The Precision Toxicology Initiative

The goal of PrecisionTox is to overcome conceptual barriers to replacing traditional mammalian chemical safety testing by accelerating the discovery of evolutionarily conserved toxicity pathways that are shared by descent among humans and more distantly related animals. An international consortium is systematically testing the toxicological effects of a diverse set of chemicals on a suite of five model species comprising fruit flies, nematodes, water fleas, and embryos of clawed frogs and zebrafish along with human cell lines. Multiple forms of omics and comparative toxicology data are integrated to map the evolutionary origins of biomolecular interactions, which are predictive of adverse health effects, to major branches of the animal phylogeny. These conserved elements of adverse outcome pathways (AOPs) and their biomarkers are expect to provide mechanistic insight useful for regulating groups of chemicals based on their shared modes of action. PrecisionTox also aims to quantify risk variation within populations by recognizing susceptibility as a heritable trait that varies with genetic diversity. This initiative incorporates legal experts and collaborates with risk managers to address specific needs within European chemicals legislation, including the uptake of new approach methodologies (NAMs) for setting precise regulatory limits on toxic chemicals.

Predicting Resistance: Quantifying the Relationship between Urban Development, Agricultural Pesticide Use, and Pesticide Resistance in a Nontarget Amphipod

Resistance alleles within the voltage-gated sodium channel (vgsc) have been correlated with pyrethroid resistance in wild populations of the nontarget amphipod, Hyalella azteca from California (CA), U.S.A. In the present study, we expand upon the relationship between land use and the evolution of pesticide resistance in H. azteca to develop a quantitative methodology to target and screen novel populations for resistance allele genotypes in a previously uninvestigated region of the U.S. (New England: NE). By incorporating urban land development and toxicity-normalized agricultural pesticide use indices into our site selection, we successfully identified three amino acid substitutions associated with pyrethroid resistance. One of the resistance mutations has been described in H. azteca from CA (L925I). We present the remaining two (vgsc I936F and I936V) as novel pyrethroid-resistance alleles in H. azteca based on previous work in insects and elevated cyfluthrin resistance in one NE population. Our results suggest that urban pesticide use is a strong driver in the evolution of resistance alleles in H. azteca. Furthermore, our method for resistance allele screening provides an applied framework for detecting ecosystem impairment on a nationwide scale that can be incorporated into ecological risk assessment decisions.

Xenobiotic metabolism and transport in Caenorhabditis elegans

Caenorhabditis elegans has emerged as a major model in biomedical and environmental toxicology. Numerous papers on toxicology and pharmacology in C. elegans have been published, and this species has now been adopted by investigators in academic toxicology, pharmacology, and drug discovery labs. C. elegans has also attracted the interest of governmental regulatory agencies charged with evaluating the safety of chemicals. However, a major, fundamental aspect of toxicological science remains underdeveloped in C. elegans: xenobiotic metabolism and transport processes that are critical to understanding toxicokinetics and toxicodynamics, and extrapolation to other species. The aim of this review was to initially briefly describe the history and trajectory of the use of C. elegans in toxicological and pharmacological studies. Subsequently, physical barriers to chemical uptake and the role of the worm microbiome in xenobiotic transformation were described. Then a review of what is and is not known regarding the classic Phase I, Phase II, and Phase III processes was performed. In addition, the following were discussed (1) regulation of xenobiotic metabolism; (2) review of published toxicokinetics for specific chemicals; and (3) genetic diversity of these processes in C. elegans. Finally, worm xenobiotic transport and metabolism was placed in an evolutionary context; key areas for future research highlighted; and implications for extrapolating C. elegans toxicity results to other species discussed.

Mixed phylogenetic signal in fish toxicity data across chemical classes

Chemical use in society is growing rapidly and is one of the five major pressures on biodiversity worldwide. Since empirical toxicity studies of pollutants generally focus on a handful of model organisms, reliable approaches are needed to assess sensitivity to chemicals across the wide variety of species in the environment. Phylogenetic comparative methods (PCM) offer a promising approach for toxicity extrapolation incorporating known evolutionary relationships among species. If phylogenetic signal in toxicity data is high, i.e., closely related species are more similarly sensitive as compared to distantly related species, PCM could ultimately help predict species sensitivity when toxicity data are lacking. Here, we present the largest ever test of phylogenetic signal in toxicity data by combining phylogenetic data from fish with acute mortality data for 42 chemicals spanning 10 different chemical classes. Phylogenetic signal is high for some chemicals, particularly organophosphate pesticides, but not necessarily for many chemicals in other classes (e.g., metals, organochlorines). These results demonstrate that PCM may be useful for toxicity extrapolation in untested species for those chemicals with clear phylogenetic signal. This study provides a framework for using PCM to understand the patterns and causes of variation in species sensitivity to pollutants.

Functional genomics to assess biological responses to marine pollution at physiological and evolutionary timescales: toward a vision of predictive ecotoxicology

Marine pollution is ubiquitous, and is one of the key factors influencing contemporary marine biodiversity worldwide. To protect marine biodiversity, how do we surveil, document and predict the short- and long-term impacts of pollutants on at-risk species? Modern genomics tools offer high-throughput, information-rich and increasingly cost-effective approaches for characterizing biological responses to environmental stress, and are important tools within an increasing sophisticated kit for surveiling and assessing impacts of pollutants on marine species. Through the lens of recent research in marine killifish, we illustrate how genomics tools may be useful for screening chemicals and pollutants for biological activity and to reveal specific mechanisms of action. The high dimensionality of transcriptomic responses enables their usage as highly specific fingerprints of exposure, and these fingerprints can be used to diagnose environmental problems. We also emphasize that molecular pathways recruited to respond at physiological timescales are the same pathways that may be targets for natural selection during chronic exposure to pollutants. Gene complement and sequence variation in those pathways can be related to variation in sensitivity to environmental pollutants within and among species. Furthermore, allelic variation associated with evolved tolerance in those pathways could be tracked to estimate the pace of environmental health decline and recovery. We finish by integrating these paradigms into a vision of how genomics approaches could anchor a modernized framework for advancing the predictive capacity of environmental and ecotoxicological science.

Evolutionary toxicology: population-level effects of chronic contaminant exposure on the marsh frogs (Rana ridibunda) of Azerbaijan

We used molecular methods and population genetic analyses to study the effects of chronic contaminant exposure in marsh frogs from Sumgayit, Azerbaijan. Marsh frogs inhabiting wetlands in Sumgayit are exposed to complex mixtures of chemical contaminants, including petroleum products, pesticides, heavy metals, and many other industrial chemicals. Previous results documented elevated estimates of genetic damage in marsh frogs from the two most heavily contaminated sites. Based on mitochondrial DNA (mtDNA) control region sequence data, the Sumgayit region has reduced levels of genetic diversity, likely due to environmental degradation. The Sumgayit region also acts as an ecological sink, with levels of gene flow into the region exceeding gene flow out of the region. Additionally, localized mtDNA heteroplasmy and diversity patterns suggest that one of the most severely contaminated sites in Sumgayit is acting as a source of new mutations resulting from an increased mutation rate. This study provides an integrated method for assessing the cumulative population impacts of chronic contaminant exposure by studying both population genetic and evolutionary effects.