Early Life Stage Bioactivity Assessment of Short-Chain Chlorinated Paraffins at Environmentally Relevant Concentrations by Concentration-Dependent Transcriptomic Analysis of Zebrafish Embryos

Insights into the synergistic toxicity mechanisms caused by nano- and microplastics with triclosan using a dose-dependent functional genomics approach in Saccharomyces cerevisiae

The emergence of polystyrene (PS) nano- and microplastics (NMPs) and triclosan (TCS) as environmental contaminants has raised concerns about their combined toxicities to organisms, but the complex toxicity arising from their interactions and the underlying molecular mechanisms remain obscure to us. In this study, we comprehensively detected the combined toxicity of PS-NMPs and TCS via the dose-dependent yeast functional genomics profiling. Firstly, our findings demonstrated that the combined exposure to PS-NMPs and TCS elicited a synergistic toxic effect in which the toxicity depended on the size of the PS-NMPs. Secondly, we found that TCS exposure, either alone or in combination with PS-NMPs, influenced lipid biosynthetic processes and ATP export pathways, while the unique responsive genes triggered by combined exposure to TCS and PS-NMPs are significantly enriched in mitochondrial translation, ribosomal small subunit assembly, and tRNA wobble uridine modification. Thirdly, our results demonstrated that point of departure (POD) at the pathway level was positively correlated with IC50, and POD was a more sensitive predictor of toxicity than the apical toxicity endpoints. More importantly, our findings suggested that the combined exposure of PS-NMPs in a size-dependent manner not only alleviated the harmful effects of TCS on glycerophospholipid metabolism, but also exacerbated its negative impact on oxidative phosphorylation. Collectively, our study not only provides new insights into the intricate molecular mechanisms that control the combined toxicity of PS-NMPs and TCS, but also confirms the effectiveness of the dose-dependent functional genomics approach in elucidating the molecular mechanisms of the combined toxicity of pollutants.

Developmental toxicity of short-chain chlorinated paraffins on early-stage chicken embryos in a shell-less (ex-ovo) incubation system

Short-chain chlorinated paraffins (SCCPs) are listed as a category of globally controlled persistent organic pollutants (POPs) by the Stockholm Convention in 2017. However, SCCP toxicity, particularly their developmental toxicity in avian embryos, has not been well studied. In this study, we observed the early development of chicken embryos (Gallus gallus domesticus) by applying a shell-less (ex-ovo) incubation system developed in our previous studies. After exposing embryos at Hamburger Hamilton stage (HHS) 1 to SCCPs (control, 0.1% DMSO; SCCPs-L, 200 ng/g; SCCPs-M, 2000 ng/g; SCCPs-H, 20,000 ng/g), we observed the development of embryos from the 3rd to 9th incubation day. Exposure to SCCPs-M and -H induced a significant reduction in survival, with an LD50 of 3100 ng/g on the 9th incubation day. Significant dose-dependent decreases in body length were observed from days 4-9. We also found that SCCPs-H decreased the blood vessel length and branch number on the 4th incubation day. Additionally, SCCPs-H significantly reduced the heart rate on the 4th and 5th incubation days. These findings suggest that SCCPs may have potential of developmental and cardiovascular toxicity during the early stages of chicken embryos. Quantitative PCR of the mRNA of genes related to embryonic development showed that SLC16A10 (a triiodothyronine transporter) level decreased in the SCCPs-H group, showing a significant positive correlation with the body length of embryos. THRA level, a thyroid hormone receptor, was significantly decreased in the SCCPs-H group, whereas that of DIO3 level, a deiodinase was significantly increased. These results suggest that SCCPs exposure induces developmental delays via the thyroxine signaling pathway. Analysis of thyroid hormones (THs) in blood plasma also indicated a significant reduction in thyroxine (T4) levels in the SCCPs-H group on the 9th incubation day of embryos. In conclusion, SCCPs induce developmental toxicity by disrupting thyroid functions at the early-life stage of chicken embryos.

Bioactivity assessment of organophosphate flame retardants via a dose-dependent yeast functional genomics approach

Organophosphate flame retardants (OPFRs) have been widely detected in multiple environment media and have many adverse effects with complex toxicity mechanisms. However, the early molecular responses to OPFRs have not been fully elucidated, thereby making it difficult to assess their risks accurately. In this work, we systematically explored the point of departure (POD) of biological pathways at genome-wide level perturbed by 14 OPFRs with three substituents (alkyl, halogen, and aryl) using a dose-dependent functional genomics approach in Saccharomyces cerevisiae at 24 h exposure. Firstly, our results demonstrated that the overall biological potency at gene level (PODDRG20) ranged from 0.013 to 35.079 μM for 14 OPFRs, especially the tributyl phosphate (TnBP) exhibited the strongest biological potency with the least PODDRG20. Secondly, we found that structural characteristics of carbon number and logKow were significantly negatively correlated with POD, and carbon number and logKow also significantly affected lipid metabolism associated processes. Thirdly, these early biological pathways of OPFRs toxification were found to be involved in lipid metabolism, oxidative stress, DNA damage, MAPK signaling pathway, and amino acid and carbohydrate metabolism, among which the lipid metabolism was the most sensitive molecular response perturbed by most OPFRs. More importantly, we identified one resistant mutant strain with knockout of ERG2 (YMR202W) gene participated in steroid biosynthesis pathway, which can serve as a key yeast strain of OPFRs toxification. Overall, our study demonstrated an effective platform for accurately assessing OPFRs risks and provided a basis for further green OPFRs development.

Characterizing temporal variability and repeatability of dose-dependent functional genomics approach for evaluating triclosan toxification

Dose-dependent functional genomics approach has shown great advantage in identifying the molecular initiating event (MIE) of chemical toxification and yielding point of departure (POD) at genome-wide scale. However, POD variability and repeatability derived from experimental design (settings of dose, replicate number, and exposure time) has not been fully determined. In this work, we evaluated POD profiles perturbed by triclosan (TCS) using dose-dependent functional genomics approach in Saccharomyces cerevisiae at multiple time points (9 h, 24 h and 48 h). The full dataset (total 9 concentrations with 6 replicates per treatment) at 9 h was subsampled 484 times to generate subsets of 4 dose groups (Dose A - Dose D with varied concentration range and spacing) and 5 replicate numbers (2 reps - 6 reps). Firstly, given the accuracy of POD and the experimental cost, the POD profiles from 484 subsampled datasets demonstrated that the Dose C group (space narrow at high concentrations and wide dose range) with three replicates was best choice at both gene and pathway levels. Secondly, the variability of POD was found to be relatively robustness and stability across different experimental designs, but POD was more dependent on the dose range and interval than the number of replicates. Thirdly, MIE of TCS toxification was identified to be the glycerophospholipid metabolism pathway at all-time points, supporting the ability of our approach to accurately recognize MIE of chemical toxification at both short- and long-term exposure. Finally, we identified and validated 13 key mutant strains involved in MIE of TCS toxification, which could serve as biomarkers for TCS exposure. Taken together, our work evaluated the repeatability of dose-dependent functional genomics approach and the variability of POD and MIE of TCS toxification, which will benefit the experimental design for future dose-dependent functional genomics study.

Are New Phthalate Ester Substitutes Safer than Traditional DBP and DiBP? Comparative Endocrine-Disrupting Analyses on Zebrafish Using In Vivo, Transcriptome, and In Silico Approaches

Although previous studies have confirmed the association between phthalate esters (PAEs) exposure and endocrine disorders in humans, few studies to date have systematically assessed the threats of new PAE alternatives to endocrine disruptions. Herein, zebrafish embryos were continuously exposed to two PAEs [di-n-butyl phthalate (DBP) and diisobutyl phthalate (DiBP)], two structurally related alternatives [diiononyl phthalate (DINP) and diisononyl hexahydrophthalate (DINCH)], and two non-PAE substitutes [dipropylene glycol dibenzoate (DGD) and glyceryl triacetate (GTA)], and the endocrine-disrupting effects were investigated during the early stages (8-48 hpf). For five endogenous hormones, including progesterone, testosterone, 17β-estradiol, triiodothyronine (T3), and cortisol, the tested chemicals disturbed the contents of at least one hormone at environmentally relevant concentrations (≤3.9 μM), except DINCH and GTA. Then, the concentration-dependent reduced zebrafish transcriptome analysis was performed. Thyroid hormone (TH)- and androgen/estrogen-regulated adverse outcome pathways (AOPs) were the two types of biological pathways most sensitive to PAE exposure. Notably, six compounds disrupted four TH-mediated AOPs, from the inhibition of deiodinases (molecular initiating event, MIE), a decrease in T3 levels (key event, KE), to mortality (adverse outcome, AO) with the quantitatively linear relationships between MIE-KE (|r| = 0.96, p = 0.002), KE-AO (|r| = 0.88, p = 0.02), and MIE-AO (|r| = 0.89, p = 0.02). Multiple structural analyses showed that benzoic acid is the critical toxicogenic fragment. Our data will facilitate the screening and development of green alternatives.

Toxic effects and toxicological mechanisms of chlorinated paraffins: A review for insight into species sensitivity and toxicity difference

Chlorinated paraffins (CPs), a group of chlorinated alkane mixtures, are frequently detected in various environmental matrices and human bodies. Recently, CPs have garnered considerable attention owing to their potential to induce health hazards in wildlife and human. Several reviews have discussed short-chain CPs (SCCPs) induced ecological risk; however, a comprehensive understanding of the underlying toxic mechanisms and a comparison among SCCPs, medium-, and long-chain CPs (MCCPs and LCCPs, respectively) are yet to be established. This review summarizes the latest research progress on the toxic effects and the underlying molecular mechanisms of CPs. The main toxicity mechanisms of CPs include activation of several receptors, oxidative stress, disturbance of energy metabolism, and inhibition of gap junction-mediated communication. The sensitivity of different species to CP-mediated toxicities varies markedly, with aquatic organisms exhibiting the highest sensitivity to CP-induced toxicity. The toxicity comparison analysis indicated that MCCPs may be unsafe as potential substitutes for SCCPs.

Prediction of zebrafish embryonic developmental toxicity by integrating omics with adverse outcome pathway

New approach methodologies (NAMs), especially omics-based high-throughput bioassays have been developed rapidly, providing rich mechanistic information such as molecular initiation events (MIEs) and (sub)cellular key events (KEs) in adverse outcome pathways (AOPs). However, how to apply the knowledge of MIEs/KEs to predict adverse outcomes (AOs) induced by chemicals represents a new challenge for computational toxicology. Here, an integrated method named ScoreAOP was developed and evaluated to predict chemicals' developmental toxicity for zebrafish embryos by integrating four related AOPs and dose-dependent reduced zebrafish transcriptome (RZT). The rules of ScoreAOP included 1) sensitivity of responsive KEs demonstrated by point of departure of KEs (POD_KE), 2) evidence reliability and 3) distance between KEs and AOs. Moreover, eleven chemicals with different modes of action (MoAs) were tested to evaluate ScoreAOP. Results showed that eight of the eleven chemicals caused developmental toxicity at tested concentration in apical tests. All the tested chemicals' developmental defects were predicted using ScoreAOP, whereas eight out of the eleven chemicals predicted by ScoreMIE which was developed to score MIEs disturbed by chemicals based on in vitro bioassays data. Finally, in terms of mechanism explanation, ScoreAOP clustered chemicals with different MoAs while ScoreMIE failed, and ScoreAOP revealed the activation of aryl hydrocarbon receptor (AhR) plays a significant role in dysfunction of cardiovascular system, resulting in zebrafish developmental defects and mortality. In conclusion, ScoreAOP represents a promising approach to apply mechanism information obtained from omics to predict AOs induced by chemicals.

Cross-Model Comparison of Transcriptomic Dose-Response of Short-Chain Chlorinated Paraffins

Short-chain chlorinated paraffins (SCCPs) have attracted attention because of their toxicological potential in humans and wildlife at environmentally relevant doses. However, limited information is available regarding mechanistic differences across species in terms of the biological pathways that are impacted by SCCP exposure. Here, a concentration-dependent reduced human transcriptome (RHT) approach was conducted to evaluate 15 SCCPs in HepG2 cells and compared with our previous results using a reduced zebrafish transcriptome (RZT) approach in zebrafish embryos (ZFEs). Generally, SCCPs induced a broader suite of biological pathways in ZFEs than HepG2 cells, and all of the 15 SCCPs were more potent in HepG2 cells compared to ZFEs. Despite these general differences, the transcriptional potency of SCCPs in both model systems showed a significant linear relationship (p = 0.0017, r² = 0.57), and the average ratios of transcriptional potency for each SCCP in RZT to that in RHT were ∼100,000. C₁₀H₁₄Cl₈ was the most potent SCCP, while C₁₀H₁₇Cl₅ was the least potent in both ZFEs and HepG2 cells. An adverse outcome pathway network-based analysis demonstrated model-specific responses, such as xenobiotic metabolism that may be mediated by different nuclear receptor-mediated pathways between HepG2 cells (e.g., CAR and AhR activation) and ZFEs (e.g., PXR activation). Moreover, induced transcriptional changes in ZFEs associated with pathways and molecular initiating events (e.g., activation of nicotinic acetylcholine receptor) suggest that SCCPs may disrupt neural development processes. The cross-model comparison of concentration-dependent transcriptomics represents a promising approach to assess and prioritize SCCPs.

Transformation pathways of chlorinated paraffins relevant for remediation: a mini-review

In the past decades, the environmental presence and ecological risks of chlorinated paraffins (CPs), an emerging class of organic halogen compounds, have been receiving increasing attention worldwide. Short-chain CPs (SCCPs) and medium-chain CPs (MCCPs) constitute the important CPs of considerable concern. In this review article, the state-of-the-art research status on the environmental transformation of CPs, including thermal decomposition, photolytic and photocatalytic degradation, biological metabolism, and atmospheric transformation, was summarized and integrated in detail. The degradation efficiency and transformation products of CPs in these environmental processes were evaluated, in which dechlorination was considered as the major reaction pathway. Notably, waste incineration of CPs has been demonstrated to generate a variety of persistent chlorinated aromatic hydrocarbons such as polychlorinated biphenyls and polychlorinated naphthalenes, which have more significant environmental impacts. Additionally, photodegradation and photocatalysis are suggested as the feasible techniques for efficient removal of SCCPs from water matrices. Overall, the current transformation studies of CPs could facilitate the comprehensive understanding of their environmental behaviors and fate as well as the development of promising remediation strategies for pollution control.

A Tiered Approach for Screening and Assessment of Environmental Mixtures by Omics and In Vitro Assays

New methodology approaches with a broad coverage of the biological effects are urgently needed to evaluate the safety of the universe of environmentally relevant chemicals. Here, we propose a tiered approach incorporating transcriptomics and in vitro bioassays to assess environmental mixtures. The mixture samples and the perturbed biological pathways are prioritized by concentration-dependent transcriptome (CDT) and then used to guide the selection of in vitro bioassays for toxicant identification. To evaluate omics' screening capability, we first applied a CDT technique to test mixture samples by HepG2 and MCF7 cells. The effect recoveries of large-volume solid-phase extraction on the overall bioactivity of the mixture were 48.9% in HepG2 and 58.3% in MCF7. The overall bioactivity potencies obtained by transcriptomics were positively correlated with the panel of 8 bioassays among 14 mixture samples combined with the previous data. Transcriptomics could predict their activation status (AUC = 0.783) and the relative potency (p < 0.05) of bioassays for four of the eight receptors (AhR, ER, AR, and Nrf2). Furthermore, the CDT identified other biological pathways perturbated by mixture samples, such as the pathway related to TP53, CAR, FXR, HIF, THRA, etc. Overall, this study demonstrates the potential of concentration-dependent omics for effect-based water quality assessment.

Advances in Studies on Toxic Effects of Short-Chain Chlorinated Paraffins (SCCPs) and Characterization of Environmental Pollution in China

Short-chain chlorinated paraffins (SCCPs) were included in the Stockholm Convention in 2017. SCCPs have persistence, bioaccumulation, long-range environmental mobility and biological toxicity, significant toxicity to aquatic organisms, and potential carcinogenicity. Little study was on the progress research on the current environmental pollution in China. We reviewed the pollution conditions of SCCPs in air, soil, and water and their accumulation in food and organisms in China, especially for the contaminations of aquatic ecosystem. Meanwhile, we summarize the recent studies on the toxic effects and toxicological mechanisms of SCCPs on aquatic organisms and mammals. Finally, the further direction and trends for SCCP research were proposed. More efforts are necessary to conduct a comprehensive risk assessment and evaluate the relative importance of the various exposure routes.