-induced effects and providing guidance for future research directions to improve the alignment.

Sublethal effects of early-life exposure to common and emerging contaminants in birds

The plight of wild birds is becoming critical due to exposure to environmental contaminants. Although laboratory studies have provided insights into the developmental effects of chemical exposures, less is known about the adverse effects of environmental chemicals in developing wild birds. Early life stages are critical windows during which long-term organization of physiological, behavioral, and neurological systems can occur. Thus, contaminant exposure at early life stages can directly influence survival and reproductive success, with consequences for population stability and resilience in wild species. This review synthesizes existing knowledge regarding both short- and long-term effects of early-life exposure to widespread contaminants in birds. We focus especially on wild birds and on contaminants of concern within the Gulf of Mexico as an example of a habitat under anthropogenic stress from exposure to a complex mixture of chemicals and changing land uses that exacerbate existing vulnerabilities of wildlife in this region. Chemical contaminants for discussion in this review are based on avian mortality records from the Wildlife Health Information Sharing Partnership (WHISPers) database and on additional review of the literature regarding avian contaminants of concern for the northern Gulf of Mexico, and include oil and associated polycyclic aromatic hydrocarbons, dioxin and dioxin-like compounds, flame retardants, pesticides, heavy metals, and plastics. We provide an overview of effects in bird species at both the pre-hatching and post-hatching early life stages, discuss differences in sensitivities by route of exposure, life stage, and life history, and provide recommendations for future research. We find that additional research is needed on altricial species, post-hatching early-life exposure, long-term effects, and on ecologically relevant contaminant concentrations and routes of exposure. Given the increasing frequency and intensity of anthropogenic stressors encountered by wild animals, understanding both lethal and sublethal impacts of contaminants on the health of individuals and populations will be critical to inform restoration, management, and mitigation efforts.

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.

Cell proliferation and carcinogenesis: an approach to screening for potential human carcinogens

Cancer arises from multiple genetic errors occurring in a single stem cell (clonality). Every time DNA replicates, mistakes occur. Thus, agents can increase the risk of cancer either by directly damaging DNA (DNA-reactive carcinogens) or increasing the number of DNA replications (increased cell proliferation). Increased cell proliferation can be achieved either by direct mitogenesis or cytotoxicity with regenerative proliferation. Human carcinogens have a mode of action of DNA reactivity, immunomodulation (mostly immunosuppression), increased estrogenic activity (mitogenesis), or cytotoxicity and regeneration. By focusing on screening for these four effects utilizing in silico, in vitro, and short-term in vivo assays, a biologically based screening for human chemical carcinogens can be accomplished with greater predictivity than the traditional 2-year bioassay with considerably less cost, less time, and the use of fewer animals.

A framework for integrating evidence to assess hazards and risk

To accurately characterize human health hazards, human, animal, and mechanistic data must be integrated and the relevance to the research question of all three lines of evidence must be considered. Mechanistic data are often critical to the full integration of animal and human data and to characterizing relevance and uncertainty. This novel evidence integration framework (EIF) provides a method for synthesizing data from comprehensive, systematic, quality-based assessments of the epidemiological and toxicological literature, including in vivo and in vitro mechanistic studies. It organizes data according to both the observed human health effects and the mechanism of action of the chemical, providing a method to support evidence synthesis. The disease-based component uses the evidence of human health outcomes studied in the best quality epidemiological literature to organize the toxicological data according to authors' stated purpose, with the pathophysiology of the disease determining the potential relevance of the toxicological data. The mechanism-based component organizes the data based on the proposed mechanisms of effect and data supporting events leading to each endpoint, with the epidemiological data potentially providing corroborating information. The EIF includes a method to cross-classify and describe the concordance of the data, and to characterize its uncertainty. At times, the two methods of organizing the data may lead to different conclusions. This facilitates identification of knowledge gaps and shows the impact of uncertainties on the strength of causal inference.

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.

Beyond Encapsulation: Exploring Macrophage-Fibroblast Cross Talk in Implant-Induced Fibrosis

The foreign body response (FBR) and organ fibrosis are complex biological processes involving the interaction between macrophages and fibroblasts. Understanding the molecular mechanisms underlying macrophage-fibroblast cross talk is crucial for developing strategies to mitigate implant encapsulation, a major cause of implant failure. This article reviews the current knowledge on the role of macrophages and fibroblasts in the FBR and organ fibrosis, highlighting the similarities between these processes. The FBR is characterized by the formation of a fibrotic tissue capsule around the implant, leading to functional impairment. Various factors, including material properties such as surface chemistry, stiffness, and topography, influence the degree of encapsulation. Cross talk between macrophages and fibroblasts plays a critical role in both the FBR and organ fibrosis. However, the precise molecular mechanisms remain poorly understood. Macrophages secrete a wide range of cytokines that modulate fibroblast behavior such as abundant collagen deposition and myofibroblast differentiation. However, the heterogeneity of macrophages and fibroblasts and their dynamic behavior in different tissue environments add complexity to this cross talk. Experimental evidence from in vitro studies demonstrates the impact of material properties on macrophage cytokine secretion and fibroblast physiology. However, the correlation between in vitro response and in vivo encapsulation outcomes is not robust. Adverse outcome pathways (AOPs) offer a potential framework to understand and predict process complexity. AOPs describe causal relationships between measurable events leading to adverse outcomes, providing mechanistic insights for in vitro testing and predictive modeling. However, the development of an AOP for the FBR does require a comprehensive understanding of the molecular initiating events and key event relationships to identify which events are essential. In this article, we describe the current knowledge on macrophage-fibroblast cross talk in the FBR and discuss how targeted research can help build an AOP for implant-related fibrosis.

Effects of petrogenic pollutants on North Atlantic and Arctic Calanus copepods: From molecular mechanisms to population impacts

Oil and gas industries in the Northern Atlantic Ocean have gradually moved closer to the Arctic areas, a process expected to be further facilitated by sea ice withdrawal caused by global warming. Copepods of the genus Calanus hold a key position in these cold-water food webs, providing an important energetic link between primary production and higher trophic levels. Due to their ecological importance, there is a concern about how accidental oil spills and produced water discharges may impact cold-water copepods. In this review, we summarize the current knowledge of the toxicity of petroleum on North Atlantic and Arctic Calanus copepods. We also review how recent development of high-quality transcriptomes from RNA-sequencing of copepods have identified genes regulating key biological processes, like molting, diapause and reproduction in Calanus copepods, to suggest linkages between exposure, molecular mechanisms and effects on higher levels of biological organization. We found that the available ecotoxicity threshold data for these copepods provide valuable information about their sensitivity to acute petrogenic exposures; however, there is still insufficient knowledge regarding underlying mechanisms of toxicity and the potential for long-term implications of relevance for copepod ecology and phenology. Copepod transcriptomics has expanded our understanding of how key biological processes are regulated in cold-water copepods. These advances can improve our understanding of how pollutants affect biological processes, and thus provide the basis for new knowledge frameworks spanning the effect continuum from molecular initiating events to adverse effects of regulatory relevance. Such efforts, guided by concepts such as adverse outcome pathways (AOPs), enable standardized and transparent characterization and evaluation of knowledge and identifies research gaps and priorities. This review suggests enhancing mechanistic understanding of exposure-effect relationships to better understand and link biomarker responses to adverse effects to improve risk assessments assessing ecological effects of pollutant mixtures, like crude oil, in Arctic areas.

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.

Short-Term Transcriptomic Points of Departure Are Consistent with Chronic Points of Departure for Three Organophosphate Pesticides across Mouse and Fathead Minnow

New approach methods (NAMs) can reduce the need for chronic animal studies. Here, we apply benchmark dose (concentration) (BMD(C))-response modeling to transcriptomic changes in the liver of mice and in fathead minnow larvae after short-term exposures (7 days and 1 day, respectively) to several dose/concentrations of three organophosphate pesticides (OPPs): fenthion, methidathion, and parathion. The mouse liver transcriptional points of departure (TPODs) for fenthion, methidathion, and parathion were 0.009, 0.093, and 0.046 mg/Kg-bw/day, while the fathead minnow larva TPODs were 0.007, 0.115, and 0.046 mg/L, respectively. The TPODs were consistent across both species and reflected the relative potencies from traditional chronic toxicity studies with fenthion identified as the most potent. Moreover, the mouse liver TPODs were more sensitive than or within a 10-fold difference from the chronic apical points of departure (APODs) for mammals, while the fathead minnow larva TPODs were within an 18-fold difference from the chronic APODs for fish species. Short-term exposure to OPPs significantly impacted acetylcholinesterase mRNA abundance (FDR p-value <0.05, |fold change| ≥2) and canonical pathways (IPA, p-value <0.05) associated with organism death and neurological/immune dysfunctions, indicating the conservation of key events related to OPP toxicity. Together, these results build confidence in using short-term, molecular-based assays for the characterization of chemical toxicity and risk, thereby reducing reliance on chronic animal studies.

Integrated physiological and metabolomic analysis reveals new insights into toxicity pathways of paraquat to Microcystis aeruginosa

Chemical pollutants, such as herbicides, released into the aquatic environment adversely affect the phytoplankton community structure. While majority of herbicides are specifically designed to target photosynthetic processes, they also can be toxic to phytoplankton; however, despite the photosynthetic toxicity, some herbicides can target multiple physiological processes. Therefore, a full picture of toxicity pathway of herbicide to phytoplankton is necessary. In the present study, the cyanobacterium Microcystis aeruginosa was exposed to two levels (17 μg L^-1 (EC₁₀) and 65 μg L^-1 (EC₅₀)) of paraquat for 72 h. The physiological and metabolic responses were analyzed to elucidate the toxicity pathway and establish the adverse outcome pathway of paraquat to M. aeruginosa. The results revealed that enhanced glycolysis (upregulation of pyruvic acid level) and tricarboxylic acid cycle (upregulation of the levels of malic acid, isocitric acid and citric acid) exposed to EC₁₀ level of paraquat, which probably acted as a temporary strategy to maintain a healthy energy status in M. aeruginosa cells. Meanwhile, the expressions of glutathione and benzoic acid were enhanced to scavenge the excessive reactive oxygen species (ROS). Additionally, the accumulation of pigments (chlorophyll a and carotenoid) might play a supplementary role in the acclimation to EC₁₀ level paraquat treatment. In cells exposed to paraquat by EC₅₀ level, the levels of SOD, CAT, glutathione and benzoic acid increased significantly; however, the ROS exceeded the tolerance level of antioxidant system in M. aeruginosa. The adverse effects were revealed by inhibition of chlorophyll a fluorescence, the decreases in several carbohydrates (e.g., glucose 1-phosphate, fructose and galactose) and total protein content. Consequently, paraquat-induced oxidative stress caused the growth inhibition of M. aeruginosa. These findings provide new insights into the mode of action of paraquat in M. aeruginosa.

Adverse Outcome Pathway 'Footprinting': A Novel Approach to the Integration of 21st Century Toxicology Information into Chemical Mixtures Risk Assessment

For over a decade, New Approach Methodologies (NAMs) such as structure-activity/read-across, -omics technologies, and Adverse Outcome Pathway (AOP), have been considered within regulatory communities as alternative sources of chemical and biological information potentially relevant to human health risk assessment. Integration of NAMs into applications such as chemical mixtures risk assessment has been limited due to the lack of validation of qualitative and quantitative application to adverse health outcomes in vivo, and acceptance by risk assessors. However, leveraging existent hazard and dose-response information, including NAM-based data, for mixture component chemicals across one or more levels of biological organization using novel approaches such as AOP 'footprinting' proposed herein, may significantly advance mixtures risk assessment. AOP footprinting entails the systematic stepwise profiling and comparison of all known or suspected AOPs involved in a toxicological effect at the level of key event (KE). The goal is to identify key event(s) most proximal to an adverse outcome within each AOP suspected of contributing to a given health outcome at which similarity between mixture chemicals can be confidently determined. These key events are identified as the 'footprint' for a given AOP. This work presents the general concept, and a hypothetical example application, of AOP footprinting as a key methodology for the integration of NAM data into mixtures risk assessment.

Advancing New Approach Methodologies (NAMs) for Tobacco Harm Reduction: Synopsis from the 2021 CORESTA SSPT-NAMs Symposium

New approach methodologies (NAMs) are emerging chemical safety assessment tools consisting of in vitro and in silico (computational) methodologies intended to reduce, refine, or replace (3R) various in vivo animal testing methods traditionally used for risk assessment. Significant progress has been made toward the adoption of NAMs for human health and environmental toxicity assessment. However, additional efforts are needed to expand their development and their use in regulatory decision making. A virtual symposium was held during the 2021 Cooperation Centre for Scientific Research Relative to Tobacco (CORESTA) Smoke Science and Product Technology (SSPT) conference (titled "Advancing New Alternative Methods for Tobacco Harm Reduction"), with the goals of introducing the concepts and potential application of NAMs in the evaluation of potentially reduced-risk (PRR) tobacco products. At the symposium, experts from regulatory agencies, research organizations, and NGOs shared insights on the status of available tools, strengths, limitations, and opportunities in the application of NAMs using case examples from safety assessments of chemicals and tobacco products. Following seven presentations providing background and application of NAMs, a discussion was held where the presenters and audience discussed the outlook for extending the NAMs toxicological applications for tobacco products. The symposium, endorsed by the CORESTA In Vitro Tox Subgroup, Biomarker Subgroup, and NextG Tox Task Force, illustrated common ground and interest in science-based engagement across the scientific community and stakeholders in support of tobacco regulatory science. Highlights of the symposium are summarized in this paper.

A new perspective on endocrine disrupting effects of triphenyltin on marine medaka: From brain transcriptome, gut content metabolome and behavior

Triphenyltin (TPT) is an endocrine contaminant that is often detected in the environment. However, the mechanism of the effects of TPT on biological systems is not fully understood. Here we exposed marine medaka (Oryzias melastigma) to TPT for 21 days. Brain transcriptome, intestinal content metabolism group, and behavior analysis were carried out. Through the comprehensive analysis of multiomics for the in-depth understanding of the ways related to health improvement, we determined that the glycine-serine-threonine metabolic axis was most perturbed by TPT. Through behavioral analysis, it was found that there was behavioral hyperactivity in the exposed group; behavioral hyperactivity may be caused by the interference of TPT with the neuroendocrine system. In order to gain a full understanding of the impacts of TPT on human health, transcriptomic screening of differential genes and an impartial attitude based on bioinformatics were used. Gene-disease interaction analysis using the Comparative Toxicogenomics Database (CTD) revealed the possible effects of TPT on human health. Finally, based on these findings, the relevant adverse outcome pathway (AOP), which is the "epigenetic modification of PPARG leading to adipogenesis," was identified from AOP Wiki. Further research is required to validate the potential AOP of TPT.

Benzo[a]pyrene inhibits testosterone biosynthesis via NDUFA10-mediated mitochondrial compromise in mouse Leydig cells: Integrating experimental and in silico toxicological approaches

Benzo[a]pyrene (B[a]P), a representative of polycyclic aromatic hydrocarbons (PAHs), is ubiquitously spread in the environment and showing deleterious impacts on male steroidogenesis, including testosterone synthesis disorder. However, the precise mechanisms involved in B[a]P-induced steroidogenesis perturbation remains obscure. In the present study, we integrated in vivo tests, transcriptome profiling, in vitro assays, and conjoint in silico toxicological approaches to delineate the detailed mechanisms. In mouse models, we observed that B[a]P administration remarkably inhibited testosterone synthesis accompanied by ultrastructural impairments of mitochondria and mitophagosome formation in mouse Leydig cells. Transcriptome profiling showed that B[a]P down-regulated the expression of Ndufa9, Ndufa6, Ndufa10, and Ndufa5 in mouse testes, which are identified as critical genes involved in the assembly and functionality of mitochondrial complex I. In the in vitro tests, the bioactive B[a]P metabolite BPDE induced perturbation of testosterone synthesis by NDUFA10-mediated mitochondrial impairment, which was further exacerbated by mitophagy in TM3 Leydig cells. The findings of in silico toxicological analyses were highly consistent with the experimental observations and further unveiled that B[a]P/BPDE-involved PPARα activation could serve as a molecular initiating event to trigger the decline in Ndufa10 expression and testosterone synthesis. Overall, we have shown the first evidence that mitochondrial compromise in Leydig cells is the extremely crucial target in B[a]P-induced steroidogenesis perturbation.

Gut as an Alternative Entry Route for SARS-CoV-2: Current Evidence and Uncertainties of Productive Enteric Infection in COVID-19

The gut has been proposed as a potential alternative entry route for SARS-CoV-2. This was mainly based on the high levels of SARS-CoV-2 receptor expressed in the gastrointestinal (GI) tract, the observations of GI disorders (such as diarrhea) in some COVID-19 patients and the detection of SARS-CoV-2 RNA in feces. However, the underlying mechanisms remain poorly understood. It has been proposed that SARS-CoV-2 can productively infect enterocytes, damaging the intestinal barrier and contributing to inflammatory response, which might lead to GI manifestations, including diarrhea. Here, we report a methodological approach to assess the evidence supporting the sequence of events driving SARS-CoV-2 enteric infection up to gut adverse outcomes. Exploring evidence permits to highlight knowledge gaps and current inconsistencies in the literature and to guide further research. Based on the current insights on SARS-CoV-2 intestinal infection and transmission, we then discuss the potential implication on clinical practice, including on long COVID. A better understanding of the GI implication in COVID-19 is still needed to improve disease management and could help identify innovative therapies or preventive actions targeting the GI tract.

Adverse Outcome Pathways Associated with the Ingestion of Titanium Dioxide Nanoparticles-A Systematic Review

Titanium dioxide nanoparticles (TiO₂-NPs) are widely used, and humans are exposed through food (E171), cosmetics (e.g., toothpaste), and pharmaceuticals. The oral and gastrointestinal (GIT) tract are the first contact sites, but it may be systemically distributed. However, a robust adverse outcome pathway (AOP) has not been developed upon GIT exposure to TiO₂-NPs. The aim of this review was to provide an integrative analysis of the published data on cellular and molecular mechanisms triggered after the ingestion of TiO₂-NPs, proposing plausible AOPs that may drive policy decisions. A systematic review according to Prisma Methodology was performed in three databases of peer-reviewed literature: Pubmed, Scopus, and Web of Science. A total of 787 records were identified, screened in title/abstract, being 185 used for data extraction. The main endpoints identified were oxidative stress, cytotoxicity/apoptosis/cell death, inflammation, cellular and systemic uptake, genotoxicity, and carcinogenicity. From the results, AOPs were proposed where colorectal cancer, liver injury, reproductive toxicity, cardiac and kidney damage, as well as hematological effects stand out as possible adverse outcomes. The recent transgenerational studies also point to concerns with regard to population effects. Overall, the findings further support a limitation of the use of TiO₂-NPs in food, announced by the European Food Safety Authority (EFSA).

Mechanisms Leading to Gut Dysbiosis in COVID-19: Current Evidence and Uncertainties Based on Adverse Outcome Pathways

Alteration in gut microbiota has been associated with COVID-19. However, the underlying mechanisms remain poorly understood. Here, we outlined three potential interconnected mechanistic pathways leading to gut dysbiosis as an adverse outcome following SARS-CoV-2 presence in the gastrointestinal tract. Evidence from the literature and current uncertainties are reported for each step of the different pathways. One pathway investigates evidence that intestinal infection by SARS-CoV-2 inducing intestinal inflammation alters the gut microbiota. Another pathway links the binding of viral S protein to angiotensin-converting enzyme 2 (ACE2) to the dysregulation of this receptor, essential in intestinal homeostasis-notably for amino acid metabolism-leading to gut dysbiosis. Additionally, SARS-CoV-2 could induce gut dysbiosis by infecting intestinal bacteria. Assessing current evidence within the Adverse Outcome Pathway framework justifies confidence in the proposed mechanisms to support disease management and permits the identification of inconsistencies and knowledge gaps to orient further research.

The path via pathway-based approaches towards safety assessment: A concise review

For decades, chemical safety assessment has been proposed to shift from animal testing to in vitro testing systems in response to the call for the 3R. In Europe, the answer was to combine various information sources in integrated testing strategies (ITS); In the US, it was in 2007 when the landmark report by the National Research Council put forward a vision of in vitro toxicity testing paradigm. Since then, efforts to develop pathway-based assessment framework have been on the track. In 2010, systems biology brought out a conceptual framework called adverse outcome pathway (AOP), which took one step further from toxicity pathway to regulatory toxicology. Computational modeling, high-throughput screening, high-content omics have all been approached to facilitate this progress. This paper briefly reviewed the achievement of pathway-based chemical assessment since 2007, discussed potential pitfalls and challenges that mechanism-driven chemical assessment may undergo, and presented future perspectives of safety assessment that is to be based on computational system biology.

Deploying elements of scoping review methods for Adverse Outcome Pathway development: A space travel case example

Purpose Health protection agencies require scientific information for evidence-based decision-making and guideline development. However, vetting and collating large quantities of published research to identify relevant high-quality studies is a challenge. One approach to address this issue is the use of Adverse Outcome Pathways (AOPs) that provide a framework to assemble toxicological knowledge into causally linked chains of key events across levels of biological organization to culminate in an adverse health outcome of significance. Traditionally, AOPs have been constructed using a narrative review approach where the collection of evidence that supports each pathway is based on prior knowledge of influential studies that can also be supplemented by individually selecting and reviewing relevant references. Objectives: We aimed to create a protocol for AOP weight of evidence gathering that harnesses elements of both scoping review methods and artificial intelligence tools to increase transparency while reducing bias and workload of human screeners. Methods: To develop this protocol, an existing space-health AOP in the workplan of the Organisation for Economic Co-operation and Development (OECD) AOP program was used as a case example. To balance the benefits of both scoping review tools and narrative approaches, a study protocol outlining a screening and search strategy was developed, and three reference collection workflows were tested to identify the most efficient method to inform weight of evidence. The workflows differed in their literature search strategies, and combinations of software tools used. Results: Across the three tested workflows, over 59 literature searches were completed, retrieving over 34000 references of which over 3300 were human reviewed. The most effective of the three methods used a search strategy with searches across each component of the AOP network, SWIFT Review as a pre-filtering software, and DistillerSR to create structured screening and data extraction forms. This methodology effectively retrieved relevant studies while balancing efficiency in data retrieval without compromising transparency, leading to a well-synthesized evidence base to support the AOP. Conclusions: The workflow is still exploratory in the context of AOP development, and we anticipate adaptations to the protocol with further experience. To further the systematicity, future iterations of the workflow could include structured quality assessment and risk of bias analysis. Overall, the workflow provides a transparent and unbiased approach to support AOP development, which in turn will support the need for rigorous methods to identify relevant scientific evidence while being practical to allow uptake by the broader community.

Old World Vultures Reflect Effects of Environmental Pollutants Through Human Encroachment

African wildlife face challenges from many stressors including current and emerging contaminants, habitat and resource loss, poaching, intentional and unintentional poisoning, and climate-related environmental change. The plight of African vultures exemplifies these challenges due to environmental contaminants and other stressors acting on individuals and populations that are already threatened or endangered. Many of these threats emanate from increasing human population size and settlement density, habitat loss from changing land use for agriculture, residential areas, and industry, and climate-related changes in resource availability. Environmental chemicals that are hazardous include legacy chemicals, emerging chemicals of concern, and high-volume-use chemicals that are employed as weed killers and in other agricultural applications. Furthermore, there are differences in risk for species living in close proximity to humans or in areas affected by habitat loss, climate, and industry. Monitoring programs are essential to track the status of nesting pairs, offspring survival, longevity, and lifetime productivity. This is important for long-lived birds, such as vultures, that may be especially vulnerable to chronic exposure to chemicals as obligate scavengers. Furthermore, their position in the food web may increase risk due to biomagnification of chemicals. We review the primary chemical hazards to Old World vultures and the interacting stressors affecting these and other birds. Habitat is a major consideration for vultures, with tree-nesters and cliff-nesters potentially experiencing different risks of exposure to environmental chemicals. The present review provides information from long-term monitoring programs and discusses a range of these threats and their effects on vulture populations. Environ Toxicol Chem 2022;41:1586-1603. © 2022 SETAC.

Investigation of a derived adverse outcome pathway (AOP) network for endocrine-mediated perturbations

An adverse outcome pathway (AOP) is a compact representation of the available mechanistic information on observed adverse effects upon environmental exposure. Sharing of events across individual AOPs has led to the emergence of AOP networks. Since AOP networks are expected to be functional units of toxicity prediction, there is current interest in their development tailored to specific research question or regulatory problem. To this end, we have developed a detailed workflow to construct an endocrine-relevant AOP (ED-AOP) network based on the existing information available in AOP-Wiki. We propose a cumulative weight of evidence (WoE) score for each ED-AOP based on the WoE scores assigned to key event relationships (KERs) by AOP-Wiki, revealing gaps in AOP development. Connectivity analysis of the ED-AOP network comprising 48 AOPs reveals 7 connected components and 12 isolated AOPs. Subsequently, we apply standard network measures to perform an in-depth analysis of the two largest connected components of the ED-AOP network. Notably, the graph-theoretic analyses led to the identification of important events including points of convergence or divergence in the ED-AOP network. These findings can suggest potential adverse outcomes and facilitate the development of new endpoints or assays for chemical risk assessment. Detailed analysis of the largest component in the ED-AOP network gives insights on the systems-level perturbations caused by endocrine disruption, emergent paths, and stressor-event associations. In sum, the derived ED-AOP network can provide a broader view of the biological events disrupted by endocrine disruption, as well as facilitate better risk assessment of environmental chemicals.

Application of an Accessible Interface for Pharmacokinetic Modeling and In Vitro to In Vivo Extrapolation

Regulatory toxicology testing has traditionally relied on in vivo methods to inform decision-making. However, scientific, practical, and ethical considerations have led to an increased interest in the use of in vitro and in silico methods to fill data gaps. While in vitro experiments have the advantage of rapid application across large chemical sets, interpretation of data coming from these non-animal methods can be challenging due to the mechanistic nature of many assays. In vitro to in vivo extrapolation (IVIVE) has emerged as a computational tool to help facilitate this task. Specifically, IVIVE uses physiologically based pharmacokinetic (PBPK) models to estimate tissue-level chemical concentrations based on various dosing parameters. This approach is used to estimate the administered dose needed to achieve in vitro bioactivity concentrations within the body. IVIVE results can be useful to inform on metrics such as margin of exposure or to prioritize potential chemicals of concern, but the PBPK models used in this approach have extensive data requirements. Thus, access to input parameters, as well as the technical requirements of applying and interpreting models, has limited the use of IVIVE as a routine part of in vitro testing. As interest in using non-animal methods for regulatory and research contexts continues to grow, our perspective is that access to computational support tools for PBPK modeling and IVIVE will be essential for facilitating broader application and acceptance of these techniques, as well as for encouraging the most scientifically sound interpretation of in vitro results. We highlight recent developments in two open-access computational support tools for PBPK modeling and IVIVE accessible via the Integrated Chemical Environment (https://ice.ntp.niehs.nih.gov/), demonstrate the types of insights these tools can provide, and discuss how these analyses may inform in vitro-based decision making.

The adverse outcome pathway (AOP) of estrogen interference effect induced by triphenyl phosphate (TPP): Integrated multi-omics and molecular dynamics approaches

Triphenyl phosphate (TPP) has been detected with increasing frequency in various biota and environmental media, and it has been confirmed that G protein-coupled estrogen receptor (GPER) was involved in the estrogenic activity of TPP. Therefore, it is necessary to link the estrogen-interfering effects and possible mechanisms of action of TPP with the molecular initiation event (MIE) to improve its adverse outcome pathway framework. In this study, transcriptomic and proteomic methods were used to analyze the estrogen interference effect of TPP mediated by GPER, and the causal relationship was supplemented by molecular dynamics simulation and fluorescence analysis. The omics results showed that TPP could regulate the response of key GPER signaling factors and the activation of downstream pathways including PI3K-Akt signaling pathway, MAPK signaling pathway, and estrogen signaling pathway. The similar activation effect of TPP and agonist G1 change of GPER was proved by molecular dynamics simulation. After TPP binding, the conformation of GPER will change from the inactive to active state. Therefore, TPP may affect cell proliferation, metastasis, and apoptosis and regulate gene transcription and kinase activity, leading to abnormal immune function and other estrogen-dependent cell processes and cancer through GPER, ultimately causing the estrogen interference effect.

From Causal Networks to Adverse Outcome Pathways: A Developmental Neurotoxicity Case Study

The last decade has seen the adverse outcome pathways (AOP) framework become one of the most powerful tools in chemical risk assessment, but the development of new AOPs remains a slow and manually intensive process. Here, we present a faster approach for AOP generation, based on manually curated causal toxicological networks. As a case study, we took a recently published zebrafish developmental neurotoxicity network, which contains causally connected molecular events leading to neuropathologies, and developed two new adverse outcome pathways: Inhibition of Fyna (Src family tyrosine kinase A) leading to increased mortality via decreased eye size (AOP 399 on AOP-Wiki) and GSK3beta (Glycogen synthase kinase 3 beta) inactivation leading to increased mortality via defects in developing inner ear (AOP 410). The approach consists of an automatic separation of the toxicological network into candidate AOPs, filtering the AOPs according to available evidence and length as well as manual development of new AOPs and weight-of-evidence evaluation. The semiautomatic approach described here provides a new opportunity for fast and straightforward AOP development based on large network resources.

High throughput data-based, toxicity pathway-oriented development of a quantitative adverse outcome pathway network linking AHR activation to lung damages

The quantitative adverse outcome pathway (qAOP) is proposed to inform dose-responses at multiple biological levels for the purpose of toxicity prediction. So far, qAOP models concerning human health are scarce. Previously, we proposed 5 key molecular pathways that led aryl hydrogen receptor (AHR) activation to lung damages. The present study assembled an AOP network based on the gene expression signatures of these toxicity pathways, and validated the network using publicly available high throughput data combined with machine learning models. In addition, the AOP network was quantitatively evaluated with omics approaches and bioassays, using 16HBE-CYP1A1 cells exposed to benzo(a)pyrene (BaP), a prototypical AHR activator. Benchmark dose (BMD) analysis of transcriptomics revealed that AHR gene held the lowest BMD value, whereas AHR pathway held the lowest point of departure (PoD) compared to the other 4 pathways. Targeted bioassays were further performed to quantitatively understand the cellular responses, including ROS generation, DNA damage, interleukin-6 production, and extracellular matrix increase marked by collagen expression. Eventually, response-response relationships were plotted using nonlinear model fitting. The present study developed a highly reliable AOP model concerning human health, and validated as well as quantitatively evaluated it, and such a method is likely to be adoptable for risk assessment.

Toxicogenomic profiling after sublethal exposure to nerve- and muscle-targeting insecticides reveals cardiac and neuronal developmental effects in zebrafish embryos

For specific primary modes of action (MoA) in environmental non-target organisms, EU legislation restricts the usage of active substances of pesticides or biocides. Corresponding regulatory hazard assessments are costly, time consuming and require large numbers of non-human animal studies. Currently, predictive toxicology of development compounds relies on their chemical structure and provides little insights into toxicity mechanisms that precede adverse effects. Using the zebrafish embryo model, we characterized transcriptomic responses to a range of sublethal concentrations of six nerve- and muscle-targeting insecticides with different MoA (abamectin, carbaryl, chlorpyrifos, fipronil, imidacloprid & methoxychlor). Our aim was to identify affected biological processes and suitable biomarker candidates for MoA-specific signatures. Abamectin showed the most divergent signature among the tested insecticides, linked to lipid metabolic processes. Differentially expressed genes (DEGs) after imidacloprid exposure were primarily associated with immune system and inflammation. In total, 222 early responsive genes to either MoA were identified, many related to three major processes: (1) cardiac muscle cell development and functioning (tcap, desma, bag3, hspb1, hspb8, flnca, myoz3a, mybpc2b, actc2, tnnt2c), (2) oxygen transport and hypoxic stress (alas2, hbbe1.1, hbbe1.3, hbbe2, hbae3, igfbp1a, hif1al) and (3) neuronal development and plasticity (npas4a, egr1, btg2, ier2a, vgf). The thyroidal function related gene dio3b was upregulated by chlorpyrifos and downregulated by higher abamectin concentrations. Important regulatory genes for cardiac muscle (tcap) and forebrain development (npas4a) were the most frequently ifferentially expressed across all insecticide treatments. We consider the identified gene sets as useful early warning biomarker candidates, i.e. for developmental toxicity targeting heart and brain in aquatic vertebrates. Our findings provide a better understanding about early molecular events in response to the analyzed MoA. Perceptively, this promotes the development for sensitive and informative biomarker-based in vitro assays for toxicological MoA prediction and AOP refinement, without the suffering of adult fish.

The Effects of Benoxacor on the Liver and Gut Microbiome of C57BL/6 Mice

The toxicity of many "inert" ingredients of pesticide formulations, such as safeners, is poorly characterized, despite evidence that humans may be exposed to these chemicals. Analysis of ToxCast data for dichloroacetamide safeners with the ToxPi tool identified benoxacor as the safener with the highest potential for toxicity, especially liver toxicity. Benoxacor was subsequently administered to mice via oral gavage for 3 days at concentrations of 0, 0.5, 5, and 50 mg/kg bodyweight (b.w.). Bodyweight-adjusted liver and testes weights were significantly increased in the 50 mg/kg b.w. group. There were no overt pathologies in either the liver or the intestine. 16S rRNA analysis of the cecal microbiome revealed no effects of benoxacor on α- or β-diversity; however, changes were observed in the abundance of certain bacteria. RNAseq analysis identified 163 hepatic genes affected by benoxacor exposure. Benoxacor exposure expressed a gene regulation profile similar to dichloroacetic acid and the fungicide sedaxane. Metabolomic analysis identified 9 serum and 15 liver metabolites that were affected by benoxacor exposure, changes that were not significant after correcting for multiple comparisons. The activity of antioxidant enzymes was not altered by benoxacor exposure. In vitro metabolism studies with liver microsomes and cytosol from male mice demonstrated that benoxacor is enantioselectively metabolized by cytochrome P450 enzymes, carboxylesterases, and glutathione S-transferases. These findings suggest that the minor toxic effects of benoxacor may be due to its rapid metabolism to toxic metabolites, such as dichloroacetic acid. This result challenges the assumption that inert ingredients of pesticide formulations are safe.

Advancing the Adverse Outcome Pathway for PPARγ Inactivation Leading to Pulmonary Fibrosis Using Bradford-Hill Consideration and the Comparative Toxicogenomics Database

Pulmonary fibrosis is regulated by transforming growth factor-β (TGF-β) and peroxisome proliferator-activated receptor-gamma (PPARγ). An adverse outcome pathway (AOP) for PPARγ inactivation leading to pulmonary fibrosis has been previously developed. To advance the development of this AOP, the confidence of the overall AOP was assessed using the Bradford-Hill considerations as per the recommendations from the Organisation for Economic Co-operation and Development (OECD) Users' Handbook. Overall, the essentiality of key events (KEs) and the biological plausibility of key event relationships (KERs) were rated high. In contrast, the empirical support of KERs was found to be moderate. To experimentally evaluate the KERs from the molecular initiating event (MIE) and KE1, PPARγ (MIE) and TGF-β (KE1) inhibitors were used to examine the effects of downstream events following inhibition of their upstream events. PPARγ inhibition (MIE) led to TGF-β activation (KE1), upregulation in vimentin expression (KE3), and an increase in the fibronectin level (KE4). Similarly, activated TGF-β (KE1) led to an increase in vimentin (KE3) and fibronectin expression (KE4). In the database analysis using the Comparative Toxicogenomics Database, 31 genes related to each KE were found to be highly correlated with pulmonary fibrosis, and the top 21 potential stressors were suggested. The AOP for pulmonary fibrosis evaluated in this study will be the basis for the screening of inhaled toxic substances in the environment.

Towards a qAOP framework for predictive toxicology - Linking data to decisions

The adverse outcome pathway (AOP) is a conceptual construct that facilitates organisation and interpretation of mechanistic data representing multiple biological levels and deriving from a range of methodological approaches including in silico, in vitro and in vivo assays. AOPs are playing an increasingly important role in the chemical safety assessment paradigm and quantification of AOPs is an important step towards a more reliable prediction of chemically induced adverse effects. Modelling methodologies require the identification, extraction and use of reliable data and information to support the inclusion of quantitative considerations in AOP development. An extensive and growing range of digital resources are available to support the modelling of quantitative AOPs, providing a wide range of information, but also requiring guidance for their practical application. A framework for qAOP development is proposed based on feedback from a group of experts and three qAOP case studies. The proposed framework provides a harmonised approach for both regulators and scientists working in this area.

Genomic comparisons between hepatocarcinogenic and non-hepatocarcinogenic organophosphate insecticides in the mouse liver

Short-term biomarkers of toxicity have an increasingly important role in the screening and prioritization of new chemicals. In this study, we examined early indicators of liver toxicity for three reference organophosphate (OP) chemicals, which are among the most widely used insecticides in the world. The OP methidathion was previously shown to increase the incidence of liver toxicity, including hepatocellular tumors, in male mice. To provide insights into the adverse outcome pathway (AOP) that underlies these tumors, effects of methidathion in the male mouse liver were examined after 7 and 28 day exposures and compared to those of two other OPs that either do not increase (fenthion) or possibly suppress liver cancer (parathion) in mice. None of the chemicals caused increases in liver weight/body weight or histopathological changes in the liver. Parathion decreased liver cell proliferation after 7 and 28 days while the other chemicals had no effects. There was no evidence for hepatotoxicity in any of the treatment groups. Full-genome microarray analysis of the livers from the 7 and 28 day treatments demonstrated that methidathion and fenthion regulated a large number of overlapping genes, while parathion regulated a unique set of genes. Examination of cytochrome P450 enzyme activities and use of predictive gene expression biomarkers found no consistent evidence for activation of AhR, CAR, PXR, or PPARα. Parathion suppressed the male-specific gene expression pattern through STAT5b, similar to genetic and dietary conditions that decrease liver tumor incidence in mice. Overall, these findings indicate that methidathion causes liver cancer by a mechanism that does not involve common mechanisms of liver cancer induction.

A Putative Adverse Outcome Pathway Network for Disrupted Female Pubertal Onset to Improve Testing and Regulation of Endocrine Disrupting Chemicals

The average age for pubertal onset in girls has declined over recent decades. Epidemiological studies in humans and experimental studies in animals suggest a causal role for endocrine disrupting chemicals (EDCs) that are present in our environment. Of concern, current testing and screening regimens are inadequate in identifying EDCs that may affect pubertal maturation, not least because they do not consider early-life exposure. Also, the causal relationship between EDC exposure and pubertal timing is still a matter of debate. To address this issue, we have used current knowledge to elaborate a network of putative adverse outcome pathways (pAOPs) to identify how chemicals can affect pubertal onset. By using the AOP framework, we highlight current gaps in mechanistic understanding that need to be addressed and simultaneously point towards events causative of pubertal disturbance that could be exploited for alternative test methods. We propose 6 pAOPs that could explain the disruption of pubertal timing by interfering with the central hypothalamic trigger of puberty, GnRH neurons, and by so doing highlight specific modes of action that could be targeted for alternative test method development.

Adverse Outcome Pathways as Versatile Tools in Liver Toxicity Testing

Adverse outcome pathways (AOPs) are tools to capture and visualize mechanisms driving toxicological effects. They share a common structure consisting of a molecular initiating event, a series of key events connected by key event relationships and an adverse outcome. Development and evaluation of AOPs ideally comply with guidelines issued by the Organization for Economic Cooperation and Development. AOPs have been introduced for major types of hepatotoxicity, which is not a surprise, as the liver is a frequent target for systemic adversity. Various applications for AOPs have been proposed in the areas of toxicology and chemical risk assessment, in particular in relation to the establishment of quantitative structure-activity relationships, the elaboration of prioritization strategies, and the development of novel in vitro toxicity screening tests and testing strategies.

In silico approaches in organ toxicity hazard assessment: current status and future needs in predicting liver toxicity

Hepatotoxicity is one of the most frequently observed adverse effects resulting from exposure to a xenobiotic. For example, in pharmaceutical research and development it is one of the major reasons for drug withdrawals, clinical failures, and discontinuation of drug candidates. The development of faster and cheaper methods to assess hepatotoxicity that are both more sustainable and more informative is critically needed. The biological mechanisms and processes underpinning hepatotoxicity are summarized and experimental approaches to support the prediction of hepatotoxicity are described, including toxicokinetic considerations. The paper describes the increasingly important role of in silico approaches and highlights challenges to the adoption of these methods including the lack of a commonly agreed upon protocol for performing such an assessment and the need for in silico solutions that take dose into consideration. A proposed framework for the integration of in silico and experimental information is provided along with a case study describing how computational methods have been used to successfully respond to a regulatory question concerning non-genotoxic impurities in chemically synthesized pharmaceuticals.

A pragmatic approach to Adverse Outcome Pathway (AOP) development and evaluation

The adverse outcome pathway (AOP) framework provides a practical means for organizing scientific knowledge that can be used to infer cause-effect relationships between stressor events and toxicity outcomes in intact organisms. It has reached wide acceptance as a tool to aid chemical safety assessment and regulatory toxicology by supporting a systematic way of predicting adverse health outcomes based on accumulated mechanistic knowledge. A major challenge for broader application of the AOP concept in regulatory toxicology, however, has been developing robust AOPs to a level where they are peer reviewed and accepted. This is because the amount of work required to substantiate the modular units of a complete AOP is considerable, to the point where it can take years from start to finish. To help alleviate this bottleneck, we propose a more pragmatic approach to AOP development whereby the focus becomes on smaller blocks. First, we argue that the key event relationship (KER) should be formally recognized as the core building block of knowledge assembly within the AOP knowledge base (AOP-KB), albeit framing them within full AOPs to ensure regulatory utility. Second, we argue that KERs should be developed using systematic review approaches, but only in cases where the underlying concept does not build on what is considered canonical knowledge. In cases where knowledge is considered canonical, rigorous systematic review approaches should not be required. It is our hope that these approaches will contribute to increasing the pace at which the AOP-KB is populated with AOPs with utility for chemical safety assessors and regulators.

Dynamic Modeling of Mitochondrial Membrane Potential Upon Exposure to Mitochondrial Inhibitors

Mitochondria are the main bioenergetic organelles of cells. Exposure to chemicals targeting mitochondria therefore generally results in the development of toxicity. The cellular response to perturbations in cellular energy production is a balance between adaptation, by reorganisation and organelle biogenesis, and sacrifice, in the form of cell death. In homeostatic conditions, aerobic mitochondrial energy production requires the maintenance of a mitochondrial membrane potential (MMP). Chemicals can perturb this MMP, and the extent of this perturbation depends both on the pharmacokinetics of the chemicals and on downstream MMP dynamics. Here we obtain a quantitative understanding of mitochondrial adaptation upon exposure to various mitochondrial respiration inhibitors by applying mathematical modeling to partially published high-content imaging time-lapse confocal imaging data, focusing on MMP dynamics in HepG2 cells over a period of 24 h. The MMP was perturbed using a set of 24 compounds, either acting as uncoupler or as mitochondrial complex inhibitor targeting complex I, II, III or V. To characterize the effect of chemical exposure on MMP dynamics, we adapted an existing differential equation model and fitted this model to the observed MMP dynamics. Complex III inhibitor data were better described by the model than complex I data. Incorporation of pharmacokinetic decay into the model was required to obtain a proper fit for the uncoupler FCCP. Furthermore, oligomycin (complex V inhibitor) model fits were improved by either combining pharmacokinetic (PK) decay and ion leakage or a concentration-dependent decay. Subsequent mass spectrometry measurements showed that FCCP had a significant decay in its PK profile as predicted by the model. Moreover, the measured oligomycin PK profile exhibited only a limited decay at high concentration, whereas at low concentrations the compound remained below the detection limit within cells. This is consistent with the hypothesis that oligomycin exhibits a concentration-dependent decay, yet awaits further experimental verification with more sensitive detection methods. Overall, we show that there is a complex interplay between PK and MMP dynamics within mitochondria and that data-driven modeling is a powerful combination to unravel such complexity.

Development of a putative adverse outcome pathway network for male rat reproductive tract abnormalities with specific considerations for the androgen sensitive window of development

Structured approaches like the adverse outcome pathway (AOP) framework offer great potential for depicting complex toxicological processes in a manner that can facilitate informed integration of mechanistic information in regulatory decisions. While this concept provides a structure for organizing evidence and facilitates consistency in evidence integration; the process, inputs, and manner in which AOPs and AOP networks are developed is still evolving. Following the OECD guiding principles of AOP development, we propose three AOPs for male reproductive tract abnormalities and derive a putative AOP network. The AOPs were developed using a fundamental understanding of the developmental biology of the organs of interest, paying close attention to the gestational timing of key events (KEs) to very specifically inform the domain of life stage applicability for the key event relationships (KERs). Chemical stressor data primarily from studies on low molecular weight phthalates (LMWPs) served to 'bound' the pathways of focus in this dynamic period of development and were integrated with the developmental biology data through an iterative process to define KEs and conclude on the extent of evidence in support of the KERs. The AOPs developed describe the linkage between 1) a decrease in Insl3 gene expression and cryptorchidism, 2) the sustained expression of Coup-tfII and hypospadias and 3) the sustained expression of Coup-tfII and altered Wolffian duct development/ epididymal agenesis. A putative AOP network linking AOP2 and AOP3 through decreased steroidogenic biosynthetic protein expression and converging of all AOPS at the population level impaired fertility adverse outcome is proposed. The network depiction specifies and displays the KEs aligned with their occurrence in gestational time. The pathways and network described herein are intended to catalyze collaborative initiatives for expansion into a larger network to enable effective data collection and inform alternative approaches for identifying stressors impacting this sensitive period of male reproductive tract development.

Lung physiology and controlled exposure study design

Controlled human inhalation exposure ( CHIE) studies provide a unique opportunity to conduct formal experiments to examine the human health effects of airborne pollutants. Lung function, easily measured using spirometry, is a common physiological variable often utilized in these studies. By design, CHIE studies only induce mild and reversible acute effects, which may or may not predict adverse effects that may develop under chronic exposure conditions. There is substantial inter- and intra-individual variability in functional capacity and symptoms such as chest tightness and dyspnea, which are complex variables that are affected by individual perception, physiological lung impairment, and other variables (e.g., concomitant health conditions, and level of conditioning/fitness). Thus, the design of the CHIE study and physiological and environmental factors of study participants can affect each CHIE study's results. Researchers can address many of these critical issues in the problem formulation phase of CHIE studies, utilizing existing information on the expected effects of the substance of interest and possible modes of action. Thoughtful design and interpretation of CHIE studies will increase their utility for evaluating and setting environmental health policy.

Application of the adverse outcome pathway framework to predict the toxicity of chemicals in the semiconductor manufacturing industry

Background

To solve current issues using big data, solve current issues related to the semiconductor and electronics industry, I tried to establish the data for each toxicity mechanism for adverse outcome pathway (AOP) for the exposure.

Objective

I planned to increase the efficiency of human hazard assessment by searching, analyzing, and linking test data on the relationship between key events occurred at each level, which are the biological targets of chemicals in semiconductor manufacturing.

Results

It was found that 48 kinds of chemicals had 11 AOPs, while 103 chemicals had multiple AOPs, and 26 had case evidence. As a result of AOP analysis, it was found that a total of 320 chemicals had 42 AOPs, and 190 major chemicals corresponded to 11 AOPs. It was found necessary to develop a complex AOP and secure an (inhalation or dermal) exposure scenario for combined exposure at work. As a comparative search (41 out of 190 chemicals) of biomarkers specific to occupational diseases, 12 biomarkers were found to be related to breast cancer. The AOPs for 50 specific chemicals were presented, together with occupational disease-specific AOPs and key events relationship from 50 chemicals, and taxonomic classification for each AOP analysis could be found. With a comparative search, 41 out of 190 chemicals were associated with specific biomarkers for occupational diseases, and 12 mRNA or protein biomarkers were found to be related to breast cancer by cross-validation with the attached Table 24 of the Enforcement Regulations of the OSHAct and the CTD.

Conclusion

The mechanism of occupational diseases caused by chemicals was presented, together with pathological preventions. I believe that a strategy is needed to expand the target organization for each chemical by linking with activities, such as work environment measurement, and cooperating with screening items and methods suitable for toxic chemicals, like AOP tools.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13273-021-00139-4.

Application of adverse outcome pathway networks to integrate mechanistic data informing the choice of a point of departure for hydrogen sulfide exposure limits

Acute exposure to hydrogen sulfide initiates a series of hallmark biological effects that occur progressively at increasing exposure levels: odor perception, conjunctivitis, olfactory paralysis, "knockdown," pulmonary edema, and apnea. Although effects of exposure to high concentrations of hydrogen sulfide are clear, effects associated with chronic, low-level exposure in humans is under debate, leading to uncertainty in the critical effect used in regulatory risk assessments addressing low dose exposures. This study integrates experimental animal, observational epidemiology, and occupational exposure evidence by applying a pathway-based approach. A hypothesized adverse outcome pathway (AOP) network was developed from 34 studies, composed of 4 AOPs sharing 1 molecular initiating events (MIE) and culminating in 4 adverse outcomes. A comparative assessment of effect levels and weight of evidence identified an AOP leading to a biologically-plausible, low-dose outcome relative to the other outcomes (nasal lesions, 30 ppm versus olfactory paralysis, >100 ppm; neurological effects, >80 ppm; pulmonary edema, >80 ppm). This AOP (i.e. AOP1) consists of the following key events: cytochrome oxidase inhibition (>10 ppm), neuronal cell loss (>30 ppm), and olfactory nasal lesions (defined as both neuronal cell loss and basal cell hyperplasia; >30 ppm) in rodents. The key event relationships in this pathway were supported by moderate empirical evidence and have high biological plausibility due to known mechanistic understanding and consistency in observations for diverse chemicals.

Applying evidence-based methods to the development and use of adverse outcome pathways

The workshop “Application of evidence-based methods to construct mechanistic frameworks for the development and use of non-animal toxicity tests” was organized by the Evidence-based Toxicology Collaboration and hosted by the Grading of Recommendations Assessment, Development and Evaluation Working Group on June 12, 2019. The purpose of the workshop was to bring together international regulatory bodies, risk assessors, academic scientists, and industry to explore how systematic review methods and the adverse outcome pathway framework could be combined to develop and use mechanistic test methods for predicting the toxicity of chemical substances in an evidence-based manner. The meeting covered the history of biological frameworks, the way adverse outcome pathways are currently developed, the basic principles of systematic methodology, including systematic reviews and evidence maps, and assessment of cer­tainty in models, and adverse outcome pathways in particular. Specific topics were discussed via case studies in small break-out groups. The group concluded that adverse outcome pathways provide an important framework to support mechanism-based assessment in environmental health. The process of their development has a few challenges that could be addressed with systematic methods and automation tools. Addressing these challenges will increase the transparency of the evidence behind adverse outcome pathways and the consistency with which they are defined; this in turn will increase their value for supporting public health decisions. It was suggested to explore the details of applying systematic methods to adverse outcome pathway development in a series of case studies and workshops.

Transcriptomics-Based and AOP-Informed Structure-Activity Relationships to Predict Pulmonary Pathology Induced by Multiwalled Carbon Nanotubes

This study presents a novel strategy that employs quantitative structure-activity relationship models for nanomaterials (Nano-QSAR) for predicting transcriptomic pathway level response using lung tissue inflammation, an essential key event (KEs) in the existing adverse outcome pathway (AOP) for lung fibrosis, as a model response. Transcriptomic profiles of mouse lungs exposed to ten different multiwalled carbon nanotubes (MWCNTs) are analyzed using statistical and bioinformatics tools. Three pathways "agranulocyte adhesion and diapedesis," "granulocyte adhesion and diapedesis," and "acute phase signaling," that (1) are commonly perturbed across the MWCNTs panel, (2) show dose response (Benchmark dose, BMDs), and (3) are anchored to the KEs identified in the lung fibrosis AOP, are considered in modelling. The three pathways are associated with tissue inflammation. The results show that the aspect ratio (κ) of MWCNTs is directly correlated with the pathway BMDs. The study establishes a methodology for QSAR construction based on canonical pathways and proposes a MWCNTs grouping strategy based on the κ-values of the specific pathway associated genes. Finally, the study shows how the AOP framework can help guide QSAR modelling efforts; conversely, the outcome of the QSAR modelling can aid in refining certain aspects of the AOP in question (here, lung fibrosis).

Stem Cells for Next Level Toxicity Testing in the 21st Century

The call for a paradigm change in toxicology from the United States National Research Council in 2007 initiates awareness for the invention and use of human-relevant alternative methods for toxicological hazard assessment. Simple 2D in vitro systems may serve as first screening tools, however, recent developments infer the need for more complex, multicellular organotypic models, which are superior in mimicking the complexity of human organs. In this review article most critical organs for toxicity assessment, i.e., skin, brain, thyroid system, lung, heart, liver, kidney, and intestine are discussed with regards to their functions in health and disease. Embracing the manifold modes-of-action how xenobiotic compounds can interfere with physiological organ functions and cause toxicity, the need for translation of such multifaceted organ features into the dish seems obvious. Currently used in vitro methods for toxicological applications and ongoing developments not yet arrived in toxicity testing are discussed, especially highlighting the potential of models based on embryonic stem cells and induced pluripotent stem cells of human origin. Finally, the application of innovative technologies like organs-on-a-chip and genome editing point toward a toxicological paradigm change moves into action.

Non-Animal Strategies for Toxicity Assessment of Nanoscale Materials: Role of Adverse Outcome Pathways in the Selection of Endpoints

Faster, cheaper, sensitive, and mechanisms-based animal alternatives are needed to address the safety assessment needs of the growing number of nanomaterials (NM) and their sophisticated property variants. Specifically, strategies that help identify and prioritize alternative schemes involving individual test models, toxicity endpoints, and assays for the assessment of adverse outcomes, as well as strategies that enable validation and refinement of these schemes for the regulatory acceptance are needed. In this review, two strategies 1) the current nanotoxicology literature review and 2) the adverse outcome pathways (AOPs) framework, a systematic process that allows the assembly of available mechanistic information concerning a toxicological response in a simple modular format, are presented. The review highlights 1) the most frequently assessed and reported ad hoc in vivo and in vitro toxicity measurements in the literature, 2) various AOPs of relevance to inhalation toxicity of NM that are presently under development, and 3) their applicability in identifying key events of toxicity for targeted in vitro assay development. Finally, using an existing AOP for lung fibrosis, the specific combinations of cell types, exposure and test systems, and assays that are experimentally supported and thus, can be used for assessing NM-induced lung fibrosis, are proposed.