A toxicity pathway-oriented approach to develop adverse outcome pathway: AHR activation as a case study

Neurotoxicity of fine and ultrafine particulate matter: A comprehensive review using a toxicity pathway-oriented adverse outcome pathway framework

Fine particulate matter (PM2.5) can cause brain damage and diseases. Of note, ultrafine particles (UFPs) with an aerodynamic diameter less than or equal to 100 nm are a growing concern. Evidence has suggested toxic effects of PM2.5 and UFPs on the brain and links to neurological diseases. However, the underlying mechanism has not yet been fully illustrated due to the variety of the study models, different endpoints, etc. The adverse outcome pathway (AOP) framework is a pathway-based approach that could systematize mechanistic knowledge to assist health risk assessment of pollutants. Here, we constructed AOPs by collecting molecular mechanisms in PM-induced neurotoxicity assessments. We chose particulate matter (PM) as a stressor in the Comparative Toxicogenomics Database (CTD) and identified the critical toxicity pathways based on Ingenuity Pathway Analysis (IPA). We found 65 studies investigating the potential mechanisms linking PM2.5 and UFPs to neurotoxicity, which contained 2, 675 genes in all. IPA analysis showed that neuroinflammation signaling and glucocorticoid receptor signaling were the common toxicity pathways. The upstream regulator analysis (URA) of PM2.5 and UFPs demonstrated that the neuroinflammation signaling was the most initially triggered upstream event. Therefore, neuroinflammation was recognized as the MIE. Strikingly, there is a clear sequence of activation of downstream signaling pathways with UFPs, but not with PM2.5. Moreover, we found that inflammation response and homeostasis imbalance were key cellular events in PM2.5 and emphasized lipid metabolism and mitochondrial dysfunction, and blood-brain barrier (BBB) impairment in UFPs. Previous AOPs, which only focused on phenotypic changes in neurotoxicity upon PM exposure, we for the first time propose AOP framework in which PM2.5 and UFPs may activate pathway cascade reactions, resulting in adverse outcomes associated with neurotoxicity. Our toxicity pathway-based approach not only advances risk assessment for PM-induced neurotoxicity but shines a spotlight on constructing AOP frameworks for new chemicals.

Hepa-ToxMOA: a pathway-screening method for evaluating cellular stress and hepatic metabolic-dependent toxicity of natural products

In the field of drug discovery, natural products have emerged as therapeutic agents for diseases such as cancer. However, their potential toxicity poses significant obstacles in the developing effective drug candidates. To overcome this limitation, we propose a pathway-screening method based on imaging analysis to evaluate cellular stress caused by natural products. We have established a cellular stress sensing system, named Hepa-ToxMOA, which utilizes HepG2 cells expressing green fluorescent protein (GFP) fluorescence under the control of transcription factor response elements (TREs) for transcription factors (AP1, P53, Nrf2, and NF-κB). Additionally, to augment the drug metabolic activity of the HepG2 cell line, we evaluated the cytotoxicity of 40 natural products with and without S9 fraction-based metabolic activity. Our finding revealed different activities of Hepa-ToxMOA depending on metabolic or non-metabolic activity, highlighting the involvement of specific cellular stress pathways. Our results suggest that developing a Hepa-ToxMOA system based on activity of drug metabolizing enzyme provides crucial insights into the molecular mechanisms initiating cellular stress during liver toxicity screening for natural products. The pathway-screening method addresses challenges related to the potential toxicity of natural products, advancing their translation into viable therapeutic agents.

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.

Abnormality of mussel in the early developmental stages induced by graphene and triphenyl phosphate: In silico toxicogenomic data-mining, in vivo, and toxicity pathway-oriented approach

Increasing number of complex mixtures of organic pollutants in coastal area (especially for nanomaterials and micro/nanoplastics associated chemicals) threaten aquatic ecosystems and their joint hazards are complex and demanding tasks. Mussels are the most sensitive marine faunal groups in the world, and their early developmental stages (embryo and larvae) are particularly susceptible to environmental contaminants, which can distinguish the probable mechanisms of mixture-induced growth toxicity. In this study, the potential critical target and biological processes affected by graphene and triphenyl phosphate (TPP) were developed by mining public toxicogenomic data. And their combined toxic effects were verified by toxicological assay at early developmental stages in filter-feeding mussels (embryo and larvae). It showed that interactions among graphene/TPP with 111 genes (ABCB1, TP53, SOD, CAT, HSP, etc.) affected phenotypes along conceptual framework linking these chemicals to developmental abnormality endpoints. The PPAR signaling pathway, monocarboxylic acid metabolic process, regulation of lipid metabolic process, response to oxidative stress, and gonad development were noted as the key molecular pathways that contributed to the developmental abnormality. Enriched phenotype analysis revealed biological processes (cell proliferation, cell apoptosis, inflammatory response, response to oxidative stress, and lipid metabolism) affected by the investigated mixture. Combined, our results supported that adverse effects induced by contaminants/ mixture could not only be mediated by single receptor signaling or be predicted by the simple additive effect of contaminants. The results offer a framework for better comprehending the developmental toxicity of environmental contaminants in mussels and other invertebrate species, which have considerable potential for hazard assessment of coastal mixture.

Benzo[b]fluoranthene induces male reproductive toxicity and apoptosis via Akt-Mdm2-p53 signaling axis in mouse Leydig cells: Integrating computational toxicology and experimental approaches

This study aims to explore the male reproductive toxicity of Benzo[b]fluoranthene (BbF) and related mechanisms. The results of computational toxicology analysis indicated male reproductive toxicity of BbF was related to apoptosis of Leydig cells and that Akt/p53 pathway might play a key role. In experiments, BbF induced testosterone decline, decreased concentration and motility of sperm and aggravated testicular pathological injury in mice. Besides, BbF led to apoptosis in Leydig cells, and decreased expressions of p-Akt and Bcl2, while improving the expressions of p53, Bax and Cleaved Caspase-3 in vivo and in vitro. Further, compared with BbF group, Akt activator SC79 significantly reduced cell apoptosis rate, improved cell viability, promoted the expressions of p-Akt and p-Mdm2, and reversed the above molecular expressions. Similarly, p53 inhibitor Pifithrin-α also significantly enhanced the cell vitality, alleviated the apoptosis of TM3 cells induced by BbF, and decreased the expressions of Bax and Cleaved Caspase-3, with the up-regulation of Bcl2. To sum up, by inhibiting Akt-Mdm2 signaling, BbF activated the p53-mediated mitochondrial apoptosis pathway, further inducing the apoptosis of Leydig cells, therefore resulting in testosterone decline and male reproductive damage. Besides, this study provided a valid mode integrating computational toxicology and experimental approaches in toxicity testing.

Potential adverse outcome pathways with hazard identification of organophosphate esters

Data-driven analysis and pathway-based approaches contribute to reasonable arrangements of limited resources and laboratory tests for continuously emerging commercial chemicals, which provides opportunities to save time and effort for toxicity research. With the widespread usage of organophosphate esters (OPEs) on a global scale, the concentrations generally reached up to micromolar range in environmental media and even in organisms. However, potential adverse effects and toxicity pathways of OPEs have not been systematically assessed. Therefore, it is necessary to review the current situation, formulate the future research priorities, and characterize toxicity mechanisms via data-driven analysis. Results showed that the early toxicity studies focused on neurotoxicity, cytotoxicity, and metabolic disorders. Then the main focus shifted to the mechanisms of cardiotoxicity, endocrine disruption, hepatocytes, reproductive and developmental toxicity to vulnerable sub-populations, such as infants and embryos, affected by OPEs. In addition, several novel OPEs have been emerging, such as bis(2-ethylhexyl)-phenyl phosphate (HDEHP) and oxidation derivatives (OPAsO) generated from organophosphite antioxidants (OPAs), leading to multiple potential ecological and human health risks (neurotoxicity, hepatotoxicity, developmental toxicity, etc.). Notably, in-depth statistical analysis was promising in encapsulating toxicological information to develop adverse outcome pathways (AOPs) frameworks. Subsequently, network-centric analysis and quantitative weight-of-evidence (QWOE) approaches were utilized to construct and evaluate the putative AOPs frameworks of OPEs, showing the moderate confidences of the developed AOPs. In addition, frameworks demonstrated that several events, such as nuclear receptor activation, reactive oxygen species (ROS) production, oxidative stress, and DNA damage, were involved in multiple different adverse outcome (AO), and these AOs had certain degree of connectivity. This study brought new insights into facilitating the complement of AOP efficiently, as well as establishing toxicity pathways framework to inform risk assessment of emerging OPEs.

Identifying microRNAs that drive BaP-induced pulmonary effects: Multiple patterns of mechanisms underlying activation of the toxicity pathways

MiRNAs are widely acknowledged as regulating gene expression and thus, being involved in broad biological functions, environmental responses, and the process of diseases. Epidemiology could provide exposure- or disease-relevant miRNAs, while toxicology could reveal the underlying mechanisms. Here, a new "Bottom-up" approach was proposed to identify miRNAs that are responsible for environmental exposure-induced adverse outcomes. In our previous study, 5 key toxicity pathways were established underlying BaP-induced lung diseases; further, genes from these 5 pathways that were responsive to BaP exposure in HBE-CYP1A1 cells were identified. In this study, we identified 26 miRNA:mRNA interactions during BaP exposure through RNA-sequencing using the same HBE-CYP1A1 cells. According to the expression alteration and regulatory mechanisms, we summarized 8 action patterns of miRNA:mRNA, which led to the induction of miRNAs that predominantly regulate target genes and responsible are for the pathway perturbations (as "drivers"), and miRNAs that subordinately regulate genes during pathway perturbations (as "symptoms"). 5 corresponding miRNAs: miR-3173-5p, miR-629-3p, miR-9-5p, miR-1343-3p and miR-219a-1-3p were identified as "drivers", and were all validated with expression alteration in lung disease patients from published studies. In conclusion, this study offers a new approach to identification of epigenetic factors that may shed light on the causation of environment-related health outcomes.

Comparative Toxicogenomics Database (CTD): update 2023

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) harmonizes cross-species heterogeneous data for chemical exposures and their biological repercussions by manually curating and interrelating chemical, gene, phenotype, anatomy, disease, taxa, and exposure content from the published literature. This curated information is integrated to generate inferences, providing potential molecular mediators to develop testable hypotheses and fill in knowledge gaps for environmental health. This dual nature, acting as both a knowledgebase and a discoverybase, makes CTD a unique resource for the scientific community. Here, we report a 20% increase in overall CTD content for 17 100 chemicals, 54 300 genes, 6100 phenotypes, 7270 diseases and 202 000 exposure statements. We also present CTD Tetramers, a novel tool that computationally generates four-unit information blocks connecting a chemical, gene, phenotype, and disease to construct potential molecular mechanistic pathways. Finally, we integrate terms for human biological media used in the CTD Exposure module to corresponding CTD Anatomy pages, allowing users to survey the chemical profiles for any tissue-of-interest and see how these environmental biomarkers are related to phenotypes for any anatomical site. These, and other webpage visual enhancements, continue to promote CTD as a practical, user-friendly, and innovative resource for finding information and generating testable hypotheses about environmental health.

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.

Chronic exposure to tralopyril induced abnormal growth and calcium regulation of turbot (Scophthalmus maximus)

Tralopyril is an emerging marine antifouling agent with limited data on its effects on fish growth and calcium regulation. To determine the changes induced by long-term exposure to tralopyril, multi-levels (such as molecular, biochemical, and individual levels) responses were measured in turbot at different concentrations (1 μg/L, 20 μg/L). The results showed that 1 μg/L mainly affected the immune response, while 20 μg/L affected the synthesis and metabolism of steroids and fat. However, different concentrations of tralopyril affected the synthesis, secretion and action of parathyroid hormone and growth hormone. The expression of GH/IGF axis gene and the level of growth hormone increased significantly, leading to abnormal growth. The energy tradeoff between immunity and growth at 1 μg/L tralopyril pressure may inhibit growth. The change of Ca²⁺ level was accompanied by the disturbance of PTH-related gene expression. The results of molecular docking showed that the disturbance of Ca²⁺ regulation might be attributed to the inhibition of vitamin D receptor by tralopyril, which affected the vitamin D signaling pathway. This study provides scientific data for the in-depth understanding and risk assessment of the toxicological effects of tralopyril and reveals the potential threat of tralopyril to environmental health.

Evaluation of dioxin induced transcriptomic responses in a 3D human liver microtissue model

Three-dimensional human liver microtissue model provides a promising method for predicting the human hepatotoxicity of environmental chemicals. However, the dynamics of transcriptional responses of 3D human liver microtissue model to dioxins exposure remain unclear. Herein, time-series transcriptomic analysis was used to characterize modulation of gene expression over 14 days in 3D human liver microtissues exposed to 2,3,7,8-tetra-chlorodibenzo-p-dioxin (TCDD, 31 nM, 10 ng/ml). Changes in gene expression and modulation of biological pathways were evaluated at several time points. The results showed that microtissues stably expressed genes related to toxicological pathways (e.g. highly of genes involved in external stimuli and maintenance of cell homeostasis pathways) during the 14-day culture period. Furthermore, a weekly phenomenon pattern was observed for the number of the differentially expressed genes in microtissues exposed to TCDD at each time point. TCDD led to an induction of genes involved in cell cycle regulation at day three. Metabolic pathways were the main significantly induced pathways during the subsequent days, with the immune/inflammatory response enriched on the fifth day, and the cellular response to DNA damage was identified at the end of the exposure. Finally, relevant transcription patterns identified in microtissues were compared with published data on rodent and human cell-line studies to elucidate potential species-specific responses to TCDD over time. Cell development and cytochrome P450 pathway were mainly affected after a 3-day exposure, with the DNA damage response identified at the end of exposure in the human microtissue system but not in mouse/rat primary hepatocytes models. Overall, the 3D human liver microtissue model is a valuable tool to predict the toxic effects of environmental chemicals with a relatively long exposure.

Associating diethylhexyl phthalate to gestational diabetes mellitus via adverse outcome pathways using a network-based approach

Gestational diabetes mellitus (GDM) is a common pregnancy complication that is harmful to both the woman and fetus. Several epidemiological studies have found that exposure to diethylhexyl phthalate (DEHP), an endocrine disruptor ubiquitous in the environment, may be associated with GDM. This study aims to investigate the mechanism between DEHP and GDM using the adverse outcome pathway (AOP) framework, which can integrate information from different sources to elucidate the causal pathways between chemicals and adverse outcomes. We applied a network-based workflow to integrate diverse information to generate computational AOPs and accelerate the AOP development. The interactions among DEHP, genes, phenotypes, and GDM were retrieved from several publicly available databases, including the Comparative Toxicogenomics Database (CTD), Computational Toxicology (CompTox) Chemicals Dashboard, DisGeNET, MalaCards, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG). Based on the above interactions, a DEHP-Gene-Phenotype-GDM network consisting of 52 nodes and 227 edges was formed to support AOP construction. The filtered genes and phenotypes were assembled as molecular initiating events (MIEs) and key events (KEs) according to the upstream and downstream relationships, generating a computational AOP (cAOP) network. Based on the Organization for Economic Co-operation and Development handbook of AOPs, a cAOP was assessed and applied to determine the effects of DEHP on GDM. DEHP could increase TNF-α, downregulate the glucose uptake process, and lead to GDM. Overall, this study revealed the utility of computational methods in integrating a variety of datasets, supporting AOP development, and facilitating a better understanding of the underlying mechanism of exposure to chemicals on human health.

Direct transcriptomic comparison of xenobiotic metabolism and toxicity pathway induction of airway epithelium models at an air-liquid interface generated from induced pluripotent stem cells and primary bronchial epithelial cells

The airway epithelium represents the main barrier between inhaled air and the tissues of the respiratory tract and is therefore an important point of contact with xenobiotic substances into the human body. Several studies have recently shown that in vitro models of the airway grown at an air-liquid interface (ALI) can be particularly useful to obtain mechanistic information about the toxicity of chemical compounds. However, such methods are not very amenable to high throughput since the primary cells cannot be expanded indefinitely in culture to obtain a sustainable number of cells. Induced pluripotent stem cells (iPSCs) have become a popular option in the recent years for modelling the airways of the lung, but despite progress in the field, such models have so far not been assessed for their ability to metabolise xenobiotic compounds and how they compare to the primary bronchial airway model (pBAE). Here, we report a comparative analysis by TempoSeq (oligo-directed sequencing) of an iPSC-derived airway model (iBAE) with a primary bronchial airway model (pBAE). The iBAE and pBAE were differentiated at an ALI and then evaluated in a 5-compound screen with exposure to a sub-lethal concentration of each compound for 24 h. We found that despite lower expression of xenobiotic metabolism genes, the iBAE similarly predicted the toxic pathways when compared to the pBAE model. Our results show that iPSC airway models at ALI show promise for inhalation toxicity assessments with further development.

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.

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.