The State-of-the Art of Environmental Toxicogenomics: Challenges and Perspectives of "Omics" Approaches Directed to Toxicant Mixtures

Metabolomics perspectives of the ecotoxicological risks of polycyclic aromatic hydrocarbons: A scoping review

Polycyclic Aromatic Hydrocarbons (PAHs) represent persistent environmental pollutants ubiquitously distributed in the environment. Their presence alongside various other contaminants gives rise to intricate interactions, culminating in profound deleterious consequences. The combination effects of different PAH mixtures on biota remains a relatively unexplored domain. Recent studies have harnessed the exceptional sensitivity of metabolomic techniques to unveil the significant ecotoxicological perils of PAH pollution confronting both human populations and ecosystems. This article furnishes a comprehensive overview of current literature focused on the metabolic repercussions stemming from exposure to complex mixtures of PAHs or PAH-pollution sources using metabolomics approaches. These insights are obtained through a wide range of models, including in vitro assessments, animal studies, investigations on human subjects, botanical specimens, and soil environments. The findings underscore that PAH mixtures induce cellular stress responses and systemic effects, leading to metabolic dysregulations in amino acids, carbohydrates, lipids, and other key metabolites (e.g., organic acids, purines), with specific variations observed based on the organism and PAH compounds involved. Additionally, the ecological consequences of PAH pollutants on plant and soil microbial responses are emphasized, revealing significant changes in stress-related metabolites and nutrient cycling in soil ecosystems. The complex interplay of various PAHs and their metabolic effects on several models, as elucidated through metabolomics, highlight the urgency of further research and the need for comprehensive strategies to mitigate the risks posed by these widespread environmental pollutants.

[Advances in the applications of exposomics in the identification of environmental pollutants and their health hazards]

Environmental pollution has become a prominent global problem, and the potential health hazards of pollutants have caused widespread concern. However, revealing the relationship between complex-pollutant exposure and disease development remains an immense challenge. The core of environmental-health research and risk assessment is the identification of contaminants and their effects. Exposomics provides a new approach in the study of the relationship between environmental factors and human health. Both "top-down" and "bottom-up" strategies are employed in exposomics research. The development of new technologies for chemical detection and "multi-omics" has greatly facilitated the implementation of these strategies. Exposomics focuses on the measurement of an individual's lifelong exposure and aims to identify the health effects of such exposure. It involves the dynamic monitoring of external and internal exposure levels at different stages of life through traditional biomonitoring and exposomic methods. It also includes the identification of biomarkers, which indicate specific environmental exposures and the adverse effects of these exposures on health. Compared with traditional environmental-health studies, exposomics can more accurately reflect the diversity of exposure factors such as pollutants, natural factors, and lifestyles in the real environment, as well as the complexity of their in vivo processes and the responses they trigger in an organism. Powerful chemical analytical tools such as high-resolution mass spectrometry (HRMS) are widely used in studies related to the field of exposomics. Liquid chromatography-mass spectrometry (LC-MS) has been applied in the detection and analysis of environmental pollutants. Proteomics and metabolomics, as two important tools for biomarker identification and effects analysis, are widely used to explore the relationship between environmental factors and diseases. Pollutants can lead to pathological changes and even toxic effects by interacting with proteins. In the case of mixed exposure, some contaminants may present joint toxicity. The interaction between contaminants may change their environmental behavior or the amount of each contaminant that enters the human body, which, in turn, affects their health effects.

Mixture effects of pharmaceuticals carbamazepine, diclofenac and venlafaxine on Mytilus galloprovincialis mussel probed by metabolomics and proteogenomics combined approach

Exposure to single molecules under laboratory conditions has led to a better understanding of the mechanisms of action (MeOAs) and effects of pharmaceutical active compounds (PhACs) on non-target organisms. However, not taking the co-occurrence of contaminants in the environment and their possible interactions into account may lead to underestimation of their impacts. In this study, we combined untargeted metabolomics and proteogenomics approaches to assess the mixture effects of diclofenac, carbamazepine and venlafaxine on marine mussels (Mytilus galloprovincialis). Our multi-omics approach and data fusion strategy highlighted how such xenobiotic cocktails induce important cellular changes that can be harmful to marine bivalves. This response is mainly characterized by energy metabolism disruption, fatty acid degradation, protein synthesis and degradation, and the induction of endoplasmic reticulum stress and oxidative stress. The known MeOAs and molecular signatures of PhACs were taken into consideration to gain insight into the mixture effects, thereby revealing a potential additive effect. Multi-omics approaches on mussels as sentinels offer a comprehensive overview of molecular and cellular responses triggered by exposure to contaminant mixtures, even at environmental concentrations.

Spirulina (Arthrospira maxima) mitigates the toxicity induced by a mixture of metal and NSAID in Xenopus laevis

Cadmium (Cd) is often detected in the environment due to its wide use in industry; also, NSAIDs are one of the most consumed pharmaceuticals, particularly diclofenac (DCF). Several studies have reported the presence of both contaminants in water bodies at concentrations ranging from ng L-1 to μg L-1; in addition, they have shown that they can induce oxidative stress in aquatic species and disturb signal transduction, cell proliferation, and intercellular communication, which could lead to teratogenesis. Spirulina has been consumed as a dietary supplement; its antioxidant, anti-inflammatory, neuroprotective, and nutritional properties are well documented. This work aimed to evaluate if Spirulina reduces the damage induced by Cd and DCF mixture in Xenopus laevis at early life stages. FETAX assay was carried out: 20 fertilized oocytes were exposed to seven different treatments on triplicate, control, Cd (24.5 μg L-1), DCF (149 μg L-1), Cd + DCF, Cd+DCF+Spirulina (2 mg L-1), Cd+DCF+Spirulina (4 mg L-1), Cd+DCF+Spirulina (10 mg L-1), malformations, mortality, and growth were evaluated after 96 h, also lipid peroxidation, superoxide dismutase and catalase activity were determined after 192 h. Cd increased DCF mortality, Cd and DCF mixture increased the incidence of malformations as well as oxidative damage; on the other hand, the results obtained show that Spirulina can be used to reduce the damage caused by the mixture of Cd and DCF since it promotes growth, reduce mortality, malformations, and oxidative stress in X. laevis.

Gene expression response of the non-target gastropod Physella acuta to Fenoxycarb, a juvenile hormone analog pesticide

Pesticides are an environmental problem. The search for new pest control methods has focused on compounds with low or no toxic effects in non-target organisms. Analogs of the juvenile hormone (JH) interfere endocrine system of arthropods. However, the lack of effect on non-target species requires confirmation. This article analyzes the impact of Fenoxycarb, an analog of JH, on Physella acuta, an aquatic gastropod. For 1 week, animals were exposed to 0.01, 1, and 100 μg/L and the RNA was isolated to analyze the gene expression by retrotranscription and Real-Time PCR. Forty genes related to the endocrine system, the DNA repair mechanisms, the detoxification mechanisms, oxidative stress, the stress response, the nervous system, hypoxia, energy metabolism, the immune system, and apoptosis were analyzed. Three of the genes, AchE, HSP17.9, and ApA, showed responses to the presence of Fenoxycarb at 1 μg/L, with no statistically significant responses in the rest of the genes and at the remaining concentrations. From the results, it can be concluded that Fenoxycarb shows a weak response at the molecular level in P. acuta in the tested time and concentrations. However, Aplysianin-A, a gene related to immunity, was altered so the long-term effect could be relevant. Therefore, additional research is required to confirm the safety of Fenoxycarb in non-arthropod species in the long term.

Metal mixtures modeling identifies birth weight-associated gene networks in the placentas of children born extremely preterm

Prenatal exposure to toxic metals is linked to numerous adverse birth and later-in-life outcomes. These outcomes are tied to disrupted biological processes in fetal-derived tissues including the placenta and umbilical cord yet the precise pathways are understudied in these target tissues. We set out to examine the relationship between metal concentrations in umbilical cord and altered gene expression networks in placental tissue. These novel relationships were investigated in a subset of the Extremely Low Gestational Age Newborn (ELGAN) cohort (n = 226). Prenatal exposure to 11 metals/metalloids was measured using inductively coupled plasma tandem-mass spectrometry (ICP-MS/MS) in cord tissue, ensuring passage through the placental barrier. RNA-sequencing was used to quantify >37,000 mRNA transcripts. Differentially expressed genes (DEGs) were identified with respect to each metal. Weighted gene co-expression analysis identified gene networks modulated by metals. Two innovative mixtures modeling techniques, namely principal components analysis and quantile-based g-computation, were employed to identify genes/gene networks associated with multi-metal exposure. Individually, lead was associated with the strongest genomic response of 191 DEGs. Joint lead and cadmium exposure was related to 657 DEGs, including DNA Methyl Transferase 1 (DNMT1). These genes were enriched for the Eukaryotic Initiation Factor 2 (EIF2) pathway. Four gene networks, each containing genes within a Nuclear Factor kappa-light-chain-enhancer of Activated B Cells (NF-kB)-mediated network, were significantly increased in average expression level in relation to increases in all metal concentrations. All four of these metal mixture-associated gene networks were negatively correlated with important predictors of neonatal health including birth weight, placenta weight, and fetal growth. Bringing together novel methodologies from epidemiological mixtures analyses and toxicogenomics, applied to a unique cohort of extremely preterm children, the present study highlighted critical genes and pathways in the placenta dysregulated by prenatal metal mixtures. These represent potential mechanisms underlying the developmental origins of metal-induced disease.

After a Century of Research into Environmental Mutagens and Carcinogens, Where Do We Stand?

Cancer is one of the longest-known human diseases, yet only in recent times have we begun to perceive that the percentage of neoplasms caused by environmental factors, lifestyle and chemicals, is likely underestimated. The first medical reports associating cancer with pollutants like tars appeared by the early 20th century, but despite initial evidence relating oncogenesis and chromosomal alterations, only after the structure of DNA had been elucidated in the 1950s have genetic disorders been fully perceived as cause. This led to a growing interest in genotoxic and mutagenic pollutants. Even though we are now familiar with a range of environmental carcinogens spanning between aromatic hydrocarbons and asbestos to radionuclides and forms of carbon nanomaterials, establishing causal networks between pollutants and cancer remains cumbersome. In most part, this is due to the complexity of toxicant matrices, unknown modes-of-action of chemicals or their mixtures, the widening array of novel pollutants plus difficulties in subtracting background effects from true aetiology of disease. Recent advances in analytical chemistry, high-throughput toxicology, next-generation sequencing, computational biology and databases that allocate whole normal and cancer genomes, all indicate that we are on the verge of a new age of research into mechanistic 'oncotoxicology', but how can it impact risk assessment and prevention?

Sublethal Exposure of Per- and Polyfluoroalkyl Substances of Varying Chain Length and Polar Functionality Results in Distinct Metabolic Responses in Daphnia magna

Per- and polyfluoroalkyl substances (PFAS) are a class of persistent organic pollutants used in industrial applications because of their physicochemical properties, which results in their ubiquitous presence across environmental matrices. To date, legacy PFAS have been well studied; however, the concentration of alternative PFAS may exceed the concentration of legacy pollutants, and more information is needed regarding the sublethal toxicity at the molecular level of aquatic model organisms, such as Daphnia magna. Perfluorobutanoic acid (PFBA), perfluorohexanoic acid (PFHxA), perfluorohexanesulfonic acid (PFHxS), and perfluorononanoic acid (PFNA) are four widely detected PFAS alternatives of varying chain length and polar functionality that are quantified in aquatic environments. The present study examines the metabolic perturbations of PFAS with varying chemistries to D. magna using targeted mass spectrometry-based metabolomics. Daphnia were acutely exposed to sublethal concentrations of PFBA, PFHxA, PFHxS, and PFNA before the polar metabolite profile was extracted from single organisms. Multivariate analysis demonstrated significant separation between the sublethal concentrations of PFHxA, PFHxS, and PFNA relative to the controls; in sum, longer chain lengths demonstrated greater overall perturbations to the extracted metabolic profiles. Univariate statistics revealed significant perturbations in the concentrations of several amino acids, nucleotides/nucleosides, and neurotransmitters with exposure to PFAS. These metabolic perturbations are consistent with disruptions in energy metabolism (pantothenate and coenzyme A metabolism, histidine metabolism) and protein synthesis (aminoacyl-transfer RNA biosynthesis and amino acid metabolism), which were identified through biochemical pathway analysis. These results provide evidence that although PFAS chemistry (chain length and polar functional group) invokes unique metabolic responses, there is also an underlying toxic mode of action that is common with select PFAS exposure. Overall, the present study highlights the capabilities of environmental metabolomics to elucidate the molecular-level perturbations of pollutants within the same chemical class to model aquatic organisms, which can be used to prioritize risk assessment of substituted PFAS alternatives. Environ Toxicol Chem 2023;42:242-256. © 2022 SETAC.

Daphnia as a Sentinel Species for Environmental Health Protection: A Perspective on Biomonitoring and Bioremediation of Chemical Pollution

Despite available technology and the knowledge that chemical pollution damages human and ecosystem health, chemical pollution remains rampant, ineffectively monitored, rarely prevented, and only occasionally mitigated. We present a framework that helps address current major challenges in the monitoring and assessment of chemical pollution by broadening the use of the sentinel species Daphnia as a diagnostic agent of water pollution. And where prevention has failed, we propose the application of Daphnia as a bioremediation agent to help reduce hazards from chemical mixtures in the environment. By applying "omics" technologies to Daphnia exposed to real-world ambient chemical mixtures, we show improvements at detecting bioactive components of chemical mixtures, determining the potential effects of untested chemicals within mixtures, and identifying targets of toxicity. We also show that using Daphnia strains that naturally adapted to chemical pollution as removal agents of ambient chemical mixtures can sustainably improve environmental health protection. Expanding the use of Daphnia beyond its current applications in regulatory toxicology has the potential to improve both the assessment and the remediation of environmental pollution.

Comparison of sub-lethal metabolic perturbations of select legacy and novel perfluorinated alkyl substances (PFAS) in Daphnia magna

Per- and polyfluoroalkyl substances (PFAS) are a class of pollutants of concern due to their ubiquitous presence, persistence, and toxicity in aquatic environments. Legacy PFAS pollutants such as perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) have been more widely studied in aquatic environments. However, replacement PFAS, such as ammonium perfluoro (2-methyl-3-oxahexanoate; GenX) are increasingly being detected with little known information surrounding their toxicity. Here, Daphnia magna, a model organism for freshwater ecotoxicology was used to compare the acute sub-lethal toxicity of PFOS, PFOA, GenX, and PFAS mixtures. Using liquid chromatography with tandem mass spectrometry (LC-MS/MS), the targeted polar metabolic profile extracted from single Daphnia was quantified to investigate perturbations in the exposure groups versus the unexposed organisms. Multivariate statistical analyses demonstrated significant non-monotonic separation in PFOA, GenX, and PFAS mixture exposures. Sub-lethal exposure to concentrations of PFOS did not lead to significant separation in multivariate analyses. Univariate statistics and pathway analyses were used to elucidate the mode of action of PFAS exposure. Exposure to all individual PFAS led to significant perturbations in many amino acids including cysteine, histidine, tryptophan, glycine, and serine. These perturbations are consistent with biochemical pathway disruptions in the pantothenate and Coenzyme A (CoA) biosynthesis, thiamine metabolism, histidine metabolism, and aminoacyl-tRNA biosynthesis pathways. Overall, the collected metabolomic data is consistent with disruptions in energy metabolism and protein synthesis as the primary mode of action of sub-lethal PFAS exposure. Secondary modes of action among individual pollutant exposures demonstrated that the structural properties (carboxylic acid vs. sulfonic acid group) may play a role in the metabolic perturbations observed. Sub-lethal exposure to PFAS mixtures highlighted a mixed response when compared to the individual pollutants (PFOS, PFOA, and GenX). Overall, this study emphasizes the niche capability of environmental metabolomics to differentiate secondary modes of action from metabolic perturbations in both single pollutant and pollutant mixtures within the same chemical class.

Mixed Contaminants: Occurrence, Interactions, Toxicity, Detection, and Remediation

The ever-increasing rate of pollution has attracted considerable interest in research. Several anthropogenic activities have diminished soil, air, and water quality and have led to complex chemical pollutants. This review aims to provide a clear idea about the latest and most prevalent pollutants such as heavy metals, PAHs, pesticides, hydrocarbons, and pharmaceuticals—their occurrence in various complex mixtures and how several environmental factors influence their interaction. The mechanism adopted by these contaminants to form the complex mixtures leading to the rise of a new class of contaminants, and thus resulting in severe threats to human health and the environment, has also been exhibited. Additionally, this review provides an in-depth idea of various in vivo, in vitro, and trending biomarkers used for risk assessment and identifies the occurrence of mixed contaminants even at very minute concentrations. Much importance has been given to remediation technologies to understand our current position in handling these contaminants and how the technologies can be improved. This paper aims to create awareness among readers about the most ubiquitous contaminants and how simple ways can be adopted to tackle the same.

Omics-based ecosurveillance for the assessment of ecosystem function, health, and resilience

Current environmental monitoring efforts often focus on known, regulated contaminants ignoring the potential effects of unmeasured compounds and/or environmental factors. These specific, targeted approaches lack broader environmental information and understanding, hindering effective environmental management and policy. Switching to comprehensive, untargeted monitoring of contaminants, organism health, and environmental factors, such as nutrients, temperature, and pH, would provide more effective monitoring with a likely concomitant increase in environmental health. However, even this method would not capture subtle biochemical changes in organisms induced by chronic toxicant exposure. Ecosurveillance is the systematic collection, analysis, and interpretation of ecosystem health-related data that can address this knowledge gap and provide much-needed additional lines of evidence to environmental monitoring programs. Its use would therefore be of great benefit to environmental management and assessment. Unfortunately, the science of ‘ecosurveillance’, especially omics-based ecosurveillance is not well known. Here, we give an overview of this emerging area and show how it has been beneficially applied in a range of systems. We anticipate this review to be a starting point for further efforts to improve environmental monitoring via the integration of comprehensive chemical assessments and molecular biology-based approaches. Bringing multiple levels of omics technology-based assessment together into a systems-wide ecosurveillance approach will bring a greater understanding of the environment, particularly the microbial communities upon which we ultimately rely to remediate perturbed ecosystems.

Thyroid Hormone Disruption by Organophosphate Esters Is Mediated by Nuclear/Membrane Thyroid Hormone Receptors: In Vitro, In Vivo, and In Silico Studies

Earlier mechanistic studies of many prohibited flame retardants (FRs) highlighted their thyroid hormone-disrupting activity through nuclear thyroid hormone receptors (nTRs), whereas some alternative FRs such as organophosphate esters (OPEs) exerted weak nTR-disrupting effects. However, an increasing number of studies have revealed that OPEs also exert thyroid hormone-disrupting effects, and the underlying mechanism is unclear. Herein, the thyroid hormone-disrupting effects and mechanisms of 8 typical OPEs were investigated using integrated in vitro, in vivo, and in silico assays. All tested chemicals competitively bound to the membrane thyroid hormone receptor (mTR) [the 20% relative inhibitory concentration (RIC20): (3.5 ± 0.2) × 10¹ to (4.9 ± 1.0) × 10⁷ nM], and Cl-OPEs and alkyl-OPEs had lower RIC20 values. In contrast, only 4 OPEs showed nTR antagonistic activities at higher concentrations [≥ (4.8 ± 0.8) × 10³ nM]. Cl-OPEs and alkyl-OPEs preferentially interacted with mTR. Molecular docking illustrated that OPEs docked into mTRs, consistent with the competitive binding assay. In vivo analyses of zebrafish embryonic development confirmed that tris(1,3-dichloro-2-propyl) phosphate induced inappropriate expression of proteins, and these protein interactions might be associated with mTR according to the quantitative proteomic analysis. Based on the results, mTR might play a critical role in mediating the thyroid hormone-disrupting effects of OPEs.

A drug discovery approach based on comparative transcriptomics between two toxin-secreting marine annelids: Glycera alba and Hediste diversicolor

While Glycera alba secretes neurotoxins, Hediste diversicolor may secrete fewer toxins with a broader action. Transcriptomics and human interactome-directed analysis unraveled promising candidates for biomedical applications from either annelid.

Current aspects of DNA damage and repair in ecotoxicology: a mini-review

The preservation of genomic stability against environmental stressors is a major adaptive feature that is well-conserved among both prokaryotes and eukaryotes. The complex and fine-tuned mechanisms that evolved to repair DNA following exposure to radiation and chemical insult are also the first line of defence against genotoxicants. Consequently, impairing the DNA damage response leads to accumulation of genomic lesions that may ultimately lead to cell death, mutagenesis and even teratogenesis and neoplasia. Understanding how pollutants affect DNA repair machinery is thus paramount to interpret the often unclear or contradictory findings from genotoxicity assessment. The main purpose of the present mini-review is to contribute to the slowly-growing awareness among ecotoxicologists that DNA damage is not limited to direct interactions of noxious compounds with the DNA molecule. Despite the limited number of studies addressing this issue in the field, special modifications of methods for genotoxicity assessment, combined with state-of-the-art molecular tools, are beginning to show promising results in the unravelling of DNA repair proteins, genes and networks in non-conventional model organisms. I will review the essentials of the most important DNA repair pathways and discuss methods and approaches that can assist steering ecotoxicologists towards a better understanding of genotoxic hazard and risk.

Prediction of adverse effects of effluents containing phenolic compounds in the Ba River on the ovary of fish (Hemiculter leucisculus) using transcriptomic and metabolomic analyses

The aim of this work was to evaluate the endocrine disrupting effects on the ovarian development of sharpbelly (Hemiculter leucisculus) caused by effluents containing phenolic compounds. This was achieved using integrated transcriptomic and metabolomic analyses, along with histopathological examinations. Sharpbelly, an indigenous freshwater fish widely distributed in East Asia, were collected by pole fishing from three sampling sites in the Ba River. These sampling sites include a mid-stream site near a wastewater outfall and a reference site located upstream and a far field comparison site located downstream. In sharpbelly collected near the wastewater discharge, the oocyte development was activated, compared to the other two sites. Histopathological alterations in the fish ovaries were likely due to the upregulated steroid hormone biosynthesis process, as suggested by the differentially expressed genes (e.g., hsd3b, hsd17b1) and differentially accumulated metabolites (e.g., pregnenolone). Additionally, under the stress of effluents containing phenolic compounds, genes related to the signaling pathways for oxidative phosphorylation and leukocyte transendothelial migration were dysregulated, suggesting the potential induction of inflammation and several ovarian diseases. Overall, these findings suggest that effluents containing phenolic compounds influence ovary development and reproductive function of female sharpbelly. Whether there is any resulting dysfunction of folliculogenesis, abnormality of ovulation, production of premature eggs and/or potential induction of ovarian cancers remains to be determined by further studies, for a better evaluation on effluents containing phenolic compounds to the fish fertility and the health of their offspring, and even the stability of the wild fish population. Notably, the integration of transcriptomics and metabolomics can complement the routine chemical analysis to comprehensively monitor the effects of wastewater treatment plant effluents on the health of wild fish.

Pollution Biomarkers in the Framework of Marine Biodiversity Conservation: State of Art and Perspectives

Marine biodiversity is threatened by several anthropogenic pressures. Pollution deriving from the discharge of chemical contaminants in the sea represents one of the main threats to the marine environment, influencing the health of organisms, their ability to recover their homeostatic status, and in turn endangering biodiversity. Molecular and cellular responses to chemical pollutants, known as biomarkers, are effect-based methodologies useful for detecting exposure and for assessing the effects of pollutants on biota in environmental monitoring. The present review analyzes and discusses the recent literature on the use of biomarkers in the framework of biodiversity conservation. The study shows that pollution biomarkers can be useful tools for monitoring and assessment of pollution threat to marine biodiversity, both in the environmental quality monitoring of protected areas and the assessment of the health status of species at risk. Moreover, key areas of the research that need further development are suggested, such as the development of omics-based biomarkers specifically addressed to conservation purposes and their validation in the field, the extension of the biomarker study to a wider number of endangered species, and the development of organic guidelines for the application of the biomarker approach in support to conservation policies and management.

Recent Advances in Immunosafety and Nanoinformatics of Two-Dimensional Materials Applied to Nano-imaging

Two-dimensional (2D) materials have emerged as an important class of nanomaterials for technological innovation due to their remarkable physicochemical properties, including sheet-like morphology and minimal thickness, high surface area, tuneable chemical composition, and surface functionalization. These materials are being proposed for new applications in energy, health, and the environment; these are all strategic society sectors toward sustainable development. Specifically, 2D materials for nano-imaging have shown exciting opportunities in in vitro and in vivo models, providing novel molecular imaging techniques such as computed tomography, magnetic resonance imaging, fluorescence and luminescence optical imaging and others. Therefore, given the growing interest in 2D materials, it is mandatory to evaluate their impact on the immune system in a broader sense, because it is responsible for detecting and eliminating foreign agents in living organisms. This mini-review presents an overview on the frontier of research involving 2D materials applications, nano-imaging and their immunosafety aspects. Finally, we highlight the importance of nanoinformatics approaches and computational modeling for a deeper understanding of the links between nanomaterial physicochemical properties and biological responses (immunotoxicity/biocompatibility) towards enabling immunosafety-by-design 2D materials.

The chemical defensome of five model teleost fish

How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal- and heat-responsive genes, and is collectively known as the chemical defensome. Teleost fish is the largest group of vertebrate species and can provide valuable insights into the evolution and functional diversity of defensome genes. We have previously shown that the xenosensing pregnane x receptor (pxr, nr1i2) is lost in many teleost species, including Atlantic cod (Gadus morhua) and three-spined stickleback (Gasterosteus aculeatus), but it is not known if compensatory mechanisms or signaling pathways have evolved in its absence. In this study, we compared the genes comprising the chemical defensome of five fish species that span the teleosteii evolutionary branch often used as model species in toxicological studies and environmental monitoring programs: zebrafish (Danio rerio), medaka (Oryzias latipes), Atlantic killifish (Fundulus heteroclitus), Atlantic cod, and three-spined stickleback. Genome mining revealed evolved differences in the number and composition of defensome genes that can have implication for how these species sense and respond to environmental pollutants, but we did not observe any candidates of compensatory mechanisms or pathways in cod and stickleback in the absence of pxr. The results indicate that knowledge regarding the diversity and function of the defensome will be important for toxicological testing and risk assessment studies.

Analysis of urinary metabolites of polycyclic aromatic hydrocarbons in precarious workers of highly exposed occupational scenarios in Mexico

Exposure to polycyclic aromatic hydrocarbons (PAHs) is a risk factor for human health. Workers are a vulnerable group due to their high exposure and therefore require special attention to mitigation measurements; however, some groups of workers are especially vulnerable, precarious workers. The objective of this research was to evaluate mixtures of hydroxylated PAHs (OH-PAHs) in precarious workers in Mexico. The following activities were evaluated: (i) brickmakers (TER), stonemasons (ESC), indigenous workers (TOC) and mercury miners (CAM). Ten OH-PAHS were analyzed: 1-hydroxynaphtalene and 2-hydroxynaphtalene; 2-,3- and 9-hydroxyfluorene; 1-,2-,3- and 4-hydroxyphenanthrene; and 1-hydroxypyrene in urine by GC-MS, chemical fingerprints of the sites were established by multivariate analysis. One hundred forty-nine precarious workers participated in the study. The populations presented total OH-PAHs concentrations of 9.20 (6.65-97.57), 14.8 (9.32-18.85), 15.7 (6.92-195.0), and 101.2 (8.02-134.4) μg/L for CAM, ESC, TER, and TOC, respectively (median (IQR)). The results of the multivariate analysis indicate that the indigenous population presented a different fingerprint compared to the three scenarios. The chemical fingerprints among the brickmakers and mercury mining population were similar. The results of the concentrations were similar and in some metabolites higher than workers in occupations classified as carcinogenic by the IARC; therefore, the control of exposure in these occupations acquires great importance and surveillance through biological monitoring of OH-PAHs should be applied to better estimate exposure in these working populations.

Proteomics in systems toxicology

Proteins are the ultimate product of gene expression. As they hinge between gene transcription and phenotype, they offer a more realistic perspective of toxicopathic effects, responses and even susceptibility to insult than targeting genes and mRNAs while dodging some inter-individual variability that hinders measuring downstream endpoints like metabolites or enzyme activity. Toxicologists have long focused on proteins as biomarkers but the advent of proteomics shifted risk assessment from narrow single-endpoint analyses to whole-proteome screening, enabling deriving protein-centric adverse outcome pathways (AOPs), which are pivotal for the derivation of Systems Biology informally named Systems Toxicology. Especially if coupled pathology, the identification of molecular initiating events (MIEs) and AOPs allow predictive modeling of toxicological pathways, which now stands as the frontier for the next generation of toxicologists. Advances in mass spectrometry, bioinformatics, protein databases and top-down proteomics create new opportunities for mechanistic and effects-oriented research in all fields, from ecotoxicology to pharmacotoxicology.

CTD Anatomy: analyzing chemical-induced phenotypes and exposures from an anatomical perspective, with implications for environmental health studies

The Comparative Toxicogenomics Database (CTD) is a freely available public resource that curates and interrelates chemical, gene/protein, phenotype, disease, organism, and exposure data. CTD can be used to address toxicological mechanisms for environmental chemicals and facilitate the generation of testable hypotheses about how exposures affect human health. At CTD, manually curated interactions for chemical-induced phenotypes are enhanced with anatomy terms (tissues, fluids, and cell types) to describe the physiological system of the reported event. These same anatomy terms are used to annotate the human media (e.g., urine, hair, nail, blood, etc.) in which an environmental chemical was assayed for exposure. Currently, CTD uses more than 880 unique anatomy terms to contextualize over 255,000 chemical-phenotype interactions and 167,000 exposure statements. These annotations allow chemical-phenotype interactions and exposure data to be explored from a novel, anatomical perspective. Here, we describe CTD's anatomy curation process (including the construction of a controlled, interoperable vocabulary) and new anatomy webpages (that coalesce and organize the curated chemical-phenotype and exposure data sets). We also provide examples that demonstrate how this feature can be used to identify system- and cell-specific chemical-induced toxicities, help inform exposure data, prioritize phenotypes for environmental diseases, survey tissue and pregnancy exposomes, and facilitate data connections with external resources. Anatomy annotations advance understanding of environmental health by providing new ways to explore and survey chemical-induced events and exposure studies in the CTD framework.

Transcriptomics analysis of hepatotoxicity induced by the pesticides imazalil, thiacloprid and clothianidin alone or in binary mixtures in a 28-day study in female Wistar rats

Co-occurrence of pesticide residues in food commodities raises a potential safety issue as their mixture effects on human health are largely unknown. In a previous study, we reported the toxicological effects (pathology and histopathology) of imazalil (IMZ), thiacloprid (THI), and clothianidin (CTD) alone and in binary mixtures in a 28-day oral gavage study in female Wistar rats. Five dose levels (up to 350 mg/kg body weight/day) ranging from a typical toxicological reference value to a clear effect dose were applied. In the present study, we undertook a transcriptomics analysis of rat livers by means of total RNA sequencing (RNA-Seq). Bioinformatic data analysis involving Ingenuity Pathway Analysis (IPA) was used to gain mechanistic information on hepatotoxicity-related pathways affected after treatment with the pesticides, alone and in mixtures. Our data show that 2986 genes were differentially regulated by CTD while IMZ and THI had effects on 194 and 225 genes, respectively. All three individual compounds shared a common subset of genes whose network is associated with xenobiotic metabolism and nuclear receptor activation. Similar networks were retrieved for the mixtures. Alterations in the expression of individual genes were in line with the assumption of dose addition. Our results bring new insight into the hepatotoxicity mechanisms of IMZ, THI, and CTD and their mixtures.

Environmental effects of offshore produced water discharges: A review focused on the Norwegian continental shelf

Produced water (PW), a large byproduct of offshore oil and gas extraction, is reinjected to formations or discharged to the sea after treatment. The discharges contain dispersed crude oil, polycyclic aromatic hydrocarbons (PAHs), alkylphenols (APs), metals, and many other constituents of environmental relevance. Risk-based regulation, greener offshore chemicals and improved cleaning systems have reduced environmental risks of PW discharges, but PW is still the largest operational source of oil pollution to the sea from the offshore petroleum industry. Monitoring surveys find detectable exposures in caged mussel and fish several km downstream from PW outfalls, but biomarkers indicate only mild acute effects in these sentinels. On the other hand, increased concentrations of DNA adducts are found repeatedly in benthic fish populations, especially in haddock. It is uncertain whether increased adducts could be a long-term effect of sediment contamination due to ongoing PW discharges, or earlier discharges of oil-containing drilling waste. Another concern is uncertainty regarding the possible effect of PW discharges in the sub-Arctic Southern Barents Sea. So far, research suggests that sub-arctic species are largely comparable to temperate species in their sensitivity to PW exposure. Larval deformities and cardiac toxicity in fish early life stages are among the biomarkers and adverse outcome pathways that currently receive much attention in PW effect research. Herein, we summarize the accumulated ecotoxicological knowledge of offshore PW discharges and highlight some key remaining knowledge needs.

Are we forgetting the "proteomics" in multi-omics ecotoxicology?

Proteomics plays a significant role in discerning the effects of chemical exposures in animal taxa. Multi-omics applications have become more pervasive in toxicology, however questions remain about whether proteomics is being utilized by the community to its full potential - are we placing too much stock in transcriptomics and other omics approaches for developing adverse outcome pathways? Proteins are more relevant than transcripts because they are direct mediators of the resulting phenotype. There is also rarely perfect stoichiometry between transcript and protein abundance and transcript abundance may not accurately predict physiologic response. Proteins direct all levels of phenotype: structural proteins dictate physical form, enzymes catalyze biochemical reactions, and proteins act as signaling proteins, antibodies, transporters, ion pumps, and transcription factors to control gene expression. Molecular initiating events (MIEs) of AOPs predominantly occur at the level of the protein (e.g. ligand-receptor binding) and proteomics can elucidate novel MIEs and mapping KEs in AOPs. This critical review highlights the need for proteomics in multi-omics studies in environmental toxicology and outlines steps required for inclusion and wider acceptance in chemical risk assessment. We also present case studies of multi-omics approaches that utilize proteomics and discuss some of the challenges and opportunities for proteomics in comparative ecotoxicology. Our intention is not to minimize the importance of other omics technologies, as each has strengths and limitations, but rather to encourage researchers to consider proteomics-based methods in multi-omics studies and AOP development.