Toward High-Throughput Fish Embryo Toxicity Tests in Aquatic Toxicology

Progress, applications, and challenges in high-throughput effect-directed analysis for toxicity driver identification - is it time for HT-EDA?

The rapid increase in the production and global use of chemicals and their mixtures has raised concerns about their potential impact on human and environmental health. With advances in analytical techniques, in particular, high-resolution mass spectrometry (HRMS), thousands of compounds and transformation products with potential adverse effects can now be detected in environmental samples. However, identifying and prioritizing the toxicity drivers among these compounds remain a significant challenge. Effect-directed analysis (EDA) emerged as an important tool to address this challenge, combining biotesting, sample fractionation, and chemical analysis to unravel toxicity drivers in complex mixtures. Traditional EDA workflows are labor-intensive and time-consuming, hindering large-scale applications. The concept of high-throughput (HT) EDA has recently gained traction as a means of accelerating these workflows. Key features of HT-EDA include the combination of microfractionation and downscaled bioassays, automation of sample preparation and biotesting, and efficient data processing workflows supported by novel computational tools. In addition to microplate-based fractionation, high-performance thin-layer chromatography (HPTLC) offers an interesting alternative to HPLC in HT-EDA. This review provides an updated perspective on the state-of-the-art in HT-EDA, and novel methods/tools that can be incorporated into HT-EDA workflows. It also discusses recent studies on HT-EDA, HT bioassays, and computational prioritization tools, along with considerations regarding HPTLC. By identifying current gaps in HT-EDA and proposing new approaches to overcome them, this review aims to bring HT-EDA a step closer to monitoring applications.

Deep learning-assisted detection of psychoactive water pollutants using behavioral profiling of zebrafish embryos

Water pollution poses a significant risk to the environment and human health, necessitating the development of innovative detection methods. In this study, a series of representative psychoactive compounds were selected as model pollutants, and a new approach combining zebrafish embryo behavioral phenotyping with deep learning was used to identify and classify water pollutants. Zebrafish embryos were exposed to 17 psychoactive compounds at environmentally relevant concentrations (1 and 10 μg/L), and their locomotor behavior was recorded at 5 and 6 days post-fertilization (dpf). We constructed six distinct zebrafish locomotor track datasets encompassing various observation times and developmental stages and evaluated multiple deep learning models on these datasets. The results demonstrated that the ResNet101 model performed optimally on the 1-min track dataset at 6 dpf, achieving an accuracy of 65.35 %. Interpretability analyses revealed that the model effectively focused on the relevant locomotor track features for classification. These findings suggest that the integration of zebrafish embryo behavioral analysis with deep learning can serve as an environmentally friendly and economical method for detecting water pollutants. This approach offers a new perspective for water quality monitoring and has the potential to assist existing chemical analytical techniques in detection, thereby advancing environmental toxicology research and water pollution control efforts.

Determining high priority disinfection byproducts based on experimental aquatic toxicity data and predictive models: Virtual screening and in vivo study

Only about 100 disinfection byproducts (DBPs) have been tested for their potential aquatic toxicity. It is not known which specific DBPs, DBP main groups, and DBP subgroups are more toxic due to the lack of experimental toxicity data. Herein, high priority specific DBPs, DBP main groups, DBP subgroups, most sensitive model aquatic species, potential PBT and PMT (persistent, bioaccumulative/mobile, and toxic) DBPs were virtually screened for 1187 updated DBPs inventory. Priority setting based on experimental and predicted acute and chronic aquatic toxicity data found that the aromatic and alicyclic DBPs in four DBPs main groups showed high priority because larger proportions of aromatic and alicyclic DBPs are in high hazard categories (i.e. Acute and/or Chronic Toxic-1 or Toxic-2) according to the criteria in GHS system compared to the aliphatic and heterocyclic DBPs. The halophenols, estrogen-DBPs, nonhalogenated esters, and nonhalogenated aldehydes were recognized as high priority DBPs subgroups. For specific DBPs, 19 and 31 DBPs should be highly concerned in the future study because both acute and chronic toxicity of those DBPs to all of the three aquatic life (algae, Daphnia magna, fish) were classified as Toxic-1 and Toxic-2, respectively. The Daphnia magna and algae were sensitive to the acute toxicity of DBPs, while the fish and Daphnia magna were sensitive to the chronic toxicity of DBPs. One potential PBT (Tetrachlorobisphenol A) and four potential PMT DBPs were identified. For verification, the acute toxicity of four DBPs on three aquatic organism were performed, and their tested acute toxicity data to three aquatic organisms were consistent with the predictions. Our results could be beneficial to government regulators to adopt effective measures to limit the discharge of high priority DBPs and help the scientific community to develop or improve disinfection processes to reduce the production of high priority DBPs.

Embryonic Zebrafish as a Model for Investigating the Interaction between Environmental Pollutants and Neurodegenerative Disorders

Environmental pollutants have been linked to neurotoxicity and are proposed to contribute to neurodegenerative disorders. The zebrafish model provides a high-throughput platform for large-scale chemical screening and toxicity assessment and is widely accepted as an important animal model for the investigation of neurodegenerative disorders. Although recent studies explore the roles of environmental pollutants in neurodegenerative disorders in zebrafish models, current knowledge of the mechanisms of environmentally induced neurodegenerative disorders is relatively complex and overlapping. This review primarily discusses utilizing embryonic zebrafish as the model to investigate environmental pollutants-related neurodegenerative disease. We also review current applicable approaches and important biomarkers to unravel the underlying mechanism of environmentally related neurodegenerative disorders. We found embryonic zebrafish to be a powerful tool that provides a platform for evaluating neurotoxicity triggered by environmentally relevant concentrations of neurotoxic compounds. Additionally, using variable approaches to assess neurotoxicity in the embryonic zebrafish allows researchers to have insights into the complex interaction between environmental pollutants and neurodegenerative disorders and, ultimately, an understanding of the underlying mechanisms related to environmental toxicants.

Zebrafish as Versatile Model for Assessing Animal Venoms and Toxins: Current Applications and Future Prospects

Animal venoms and toxins hold promise as sources of novel drug candidates, therapeutic agents, and biomolecules. To fully harness their potential, it is crucial to develop reliable testing methods that provide a comprehensive understanding of their effects and mechanisms of action. However, traditional rodent assays encounter difficulties in mimicking venom-induced effects in human due to the impractical venom dosage levels. The search for reliable testing methods has led to the emergence of zebrafish (Danio rerio) as a versatile model organism for evaluating animal venoms and toxins. Zebrafish possess genetic similarities to humans, rapid development, transparency, and amenability to high-throughput assays, making it ideal for assessing the effects of animal venoms and toxins. This review highlights unique attributes of zebrafish and explores their applications in studying venom- and toxin-induced effects from various species, including snakes, jellyfish, cuttlefish, anemones, spiders, and cone snails. Through zebrafish-based research, intricate physiological responses, developmental alterations, and potential therapeutic interventions induced by venoms are revealed. Novel techniques such as CRISPR/Cas9 gene editing, optogenetics, and high-throughput screening hold great promise for advancing venom research. As zebrafish-based insights converge with findings from other models, the comprehensive understanding of venom-induced effects continues to expand, guiding the development of targeted interventions and promoting both scientific knowledge and practical applications.

A Mechanistic Study of the Osteogenic Effect of Arecoline in an Osteoporosis Model: Inhibition of Iron Overload-Induced Osteogenesis by Promoting Heme Oxygenase-1 Expression

Iron overload-associated osteoporosis presents a significant challenge to bone health. This study examines the effects of arecoline (ACL), an alkaloid found in areca nut, on bone metabolism under iron overload conditions induced by ferric ammonium citrate (FAC) treatment. The results indicate that ACL mitigates the FAC-induced inhibition of osteogenesis in zebrafish larvae, as demonstrated by increased skeletal mineralization and upregulation of osteogenic genes. ACL attenuates FAC-mediated suppression of osteoblast differentiation and mineralization in MC3T3-E1 cells. RNA sequencing analysis suggests that the protective effects of ACL are related to the regulation of ferroptosis. We demonstrate that ACL inhibits ferroptosis, including oxidative stress, lipid peroxidation, mitochondrial damage, and cell death under FAC exposure. In this study, we have identified heme oxygenase-1 (HO-1) as a critical mediator of ACL inhibiting ferroptosis and promoting osteogenesis, which was validated by HO-1 knockdown and knockout experiments. The study links ACL to HO-1 activation and ferroptosis regulation in the context of bone metabolism. These findings provide new insights into the mechanisms underlying the modulation of osteogenesis by ACL. Targeting the HO-1/ferroptosis axis is a promising therapeutic approach for treating iron overload-induced bone diseases.

Methods: A bioinformatic protocol for rapid analysis of zebrafish embryo photo-motory responses (PMR) in neurotoxicity testing

Chemobehavioural phenotyping presents unique opportunities for analyzing neurotoxicants and discovering behavior-modifying neuroceuticals in small aquatic model organisms such as zebrafish (Danio rerio). A recently popularized approach in this field involves the utilization of zebrafish embryos for a photo-motor response (PMR) bioassay. The PMR bioassay entails stimulating zebrafish embryos between 24 and 36 h post fertilization (hpf) with a high-intensity light stimulus, inducing a transient increase in the frequency of photo-induced embryo body flexions. These flexions can be computationally analyzed to derive behavioral signatures, enabling the categorization of neuromodulating chemicals. Despite the significant advantages of the PMR bioassay, its widespread implementation is hindered by lack of well described and straightforward high-throughput bioinformatic analysis of behavioral data. In this methods article, we present an easily implementable bioinformatics protocol specifically designed for rapid behavioral analysis of large cohorts of zebrafish specimens in PMR bioassays. We also address common pitfalls encountered during PMR analysis, discuss its limitations, and propose future directions for developing next-generation biometric analysis techniques in chemobehavioural assays utilizing zebrafish embryos.

Deep Learning-Enabled Morphometric Analysis for Toxicity Screening Using Zebrafish Larvae

Toxicology studies heavily rely on morphometric analysis to detect abnormalities and diagnose disease processes. The emergence of ever-increasing varieties of environmental pollutants makes it difficult to perform timely assessments, especially using in vivo models. Herein, we propose a deep learning-based morphometric analysis (DLMA) to quantitatively identify eight abnormal phenotypes (head hemorrhage, jaw malformation, uninflated swim bladder, pericardial edema, yolk edema, bent spine, dead, unhatched) and eight vital organ features (eye, head, jaw, heart, yolk, swim bladder, body length, and curvature) of zebrafish larvae. A data set composed of 2532 bright-field micrographs of zebrafish larvae at 120 h post fertilization was generated from toxicity screening of three categories of chemicals, i.e., endocrine disruptors (perfluorooctanesulfonate and bisphenol A), heavy metals (CdCl2 and PbI2), and emerging organic pollutants (acetaminophen, 2,7-dibromocarbazole, 3-monobromocarbazo, 3,6-dibromocarbazole, and 1,3,6,8-tetrabromocarbazo). Two typical deep learning models, one-stage and two-stage models (TensorMask, Mask R-CNN), were trained to implement phenotypic feature classification and segmentation. The accuracy was statistically validated with a mean average precision >0.93 in unlabeled data sets and a mean accuracy >0.86 in previously published data sets. Such a method effectively enables subjective morphometric analysis of zebrafish larvae to achieve efficient hazard identification of both chemicals and environmental pollutants.

Developmental toxicity of the emerging contaminant cyclophosphamide and the integrated biomarker response (IBRv2) in zebrafish

The safety of cyclophosphamide (CP) in the early developmental stages is not studied yet; it is important to study the responses at these stages because they might have relevance to CP-administered humans. We studied the developmental toxicity of CP by analysing physiological, morphological, and oxidative stress, neurotransmission enzymes, gene expression and histological endpoints in zebrafish embryos/larvae. The study lasted for 120 hpf at environmentally relevant concentrations of CP. No visible alterations were noticed in the control group. Delayed hatching, slow heart rate, yolk sac oedema, pericardial oedema, morphological deformities, the incompetence of oxidative stress biomarkers, excessive generation of ROS, apoptosis, inhibition of neurotransmitters and histopathological anomalies were observed in CP-treated groups. These alterations were found to be concentration- and duration-dependent effects for physiological and morphological endpoints, whereas concentration-dependent effects were antioxidants, ROS, apoptosis and histological endpoints. Biomarkers and gene expression were standardised using the integrated biomarker response-IBRv2 index. The IBRv2 index showed a concentration-dependent behaviour. A non-lethal developmental and teratogenic effect was observed in CP-treated zebrafish embryos/larvae at the studied concentrations. The studied biomarkers are sensitive, and the responses are interrelated; thus, their responses are useful to assess veiled and unseen hazards of pharmaceuticals.

Progress on the toxicity of quantum dots to model organism-zebrafish

In vivo toxicological studies are currently necessary to analyze the probable dangers of quantum dots (QDs) to the environment and human safety, due to the fast expansion of QDs in a range of applications. Because of its high fecundity, cost-effectiveness, well-defined developmental phases, and optical transparency, zebrafish has long been considered the "gold standard" for biosafety assessment of chemical substances and pollutants. In this review, the advantages of using zebrafish in QD toxicity assessment were explored. Then, the target organ toxicities such as developmental toxicity, immunotoxicity, cardiovascular toxicity, neurotoxicity, and hepatotoxicity were summarized. The hazardous effects of different QDs, including cadmium-containing QDs like CdTe, CdSe, and CdSe/ZnS, as well as cadmium-free QDs like graphene QDs (GQDs), graphene oxide QDs (GOQDs), and others, were emphasized and described in detail, as well as the underlying mechanisms of QDs generating these effects. Furthermore, general physicochemical parameters determining QD-induced toxicity in zebrafish were introduced, such as chemical composition and surface coating/modification. The limitations and special concerns of using zebrafish in QD toxicity studies were also mentioned. Finally, we predicted that the utilization of high-throughput screening assays and omics, such as transcriptome sequencing, proteomics, and metabolomics will be popular topic in nanotoxicology.

High-throughput screening paradigms in ecotoxicity testing: Emerging prospects and ongoing challenges

The rapidly increasing number of new production chemicals coupled with stringent implementation of global chemical management programs necessities a paradigm shift towards boarder uses of low-cost and high-throughput ecotoxicity testing strategies as well as deeper understanding of cellular and sub-cellular mechanisms of ecotoxicity that can be used in effective risk assessment. The latter will require automated acquisition of biological data, new capabilities for big data analysis as well as computational simulations capable of translating new data into in vivo relevance. However, very few efforts have been so far devoted into the development of automated bioanalytical systems in ecotoxicology. This is in stark contrast to standardized and high-throughput chemical screening and prioritization routines found in modern drug discovery pipelines. As a result, the high-throughput and high-content data acquisition in ecotoxicology is still in its infancy with limited examples focused on cell-free and cell-based assays. In this work we outline recent developments and emerging prospects of high-throughput bioanalytical approaches in ecotoxicology that reach beyond in vitro biotests. We discuss future importance of automated quantitative data acquisition for cell-free, cell-based as well as developments in phytotoxicity and in vivo biotests utilizing small aquatic model organisms. We also discuss recent innovations such as organs-on-a-chip technologies and existing challenges for emerging high-throughput ecotoxicity testing strategies. Lastly, we provide seminal examples of the small number of successful high-throughput implementations that have been employed in prioritization of chemicals and accelerated environmental risk assessment.

Transcriptomic signaling in zebrafish (Danio rerio) embryos exposed to environmental concentrations of glyphosate

Glyphosate [N-(phosphonomethyl)glycine] is one of the most popular herbicides worldwide. Globally, the use of glyphosate is increasing, and its residues have been found in drinking water and food products. The data regarding the possible toxic effects of this herbicide are controversial. Therefore, the aim of this study was to evaluate the effects of glyphosate at environmental concentrations in zebrafish (Danio rerio) embryos. Embryos were exposed to 0, 1, 100, and 1,000 µg/L glyphosate for 96 h, and mortality, heart rate, and hatching rate were evaluated. After the experiment, RNA was extracted from the embryos for transcriptional analysis. No mortality was recorded, and exposure to 100 µg/L and 1,000 µg/L of glyphosate resulted in lower heart rates at 48 h. In addition, RNA-seq analysis revealed that glyphosate exposure induced subtle changes in gene transcription profiles. We found 30 differentially expressed genes; however, the highest glyphosate concentration (1,000 µg/L) induced the greatest number of differentially expressed genes involved in oocyte maturation, metabolic processes, histone deacetylation, and nervous system development.

Beyond the behavioural phenotype: Uncovering mechanistic foundations in aquatic eco-neurotoxicology

During the last decade, there has been an increase in awareness of how anthropogenic pollution can alter behavioural traits of diverse aquatic organisms. Apart from understanding profound ecological implications, alterations in neuro-behavioural indices have emerged as sensitive and physiologically integrative endpoints in chemical risk assessment. Accordingly, behavioural ecotoxicology and broader eco-neurotoxicology are becoming increasingly popular fields of research that span a plethora of fundamental laboratory experimentations as well as applied field-based studies. Despite mounting interest in aquatic behavioural ecotoxicology studies, there is, however, a considerable paucity in deciphering the mechanistic foundations underlying behavioural alterations upon exposure to pollutants. The behavioural phenotype is indeed the highest-level integrative neurobiological phenomenon, but at its core lie myriads of intertwined biochemical, cellular, and physiological processes. Therefore, the mechanisms that underlie changes in behavioural phenotypes can stem among others from dysregulation of neurotransmitter pathways, electrical signalling, and cell death of discrete cell populations in the central and peripheral nervous systems. They can, however, also be a result of toxicity to sensory organs and even metabolic dysfunctions. In this critical review, we outline why behavioural phenotyping should be the starting point that leads to actual discovery of fundamental mechanisms underlying actions of neurotoxic and neuromodulating contaminants. We highlight potential applications of the currently existing and emerging neurobiology and neurophysiology analytical strategies that should be embraced and more broadly adopted in behavioural ecotoxicology. Such strategies can provide new mechanistic discoveries instead of only observing the end sum phenotypic effects.

Technologies bringing young Zebrafish from a niche field to the limelight

Fundamental life science and pharmaceutical research are continually striving to provide physiologically relevant context for their biological studies. Zebrafish present an opportunity for high-content screening (HCS) to bring a true in vivo model system to screening studies. Zebrafish embryos and young larvae are an economical, human-relevant model organism that are amenable to both genetic engineering and modification, and direct inspection via microscopy. The use of these organisms entails unique challenges that new technologies are overcoming, including artificial intelligence (AI). In this perspective article, we describe the state-of-the-art in terms of automated sample handling, imaging, and data analysis with zebrafish during early developmental stages. We highlight advances in orienting the embryos, including the use of robots, microfluidics, and creative multi-well plate solutions. Analyzing the micrographs in a fast, reliable fashion that maintains the anatomical context of the fluorescently labeled cells is a crucial step. Existing software solutions range from AI-driven commercial solutions to bespoke analysis algorithms. Deep learning appears to be a critical tool that researchers are only beginning to apply, but already facilitates many automated steps in the experimental workflow. Currently, such work has permitted the cellular quantification of multiple cell types in vivo, including stem cell responses to stress and drugs, neuronal myelination and macrophage behavior during inflammation and infection. We evaluate pro and cons of proprietary versus open-source methodologies for combining technologies into fully automated workflows of zebrafish studies. Zebrafish are poised to charge into HCS with ever-greater presence, bringing a new level of physiological context.

Agricultural surface water, imidacloprid, and chlorantraniliprole result in altered gene expression and receptor activation in Pimephales promelas

The toxicity of single pesticides is likely underestimated when considering complex pesticide mixtures found in agricultural runoff and this is especially true for newer pesticides with little toxicity data on non-target species. The goal of our study was to compare the toxicity of two newer pesticides, imidacloprid (IMI) and chlorantraniliprole (CHL), when an invertebrate and fish were exposed to single compounds, binary mixtures or surface water collected near agricultural fields. A secondary goal was to determine whether changes in select subcellular molecular pathways correspond to the insecticides' mechanisms of activity in aquatic organisms. We conducted acute (96 h) exposures using a dilution series of field water and environmentally relevant concentrations of single and binary mixtures of IMI and CHL. We then evaluated survival, gene expression and the activity of IMI toward the n-acetylcholine receptor (nAChR) and CHL activity toward the ryanodine receptor (RyR). Both IMI and CHL were detected at all sampling locations for May 2019 and September 2019 sampling dates and exposure to field water led to high invertebrate but not fish mortality. Fish exposed to field collected water had significant changes in the relative expression of genes involved with detoxification and neuromuscular function. Exposure of fish to single compounds or binary mixtures of IMI and CHL led to increased relative gene expression of RyR in fish. Furthermore, we found that IMI targets the nAChR in aquatic invertebrates and that CHL can cause overactivation of the RyR in invertebrates and fish. Overall, our finding suggests that IMI and CHL may impact neuromuscular health in fish. Expanding monitoring efforts to include sublethal and molecular assays would allow the detection of subcellular level effects due to complex mixtures present in surface water near agricultural areas.

Accelerating Chemobehavioral Phenotypic Screening in Neurotoxicology Using a Living Embryo Array System

Large-scale chemobehavioral phenotyping with zebrafish embryos is a promising avenue for accelerated neurotoxicity testing and discovery of behavior-modifying neuroceuticals. These strategies are hampered by lack of effective embryo in-test positioning, wide-field imaging, and high-throughput bioinformatic analytics. In this study, we demonstrate advantages of using custom large-density embryo arrays in conjunction with an open-source ultra-high-definition video imaging system. Moreover, we present a high-throughput bioinformatics workflow for rapid behavioral analysis of large cohorts of specimens in photomotor response bioassays. The system validation was showcased in a proof-of-concept neurotoxicity analysis.

Recent progress in cytometric technologies and their applications in ecotoxicology and environmental risk assessment

Environmental toxicology focuses on identifying and predicting impact of potentially toxic anthropogenic chemicals on biosphere at various levels of biological organization. Presently there is a significant drive to gain deeper understanding of cellular and sub-cellular mechanisms of ecotoxicity. Most notable is increased focus on elucidation of cellular-response networks, interactomes, and greater implementation of cell-based biotests using high-throughput procedures, while at the same time decreasing the reliance on standard animal models used in ecotoxicity testing. This is aimed at discovery and interpretation of molecular pathways of ecotoxicity at large scale. In this regard, the applications of cytometry are perhaps one of the most fundamental prospective analytical tools for the next generation and high-throughput ecotoxicology research. The diversity of this modern technology spans flow, laser-scanning, imaging, and more recently, Raman as well as mass cytometry. The cornerstone advantages of cytometry include the possibility of multi-parameter measurements, gating and rapid analysis. Cytometry overcomes, thus, limitations of traditional bulk techniques such as spectrophotometry or gel-based techniques that average the results from pooled cell populations or small model organisms. Novel technologies such as cell imaging in flow, laser scanning cytometry, as well as mass cytometry provide innovative and tremendously powerful capabilities to analyze cells, tissues as well as to perform in situ analysis of small model organisms. In this review, we outline cytometry as a tremendously diverse field that is still vastly underutilized and often largely unknown in environmental sciences. The main motivation of this work is to highlight the potential and wide-reaching applications of cytometry in ecotoxicology, guide environmental scientists in the technological aspects as well as popularize its broader adoption in environmental risk assessment.