Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay

Application of transcriptomics concentration-response modeling for prioritization of contaminants detected in tributaries of the North American Great Lakes

As part of the Great Lakes Restoration Initiative, chemical monitoring and surveillance efforts have detected approximately 330 chemicals in surface water of Great Lakes tributaries. There were 140 chemicals for which no empirical toxicity data were available. The aim of this study was to generate transcriptomic points of departure (tPODs) for 10 of these compounds and demonstrate how they could be applied in a screening-level prioritization. Organisms representing three trophic levels of the aquatic food web (Pimephales promelas, Daphnia magna, and Raphidocelis subcapitata) were exposed for 24 hr to a half-log dilution series of nominal exposure concentrations typically ranging from 66.7-0.021 µM of each chemical. In addition to observations of apical effects (e.g., survival and morphology), whole body transcriptomic responses (tPODs) to each chemical were evaluated with targeted analysis using TempO-seq for P. promelas and D. magna and nontargeted RNA-seq for R. subcapitata. The tPODs ranged from 0.18-10.8 µM for P. promelas and 0.32-29 µM for D. magna, with the most potent of the chemicals tested being fipronil carboxamide for both species. For R. subcapitata, the tPODs ranged from 0.04-1.77 µM, with gabapentin as the most potent chemical tested. Empirically derived tPODs from these data-poor chemicals were compared with concentrations detected in the Great Lakes basin. Environmental concentrations were less than the tPODs except for R. subcapitata and 3,4-dichlorophenyl isocyanate. Similarly, tPODs from previously tested data-rich chemicals were compared with environmental concentrations, in which case tPODs from several chemicals overlapped environmental concentrations. This work demonstrates the potential utility of emerging ecological high-throughput transcriptomics assays to support screening and prioritization of data-poor environmental contaminants.

Bioactivity of the ubiquitous tire preservative 6PPD and degradant, 6PPD-quinone in fish- and mammalian-based assays

6PPD-quinone (N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone), a transformation product of the antiozonant 6PPD (N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine) is a likely causative agent of coho salmon (Oncorhynchus kisutch) pre-spawn mortality. Stormwater runoff transports 6PPD-quinone into freshwater streams, rapidly leading to neurobehavioral, respiratory distress, and rapid mortality in laboratory-exposed coho salmon, but causing no mortality in many laboratory-tested species. Given this identified hazard, and potential for environmental exposure, we evaluated a set of U.S. Environmental Protection Agency's high-throughput assays for their capability to detect the large potency difference between 6PPD and 6PPD-quinone observed in coho salmon and screen for bioactivities of concern. Assays included transcriptomics in larval fathead minnow (FHM), developmental and behavioral toxicity in larval zebrafish, phenotypic profiling in a rainbow trout gill cell line, acute and developmental neurotoxicity in mammalian cells, and reporter transcription factor activity in HepG2 cells. 6PPD was more consistently bioactive across assays, with distinct activity in the developmental neurotoxicity assay (mean 50th centile activity concentration = 0.91 µM). Although 6PPD-quinone was less potent in FHM and zebrafish, and displayed minimal neurotoxic activity in mammalian cells, it was highly potent in altering organelle morphology in RTgill-W1 cells (phenotype-altering concentration = 0.024 µM compared with 0.96 µM for 6PPD). Although in vitro sensitivity of RTgill-W1 cells may not be as sensitive as intact Coho salmon, the assay may be a promising approach to test chemicals for 6PPD-quinone-like activities. The other assays each identified unique bioactivities of 6PPD, with neurobehavioral and developmental neurotoxicity being most affected, indicating a need for further assessment of this chemical. Our results demonstrate that the common tire additive, 6PPD, is bioactive in a broader set of assays than the environmental transformation product 6PPD-quinone and that it may be a developmental neurotoxicant in mammals, whereas 6PPD-quinone was much more potent than 6PPD in altering the intracellular phenotype of rainbow trout gill cells. Application of the set of high-throughput and high-content bioassays to test the bioactivity of this emerging pollutant has provided data to inform both ecological and human health assessments.

Transcriptomic response of an algal species (Raphidocelis subcapitata) exposed to 22 per- and polyfluoroalkyl substances

Per- and polyfluoroalkyl substances (PFAS) are a large class of chemicals of concern for both human and environmental health because of their ubiquitous presence in the environment, persistence, and potential toxicological effects. Despite this, ecological hazard data are limited to a small number of PFAS although there are over 4,000 identified PFAS. Traditional toxicity testing will likely be inadequate to generate necessary hazard information for risk assessment. Therefore, this study investigated the utility of using transcriptomic points of departure (tPODs) for informing PFAS algal toxicity. Raphidocelis subcapitata, a freshwater green algal species, were exposed for 24 hr in 96-well microplates to multiple concentrations of 22 different PFAS. Following exposure, RNA was extracted, and the transcriptome was evaluated by RNA sequencing followed by concentration response modeling to determine a tPOD for each PFAS. Per- and polyfluoroalkyl substance tPODs, based on measured concentrations, ranged from 0.9 µg/L for perfluorotridecanoic acid to 1 mg/L for perfluorononanoic acid. These values derived from R. subcapitata exposures were compared with published hazard benchmarks from other taxa (larval fathead minnow and Daphnia magna) and in vitro data. Although R. subcapitata was generally more sensitive to the tested PFAS than previously tested taxa and in vitro assays, the algal tPODs were, on average, three orders magnitude greater than the maximum concentrations of PFAS detected in Great Lakes tributaries. This high throughput transcriptomics assay with algae is a promising new approach method for an ecologically relevant tiered hazard evaluation strategy.

Bioinformatic workflows for deriving transcriptomic points of departure: current status, data gaps, and research priorities

There is a pressing need to increase the efficiency and reliability of toxicological safety assessment for protecting human health and the environment. Although conventional toxicology tests rely on measuring apical changes in vertebrate models, there is increasing interest in the use of molecular information from animal and in vitro studies to inform safety assessment. One promising and pragmatic application of molecular information involves the derivation of transcriptomic points of departure (tPODs). Transcriptomic analyses provide a snapshot of global molecular changes that reflect cellular responses to stressors and progression toward disease. A tPOD identifies the dose level below which a concerted change in gene expression is not expected in a biological system in response to a chemical. A common approach to derive such a tPOD consists of modeling the dose-response behavior for each gene independently and then aggregating the gene-level data into a single tPOD. Although different implementations of this approach are possible, as discussed in this manuscript, research strongly supports the overall idea that reference doses produced using tPODs are health protective. An advantage of this approach is that tPODs can be generated in shorter term studies (e.g. days) compared with apical endpoints from conventional tests (e.g. 90-d subchronic rodent tests). Moreover, research strongly supports the idea that reference doses produced using tPODs are health protective. Given the potential application of tPODs in regulatory toxicology testing, rigorous and reproducible wet and dry laboratory methodologies for their derivation are required. This review summarizes the current state of the science regarding the study design and bioinformatics workflows for tPOD derivation. We identify standards of practice and sources of variability in tPOD generation, data gaps, and areas of uncertainty. We provide recommendations for research to address barriers and promote adoption in regulatory decision making.

A combination of high-throughput in vitro and in silico new approach methods for ecotoxicology hazard assessment for fish

Fish acute toxicity testing is used to inform environmental hazard assessment of chemicals. In silico and in vitro approaches have the potential to reduce the number of fish used in testing and increase the efficiency of generating data for assessing ecological hazards. Here, two in vitro bioactivity assays were adapted for use in high-throughput chemical screening. First, a miniaturized version of the Organisation for Economic Co-operation and Development (OECD) test guideline 249 plate reader-based acute toxicity assay in RTgill-W1 cells was developed. Second, the Cell Painting (CP) assay was adapted for use in RTgill-W1 cells along with an imaging-based cell viability assay. Then, 225 chemicals were tested in each assay. Potencies and bioactivity calls from the plate reader and imaging-based cell viability assays were comparable. The CP assay was more sensitive than either cell viability assay in that it detected a larger number of chemicals as bioactive, and phenotype altering concentrations (PACs) were lower than concentrations that decreased cell viability. An in vitro disposition (IVD) model that accounted for sorption of chemicals to plastic and cells over time was applied to predict freely dissolved PACs and compared with in vivo fish toxicity data. Adjustment of PACs using IVD modeling improved concordance of in vitro bioactivity and in vivo toxicity data. For the 65 chemicals where comparison of in vitro and in vivo values was possible, 59% of adjusted in vitro PACs were within one order of magnitude of in vivo toxicity lethal concentrations for 50% of test organisms. In vitro PACs were protective for 73% of chemicals. This combination of in vitro and in silico approaches has the potential to reduce or replace the use of fish for in vivo toxicity testing.

A tiered toxicity testing strategy for assessing early life stage toxicity in estuarine fish (Mugilogobius chulae): A case study on tris (1-chloro-2-propyl) phosphate ester

The estuarine ecological environment faces significant threats from contaminants of emerging concern (CECs); yet, the risk posed by CECs to resident organisms remains poorly understood. Here, we employed tiered toxicity testing to investigate the adverse effects and potential mechanisms of tris (1-chloro-2-propyl) phosphate (TCPP) on the early life stages of an estuarine fish, Mugilogobius chulae. TCPP affected the development of M. chulae embryos, including survival, morphology, hatching, and behavior. A concentration-dependent transcriptomic analysis showed that TCPP disrupted 12 neurodevelopment-related KEGG pathways in M. chulae embryos, with five of the 30 % top-ranked pathways related to neurotransmitter signaling. Besides the cholinergic synapse signaling pathway, the glutamatergic signaling pathway (including NMDAR and AMPAR subtypes) may also mediate TCPP-induced neurodevelopmental toxicity. The NMDAR subtype GRIN2B was downregulated at high concentrations. Molecular dynamics simulations revealed a strong interaction between TCPP and GRIN2B, with TCPP binding to the residues Ile153 and Ile188. The results suggest that NMDARs play a crucial role in TCPP-induced neurodevelopmental toxicity toward M. chulae. AOP network analysis predicted that TCPP may impact cognitive functions and memory. Our study provides a novel testing strategy for identifying the mechanisms of toxicity of CECs, a crucial component of ecological risk assessment.

Cytotoxic and Molecular Effects of Soil Extracts from the Agbogbloshie Electronic-Waste Site on Fish and Human Cell Lines

Effect-based methods (EBM) are of growing interest in environmental monitoring programs. Few EBM have incorporated transcriptomics even though these provide a wealth of biological information and can be modeled to yield transcriptomic points of departure (tPODs). The study objectives were to: A) characterize cytotoxic effects of soil extracts on the rainbow trout RTgill-W1 and the human Caco-2 cell lines; B) measure gene expression changes and calculate tPODs; and C) compare in vitro responses to available measures of plastic-related compounds and metals. Extracts were prepared from 35 soil samples collected at the Agbogbloshie E-waste site (Accra, Ghana). Cells were exposed to six soil concentrations (0.3 to 9.4 mg dry weight of extract (eQsed)/ml). Many samples caused cytotoxicity with RTgill cells being more sensitive than Caco-2 cells. Eleven samples were analyzed for transcriptomics in both cell lines, with responses measured in all samples (52 to 5925 differentially expressed genes) even in the absence of cytotoxicity. In RTgill cells there was concordance between cytotoxic measures in tPOD values (spearman = 0.85). Though trends between in vitro measures and contaminant data were observed, more work is needed in this area before definitive conclusions are drawn. Nonetheless, this study helps support ongoing efforts in establishing alternative testing strategies (e.g., alternative to animal methods; toxicogenomics) for the assessment of complex environmental samples.

Far from Their Origins: A Transcriptomic Investigation on How 2,4-Di-tert-butyl-6-(5-chloro-2H-benzotriazol-2-yl) Phenol Affects Rainbow Trout Alevins

Benzotriazole ultraviolet stabilizers (BUVSs) are a group of widely used chemicals added to a variety of consumer (e.g., plastics) and industrial (e.g., metal coating) goods. Although detected globally as an environmentally persistent pollutant, BUVSs have received relatively little toxicological attention and only recently have been acknowledged to affect development and the endocrine system in vivo. In our previous study, altered behavior, indicative of potential neurotoxicity, was observed among rainbow trout alevins (day 14 posthatching) that were microinjected as embryos with a single environmentally relevant dose of 2,4-di-tert-butyl-6-(5-chloro-2H-benzotriazol-2-yl) phenol (UV-327). In the present follow-up study, we performed whole-transcriptome profiling (RNA sequencing) of newly hatched alevins from the same batch. The primary aim was to identify biomarkers related to behavior and neurology. Dose-specifically, 1 to 176 differentially expressed genes (DEGs) were identified. In the group presenting altered behavior (273.4 ng g-1), 176 DEGs were identified, yet only a fraction was related to neurological functions, including water, calcium, and potassium homeostasis; acetylcholine transmission and signaling; as well insulin and energy metabolism. The second objective was to estimate the transcriptomic point of departure (tPOD) and assess if point estimate(s) are protective of altered behavior. A tPOD was established at 35 to 94 ng UV-327 g-1 egg, making this tPOD protective of behavioral alterations. Holistically, these transcriptomic alterations provide a foundation for future research on how BUVSs can influence rainbow trout alevin development, while providing support to the hypothesis that UV-327 can influence neurogenesis and subsequent behavioral endpoints. The exact structural and functional changes caused by embryonic exposure to UV-327 remain enigmatic and will require extensive investigation before being deciphered and understood toxicologically. Environ Toxicol Chem 2024;43:2026-2038. © 2024 The Author(s). Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Comparing Transcriptomic Points of Departure to Apical Effect Concentrations For Larval Fathead Minnow Exposed to Chemicals with Four Different Modes Of Action

It is postulated that below a transcriptomic-based point of departure, adverse effects are unlikely to occur, thereby providing a chemical concentration to use in screening level hazard assessment. The present study extends previous work describing a high-throughput fathead minnow assay that can provide full transcriptomic data after exposure to a test chemical. One-day post-hatch fathead minnows were exposed to ten concentrations of three representatives of four chemical modes of action: organophosphates, ecdysone receptor agonists, plant photosystem II inhibitors, and estrogen receptor agonists for 24 h. Concentration response modeling was performed on whole body gene expression data from each exposure, using measured chemical concentrations when available. Transcriptomic points of departure in larval fathead minnow were lower than apical effect concentrations across fish species but not always lower than toxic effect concentrations in other aquatic taxa like crustaceans and insects. The point of departure was highly dependent on measured chemical concentration which were often lower than the nominal concentration. Differentially expressed genes between chemicals within modes of action were compared and often showed statistically significant overlap. In addition, reproducibility between identical exposures using a positive control chemical (CuSO4) and variability associated with the transcriptomic point of departure using in silico sampling were considered. Results extend a transcriptomic-compatible fathead minnow high-throughput assay for possible use in ecological hazard screening.

Effects of Age and Exposure Duration on the Sensitivity of Early Life Stage Fathead Minnow (Pimephales promelas) to Waterborne Propranolol Exposure

Propranolol is a heavily prescribed, nonspecific beta-adrenoceptor (bAR) antagonist frequently found in wastewater effluents, prompting concern over its potential to adversely affect exposed organisms. In the present study, the transcriptional responses of 4, 5, and 6 days postfertilization (dpf) ±1 h fathead minnow, exposed for 6, 24, or 48 h to 0.66 or 3.3 mg/L (nominal) propranolol were characterized using RNA sequencing. The number of differentially expressed genes (DEGs) was used as an estimate of sensitivity. A trend toward increased sensitivity with age was observed; fish >7 dpf at the end of exposure were particularly sensitive to propranolol. The DEGs largely overlapped among treatment groups, suggesting a highly consistent response that was independent of age. Cluster analysis was performed using normalized count data for unexposed and propranolol-exposed fish. Control fish clustered tightly by age, with fish ≥7 dpf clustering away from younger fish, reflecting developmental differences. When clustering was conducted using exposed fish, in cases where propranolol induced a minimal or no transcriptional response, the results mirrored those of the control fish and did not appreciably cluster by treatment. In treatment groups that displayed a more robust transcriptional response, the effects of propranolol were evident; however, fish <7 dpf clustered away from older fish, despite having similar numbers of DEGs. Increased sensitivity at 7 dpf coincided with developmental milestones with the potential to alter propranolol pharmacokinetics or pharmacodynamics, such as the onset of exogenous feeding and gill functionality as well as increased systemic expression of bAR. These results may have broader implications because toxicity testing often utilizes fish <4 dpf, prior to the onset of these potentially important developmental milestones, which may result in an underestimation of risk for some chemicals. Environ Toxicol Chem 2024;43:807-820. Published 2023. This article is a U.S. Government work and is in the public domain in the USA.

Derivation of Transcriptomics-Based Points of Departure for 20 Per- or Polyfluoroalkyl Substances Using a Larval Fathead Minnow (Pimephales promelas) Reduced Transcriptome Assay

Traditional toxicity testing has been unable to keep pace with the introduction of new chemicals into commerce. Consequently, there are limited or no toxicity data for many chemicals to which fish and wildlife may be exposed. Per- and polyfluoroalkyl substances (PFAS) are emblematic of this issue in that ecological hazards of most PFAS remain uncharacterized. The present study employed a high-throughput assay to identify the concentration at which 20 PFAS, with diverse properties, elicited a concerted gene expression response (termed a transcriptomics-based point of departure [tPOD]) in larval fathead minnows (Pimephales promelas; 5-6 days postfertilization) exposed for 24 h. Based on a reduced transcriptome approach that measured whole-body expression of 1832 genes, the median tPOD for the 20 PFAS tested was 10 µM. Longer-chain carboxylic acids (12-13 C-F); an eight-C-F dialcohol, N-alkyl sulfonamide; and telomer sulfonic acid were among the most potent PFAS, eliciting gene expression responses at concentrations <1 µM. With a few exceptions, larval fathead minnow tPODs were concordant with those based on whole-transcriptome response in human cell lines. However, larval fathead minnow tPODs were often greater than those for Daphnia magna exposed to the same PFAS. The tPODs overlapped concentrations at which other sublethal effects have been reported in fish (available for 10 PFAS). Nonetheless, fathead minnow tPODs were orders of magnitude higher than aqueous PFAS concentrations detected in tributaries of the North American Great Lakes, suggesting a substantial margin of safety. Overall, results broadly support the use of a fathead minnow larval transcriptomics assay to derive screening-level potency estimates for use in ecological risk-based prioritization. Environ Toxicol Chem 2024;00:1-16. © 2024 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

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.

Using Transcriptomics and Cell Morphology Data in Drug Discovery: The Long Road to Practice

Gene expression and cell morphology data are high-dimensional biological readouts of much recent interest for drug discovery. They are able to describe biological systems in different states (e.g., healthy and diseased), as well as biological systems before and after compound treatment, and they are hence useful for matching both spaces (e.g., for drug repurposing) as well as for characterizing compounds with respect to efficacy and safety endpoints. This Microperspective describes recent advances in this direction with a focus on applied drug discovery and drug repurposing, as well as outlining what else is needed to advance further, with a particular focus on better understanding the applicability domain of readouts and their relevance for decision making, which is currently often still unclear.