Combining time-resolved transcriptomics and proteomics data for Adverse Outcome Pathway refinement in ecotoxicology

Key events relating to homeostasis and regeneration of freshwater planarians (Dugesia Japonica) after exposure to various ZnO-forms

This study aims to investigate the toxicity and underlying mechanisms of ZnO nanoparticles (ZnO NPs), bulk ZnO (ZnO MPs), and zinc ions (Zn2 +) on Dugesia japonica planarians, with a focus on their bioaccumulation, transformation, and associated biological effects. Using advanced techniques such as synchrotron X-ray fluorescence (XRF), X-ray Absorption Near Edge Structure (XANES) and single particle ICP-MS (sp-ICP-MS), we measured the accumulation, distribution, and transformation of these materials in planarians. All treatments caused significant Zn accumulation: ZnO NPs increased Zn by 120-fold, ZnO MPs by 100-fold, and Zn2+ by 430-fold. XANES and sp-ICP-MS analysis confirmed that ZnO NPs remained largely in particulate form (40-60 %) following uptake by planarians. Toxicity tests revealed that all treatments impaired blastema growth, locomotion, stem cell proliferation, differentiation, and neural regeneration. ZnO MPs exhibited higher toxicity than ZnO NPs, while Zn2+ resulted in elevated oxidative stress. ZnO NPs induced severe energy damage and triggered cell apoptosis, whereas ZnO MPs caused more pronounced necrosis cell death. Transcriptomic and proteomic analyses showed that all treatments disrupted pathways related to oxidative stress response, energy metabolism and cell apoptosis. ZnO NPs primarily affected the membrane integrity pathway, ZnO MPs altered cell homeostasis and membrane potential, while Zn2+ exposure triggered metal ion-specific cellular reactions. These molecular and cellular changes collectively explain the observed phenotypic outcomes, which align with the Adverse Outcome Pathway framework. The findings provide insights into the environmental risks of different ZnO forms and highlight their distinct toxicity mechanisms.

Progress in toxicogenomics to protect human health

Toxicogenomics measures molecular features, such as transcripts, proteins, metabolites and epigenomic modifications, to understand and predict the toxicological effects of environmental and pharmaceutical exposures. Transcriptomics has become an integral tool in contemporary toxicology research owing to innovations in gene expression profiling that can provide mechanistic and quantitative information at scale. These data can be used to predict toxicological hazards through the use of transcriptomic biomarkers, network inference analyses, pattern-matching approaches and artificial intelligence. Furthermore, emerging approaches, such as high-throughput dose-response modelling, can leverage toxicogenomic data for human health protection even in the absence of predicting specific hazards. Finally, single-cell transcriptomics and multi-omics provide detailed insights into toxicological mechanisms. Here, we review the progress since the inception of toxicogenomics in applying transcriptomics towards toxicology testing and highlight advances that are transforming risk assessment.

Bioactivity Profiling of Chemical Mixtures for Hazard Characterization

The assessment and regulation of chemical toxicity to protect human health and the environment are done one chemical at a time and seldom at environmentally relevant concentrations. However, chemicals are found in the environment as mixtures, and their toxicity is largely unknown. Understanding the hazard posed by chemicals within the mixture is critical to enforce protective measures. Here, we demonstrate the application of bioactivity profiling of environmental water samples using the sentinel and ecotoxicology model species Daphnia to reveal the biomolecular response induced by exposure to real-world mixtures. We exposed a Daphnia strain to 30 sampled waters of the Chaobai River and measured the gene expression response profiles. Using a multiblock correlation analysis, we establish correlations between chemical mixtures identified in 30 water samples with gene expression patterns induced by these chemical mixtures. We identified 80 metabolic pathways putatively activated by mixtures of inorganic ions, heavy metals, polycyclic aromatic hydrocarbons, industrial chemicals, and a set of biocides, pesticides, and pharmacologically active substances. Our data-driven approach discovered both known bioactivity signatures with previously described modes of action and new pathways linked to undiscovered potential hazards. This study demonstrates the feasibility of reducing the complexity of real-world mixture toxicity to characterize the biomolecular effects of a defined number of chemical components based on gene expression monitoring of the sentinel species Daphnia.

Molecular Mechanism of Indoor Exposure to Airborne Halogenated Flame Retardants TCIPP (Tris(1,3-Dichloro-2-Propyl) Phosphate) and TCEP Tris(2-chloroethyl) Phosphate and Their Hazardous Effects on Biological Systems

TCIPP (tris(1,3-dichloro-2-propyl) phosphate) and TCEP (tris(2-chloroethyl) phosphate) are organophosphate ester flame retardants found in various consumer products, posing significant health and environmental risks through inhalation, ingestion, and dermal exposure. Research reveals these compounds cause oxidative stress, inflammation, endocrine disruption, genotoxicity, neurotoxicity, and potentially hepatotoxicity, nephrotoxicity, cardiotoxicity, developmental, reproductive, and immunotoxicity. This review summarizes the current knowledge on the toxicological mechanisms of TCIPP and TCEP and presents the latest data on their toxicological effects obtained in vitro and in vivo, using omic systems, and on the basis of computational modelling. It also elaborates on the scope of further toxicities and highlights the necessity of ongoing mechanistic research, integration of new technologies, and successful transfer of the acquired knowledge into risk evaluation, policies and regulations, and the creation of safer products. Since flame retardants are already present in homes, schools, offices, and daycare centres, efforts to scale back the exposure to these chemicals, most especially the hazardous ones, must be made to protect human health and the environment. Therefore, effective and timely prevention, based upon a deep knowledge of the entire toxicological profile of these substances, is the only way to face this difficult toxicological issue and provide for a healthy and safe future.

FengycinA-M3 Inhibits Listeria monocytogenes by Binding to Penicillin-Binding Protein 2B Targets to Disrupt Cell Structure

The contamination of food with Listeria monocytogenes threatens food safety and human health, and developing a novel, green, and safe antimicrobial substance will offer a new food preservation strategy. FengycinA-M3 is a novel lipid peptide with low cytotoxicity and resistance and has effective antibacterial activity against L. monocytogenes with a minimum inhibitory concentration (MIC) of 4 µg/mL. Further combined transcriptomics and proteomics analysis yielded 20 differentially expressed genes (DEGs). The MICs of the combined use of FengycinA-M3 and Cefalexin on L. monocytogenes were further determined as FengycinA-M3 (2 µg/mL) and Cefalexin (8 µg/mL) using the checkerboard method. In addition, FengycinA-M3 was found to play a role in delaying pork deterioration. This study explored the inhibitory effect of FengycinA-M3 on L. monocytogenes and its mechanism of action. FengycinA-M3 interacted with penicillin-binding protein 2B on the cell membrane of L. monocytogenes, destroying the permeability of the membrane, causing cell membrane rupture, thereby inhibiting the growth of L. monocytogenes. Overall, FengycinA-M3 is a promising candidate for preventing the emergence and spread of L. monocytogenes with potential applications in food processing.

A Dirt(y) World in a Changing Climate: Importance of Heat Stress in the Risk Assessment of Pesticides for Soil Arthropods

The rise in global temperatures and increasing severity of heat waves pose significant threats to soil organisms, disrupting ecological balances in soil communities. Additionally, the implications of environmental pollution are exacerbated in a warmer world, as changes in temperature affect the uptake, transformation and elimination of toxicants, thereby increasing the vulnerability of organisms. Nevertheless, our understanding of such processes remains largely unexplored. The present study examines the impact of high temperatures on the uptake and effects of the fungicide fluazinam on the springtail Folsomia candida (Collembola, Isotomidae). Conducted under non-optimum but realistic high temperatures, the experiments revealed that increased temperature hampered detoxification processes in F. candida, enhancing the toxic effects of fluazinam. High temperatures and the fungicide exerted synergistic interactions, reducing F. candida's reproduction and increasing adult mortality beyond what would be predicted by simple addition of the heat and chemical effects. These findings highlight the need to reevaluate the current ecological risk assessment and the regulatory framework in response to climate changes. This research enhances our understanding of how global warming affects the toxicokinetics and toxicodynamics (TK-TD) of chemicals in terrestrial invertebrates. In conclusion, our results suggest that adjustments to regulatory threshold values are necessary to address the impact of a changing climate.

Porphyrin metabolism and carbon fixation response of Skeletonema costatum at different growth phases to mixed emerging PFASs at environmental concentrations

Per- and polyfluoroalkyl substances (PFASs), especially as emerging compounds, have been widely detected in coastal seawater. However, the awareness of the interaction between PFASs at environmental concentrations and marine diatoms is still limited. In this study, Skeletonema costatum was exposed to three co-existing PFASs, namely hexafluoropropylene oxide dimer acid (HFPO-DA), 6 : 2 chlorinated polyfluorinated ether sulfonate (Cl-PFAES), and perfluoroethylcyclohexane sulfonate (PFECHS) (15-300 ng L-1 in total), for 14 days. In the 300 ng L-1 test group, the significant down-regulation of chlorophyllide a in porphyrin metabolism, light-harvesting capacity and carbon fixation were the main inhibitory mechanisms of photosynthesis by emerging PFASs at the 14th day compared to the 8th day, which indicated that they may have a shading effect on S. costatum. Additionally, mixed PFASs could also activate nicotinamide adenine dinucleotide phosphate (NADPH) oxidase by up-regulating gene gp91 and down-regulating genes CaM4 and NDPK2 to generate excessive ROS. This resulted in a decrease in the algal biomass, which would further weaken the primary productivity of S. costatum. Our findings illustrated that mixed emerging PFASs at environmental concentrations may interfere with the carbon balance of marine diatoms.

Construction of an adverse outcome pathway framework for arsenic-induced lung cancer using a network-based approach

Environmental pollutants are considered as a cause of tumorigenesis, but approaches to assess their risk of causing tumors remain insufficient. As an alternative approach, the adverse outcome pathway (AOP) framework is used to assess the risk of tumors caused by environmental pollutants. Arsenic is a pollutant associated with lung cancer, but early assessment of lung cancer risk is lacking. Therefore, we applied the AOP framework to arsenic-induced lung cancer. A systematic review revealed increased risks of lung cancer following exposure to a range of arsenic concentrations in drinking water (OR = 1.83, 95 % CI = 1.46-2.30). We obtained, from public databases, genes related to risk of arsenic-induced lung cancer. Then, Cox and LASSO regressions were used to screen target genes from the risk genes. Subsequently, target genes, phenotypes, and pathways were used to construct the computational AOP network, which was determined by Cytoscape to have 156 edges and 45 nodes. Further, target genes, phenotypes, and pathways were used as molecular initiating events and key events to construct the AOP framework depending on upstream and downstream relationships. In the AOP framework, by Weight of Evidence, arsenic exposure increased levels of EGFR, activated the PI3K/AKT pathway, regulated cell proliferation by promoting the G1/S phase transition, and caused generation of lung cancers. External validation was achieved through arsenite-induced, malignant transformed human bronchial epithelial (HBE) cells. Overall, these results, by integration into existing data to construct an AOP framework, provide insights into the assessment of lung cancer risk for arsenic exposure. Special attention needs to be focused on populations with low-dose arsenic exposure.

Transcriptome-centric approach to the derivation of adverse outcome pathway networks of vascular dysfunction after long-term low-level exposure of human endothelial cells to dibutyl phthalate

Dibutyl phthalate (DBP) is an endocrine disruptor that adversely affects reproduction; however, evidence suggests it can also impact other systems, including vascular function. The mechanisms underlying DBP-induced vascular dysfunction, particularly after long-term low-level exposure of endothelial cells to this phthalate, remain largely unknown. To address this gap, we used experimentally derived data on differentially expressed genes (DEGs) obtained after 12 weeks of exposure of human vascular endothelial cells EA.hy926 to the concentrations of DBP to which humans are routinely exposed (10-9 M, 10-8 M, and 10-7 M) and various computational tools and manual data curation to build the first adverse outcome pathway (AOP) network relevant to DBP-induced vascular toxicity. DEGs were used to infer transcription factors (molecular initiating events) and molecular functions and biological processes (key events, KEs) using the Enrichr database. The AOP-helpFinder 2.0, an artificial intelligence-based web tool, was used to link genes and KEs and assign confidence scores to co-occurred terms. We constructed the AOP networks using Cytoscape and then manually arranged KEs to depict the flow of mechanistic information across different levels of network organization. An AOP network was created for each DBP concentration, revealing several distinct high-confidence subnetworks that could be involved in DBP-induced vascular toxicity: the insulin-like growth factor subnetwork for 10-7 M DBP, the CXCL8-dependent chemokine subnetwork for 10-8 M DBP, and the fatty acid subnetwork for 10-9 M DBP. We also developed an AOP network providing a mechanistic insight into the dose-dependent effects of DBP in endothelial cells leading to vascular dysfunction. In summary, we present novel putative AOP networks describing the mechanistic flow of information involved in DBP-induced vascular dysfunction in a long-term low-level exposure scenario.

Proteomic and transcriptomic analyses of Cutibacterium acnes biofilms and planktonic cultures in presence of epinephrine

Transcriptomic and proteomic analysis were performed on 72 h biofilms of the acneic strain Cutibacterium acnes and planktonic cultures in the presence of epinephrine. Epinephrine predominantly downregulated genes associated with various transporter proteins. No correlation was found between proteomic and transcriptomic profiles. In control samples, the expression of 51 proteins differed between planktonic cultures and biofilms. Addition of 5 nM epinephrine reduced this number, and in the presence of 5 µM epinephrine, the difference in proteomic profiles between planktonic cultures and biofilms disappeared. According to the proteomic profiling, epinephrine itself was more effective in the case of C. acnes biofilms and potentially affected the tricarboxylic acid cycle (as well as alpha-ketoglutarate decarboxylase Kgd), biotin synthesis, cell division, and transport of different compounds in C. acnes cells. These findings are consistent with recent research on Micrococcus luteus, suggesting that the effects of epinephrine on actinobacteria may be universal.

Behavioural and physiological impacts of low salinity on the sea urchin Echinus esculentus

Reduced seawater salinity as a result of freshwater input can exert a major influence on the ecophysiology of benthic marine invertebrates, such as echinoderms. While numerous experimental studies have explored the physiological and behavioural effects of short-term, acute exposure to low salinity in echinoids, surprisingly few have investigated the consequences of chronic exposure, or compared the two. In this study, the European sea urchin, Echinus esculentus, was exposed to low salinity over the short term (11‰, 16‰, 21‰, 26‰ and 31‰ for 24 h) and longer term (21, 26 and 31‰ for 25 days). Over the short term, oxygen consumption, activity coefficient and coelomic fluid osmolality were directly correlated with reduced salinity, with 100% survival at ≥21‰ and 0% at ≤16‰. Over the longer term at 21‰ (25 days), oxygen consumption was significantly higher, feeding was significantly reduced and activity coefficient values were significantly lower than at control salinity (31‰). At 26‰, all metrics were comparable to the control by the end of the experiment, suggesting acclimation. Furthermore, beneficial functional resistance (righting ability and metabolic capacity) to acute low salinity was observed at 26‰. Osmolality values were slightly hyperosmotic to the external seawater at all acclimation salinities, while coelomocyte composition and concentration were unaffected by chronic low salinity. Overall, E. esculentus demonstrate phenotypic plasticity that enables acclimation to reduced salinity around 26‰; however, 21‰ represents a lower acclimation threshold, potentially limiting its distribution in coastal areas prone to high freshwater input.