Comparative Toxicogenomic Responses to the Flame Retardant mITP in Developing Zebrafish

Gene co-expression network analysis in zebrafish reveals chemical class specific modules

BACKGROUND

Zebrafish is a popular animal model used for high-throughput screening of chemical hazards, however, investigations of transcriptomic mechanisms of toxicity are still needed. Here, our goal was to identify genes and biological pathways that Aryl Hydrocarbon Receptor 2 (AHR2) Activators and flame retardant chemicals (FRCs) alter in developing zebrafish. Taking advantage of a compendium of phenotypically-anchored RNA sequencing data collected from 48-h post fertilization (hpf) zebrafish, we inferred a co-expression network that grouped genes based on their transcriptional response.

RESULTS

Genes responding to the FRCs and AHR2 Activators localized to distinct regions of the network, with FRCs inducing a broader response related to neurobehavior. AHR2 Activators centered in one region related to chemical stress responses. We also discovered several highly co-expressed genes in this module, including cyp1a, and we subsequently show that these genes are definitively within the AHR2 signaling pathway. Systematic removal of the two chemical types from the data, and analysis of network changes identified neurogenesis associated with FRCs, and regulation of vascular development associated with both chemical classes. We also identified highly connected genes responding specifically to each class that are potential biomarkers of exposure.

CONCLUSIONS

Overall, we created the first zebrafish chemical-specific gene co-expression network illuminating how chemicals alter the transcriptome relative to each other. In addition to our conclusions regarding FRCs and AHR2 Activators, our network can be leveraged by other studies investigating chemical mechanisms of toxicity.

Phenotypically Anchored mRNA and miRNA Expression Profiling in Zebrafish Reveals Flame Retardant Chemical Toxicity Networks

The ubiquitous use of flame retardant chemicals (FRCs) in the manufacture of many consumer products leads to inevitable environmental releases and human exposures. Studying toxic effects of FRCs as a group is challenging since they widely differ in physicochemical properties. We previously used zebrafish as a model to screen 61 representative FRCs and showed that many induced behavioral and teratogenic effects, with aryl phosphates identified as the most active. In this study, we selected 10 FRCs belonging to diverse physicochemical classes and zebrafish toxicity profiles to identify the gene expression responses following exposures. For each FRC, we executed paired mRNA-micro-RNA (miR) sequencing, which enabled us to study mRNA expression patterns and investigate the role of miRs as posttranscriptional regulators of gene expression. We found widespread disruption of mRNA and miR expression across several FRCs. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs (e.g., osbpl2a) and miRs (e.g., mir-125b-5p), showed differential expression common to multiple FRCs (10 and 7 respectively). These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions, including apoptosis, neurodevelopment, lipid regulation and inflammation. Commonly disrupted transcription factors (TFs) such as retinoic acid receptor, retinoid X receptor, and vitamin D regulator were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA-TF and mRNA-miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA-DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE-47. Our study is the first to establish a mRNA-miR-TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals and establish this approach as an important tool for better understanding toxic effects of environmental contaminants.

Translational Toxicology in Zebrafish

A major goal of translational toxicology is to identify adverse chemical effects and determine whether they are conserved or divergent across experimental systems. Translational toxicology encompasses assessment of chemical toxicity across multiple life stages, determination of toxic mode-of-action, computational prediction modeling, and identification of interventions that protect or restore health following toxic chemical exposures. The zebrafish is increasingly used in translational toxicology because it combines the genetic and physiological advantages of mammalian models with the higher-throughput capabilities and genetic manipulability of invertebrate models. Here, we review recent literature demonstrating the power of the zebrafish as a model for addressing all four activities of translational toxicology. Important data gaps and challenges associated with using zebrafish for translational toxicology are also discussed.

Assessing the hazard of E-Cigarette flavor mixtures using zebrafish

Since 2007, electronic cigarette (e-cigarette) sales in the U.S. have surpassed those of tobacco cigarettes. This is due, in part, to manufacturer's claims that they are a safer alternative to tobacco cigarettes. However, formaldehyde, acrolein, and diacetyl have been detected in e-cigarettes and public knowledge of e-cigarette composition and ingredient bioactivity is conspicuously lacking. We evaluated the toxicity of nine e-cigarette flavor mixtures and their constituents in the developmental zebrafish, an excellent whole animal biosensor of chemical hazard. Seven of the nine flavors (78%) elicited adverse developmental responses at 1% by volume. The number of toxic endpoints varied greatly between flavors. Two flavors, Grape and Bubble Gum, had similar chemical compositions, but different toxicity profiles. We hypothesized that the toxicity was driven by a constituent present only in the Bubble Gum flavor, cinnamaldehyde. To replicate this toxicity, we built our own defined mixture. The addition of varying concentrations of cinnamaldehyde suggested that it drove the toxicity of these mixtures and that e-cigarette hazard can be flavor dependent.

Coupling Genome-wide Transcriptomics and Developmental Toxicity Profiles in Zebrafish to Characterize Polycyclic Aromatic Hydrocarbon (PAH) Hazard

Polycyclic Aromatic Hydrocarbons (PAHs) are diverse environmental pollutants associated with adverse human health effects. Many studies focus on the carcinogenic effects of a limited number of PAHs and there is an increasing need to understand mechanisms of developmental toxicity of more varied yet environmentally relevant PAHs. A previous study characterized the developmental toxicity of 123 PAHs in zebrafish. Based on phenotypic responses ranging from complete inactivity to acute mortality, we classified these PAHs into eight bins, selected 16 representative PAHs, and exposed developing zebrafish to the concentration of each PAH that induced 80% phenotypic effect. We conducted RNA sequencing at 48 h post fertilization to identify gene expression changes as a result of PAH exposure. Using the Context Likelihood of Relatedness algorithm, we inferred a network that links the PAHs based on coordinated gene responses to PAH exposure. The 16 PAHs formed two broad clusters: Cluster A was transcriptionally more similar to the controls, while Cluster B consisted of PAHs that were generally more developmentally toxic, significantly elevated cyp1a transcript levels, and induced Ahr2-dependent Cyp1a protein expression in the skin confirmed by gene-silencing studies. We found that cyp1a transcript levels were associated with transcriptomic response, but not with PAH developmental toxicity. While all cluster B PAHs predominantly activated Ahr2, they also each enriched unique pathways like ion transport signaling, which likely points to differing molecular events between the PAHs downstream of Ahr2. Thus, using a systems biology approach, we have begun to evaluate, classify, and define mechanisms of PAH toxicity.

Characterization of the Fundulus heteroclitus embryo transcriptional response and development of a gene expression-based fingerprint of exposure for the alternative flame retardant, TBPH (bis (2-ethylhexyl)-tetrabromophthalate)

Although alternative Flame Retardant (FR) chemicals are expected to be safer than the legacy FRs they replace, their risks to human health and the environment are often poorly characterized. This study used a small volume, fish embryo system to reveal potential mechanisms of action and diagnostic exposure patterns for TBPH (bis (2-ethylhexyl)-tetrabromophthalate), a component of several widely-used commercial products. Two different concentration of TBPH were applied to sensitive early life stages of an ecologically important test species, Fundulus heteroclitus (Atlantic killifish), with a well-annotated genome. Exposed fish embryos were sampled for transcriptomics or chemical analysis of parent compound and primary metabolite or observed for development and survival through larval stage. Global transcript profiling using RNA-seq was conducted (n = 16 per treatment) to provide a non-targeted and statistically robust approach to characterize TBPH gene expression patterns. Transcriptomic analysis revealed a dose-response in the expression of genes associated with a surprisingly limited number of biological pathways, but included the aryl hydrocarbon receptor signal transduction pathway, which is known to respond to several toxicologically-important chemical classes. A transcriptional fingerprint using Random Forests was developed that was able to perfectly discriminate exposed vs. non-exposed individuals in test sets. These results suggest that TBPH has a relatively low potential for developmental toxicity (at least in fishes), despite concerns related to its structural similarities to endocrine disrupting chemicals and that the early life stage Fundulus system may provide a convenient test system for exposure characterization. More broadly, this study advances the usefulness of a biological testing and analysis system utilizing non-targeted transcriptomics profiling and early developmental endpoints that complements current screening methods to characterize chemicals of ecological and human health concern.

Aryl hydrocarbon receptor-mediated activity of gas-phase ambient air derived from passive sampling and an in vitro bioassay

The gaseous fraction of hydrophobic organic contaminants (HOCs) in ambient air appears to be responsible for a significant portion of aryl hydrocarbon receptor (AhR)-mediated activity, but the majority of compounds contributing to this activity remain unidentified. The present study investigated the use of polyethylene passive samplers to isolate gaseous HOCs from ambient air for use in in vitro bioassays and to improve our understanding of the toxicological relevance of the gaseous fraction of ambient air in urban and residential environments. Concentrations of polycyclic aromatic hydrocarbons (PAHs) and organic flame retardants were measured in polyethylene passive sampler extracts. Extracts were also analyzed using an in vitro bioassay to measure AhR-mediated activity. Bioassay-derived benzo[a]pyrene (BaP) equivalents (BaP-Eq_bio ), a measure of potency of HOC mixtures, were greatest in the downtown Cleveland area and lowest at rural/residential sites further from the city center. The BaP-Eq_bio was weakly correlated with concentrations of 2-ring alkyl/substituted PAHs and one organophosphate flame retardant, ethylhexyl diphenyl phosphate. Potency predicted based on literature-derived induction equivalency factors (IEFs) explained only 2 to 23% of the AhR-mediated potency observed in bioassay experiments. Our results suggests that health risks of gaseous ambient air pollution predicted using data from targeted chemical analysis may underestimate risks of exposure, most likely due to augmentation of potency by unmonitored chemicals in the mixture, and the lack of relevant IEFs for many targeted analytes. Environ Toxicol Chem 2019;38:748-759. © 2019 SETAC.