Hepatic transcriptomic alterations for N,N-dimethyl-p-toluidine (DMPT) and p-toluidine after 5-day exposure in rats

Diverse N-Oxidation of Primary Aromatic Amines Controlled by Engineered P450 Peroxizyme Variants Facilitated by Dual-Functional Small Molecule

Amine oxidation is an important organic reaction for the production of high-value N-containing compounds. However, it is still challenging to control the reactivity of active N-centered radicals to selectively access N-oxidation products. Herein, this study reports the engineering of cytochrome P450BM3 into multifunctional N-oxidizing enzymes with the assistance of dual-functional small molecules (DFSM) to selectively produce N-oxygenation (i.e., p-nitrosobenzene, p-nitrobenzene, and azoxybenzene) and one-electron oxidation products (i.e., oligomeric quinones and azobenzene) from aromatic amines. The best mutant, F87A/T268V/V78T/A82T, exclusively gives p-nitrosobenzene (up to 98% selectivity), whereas the selectivity for p-nitrobenzene is >99% using the mutant F87A/T268V/A82T/I263L. Crystal structure analysis reveals that key mutations and DFSM exert synergistic effects on catalytic promiscuity by controlling the substrate orientation in active center. This study highlights the potential of DFSM-facilitated P450 peroxygenase and peroxidase for the synthesis of N-containing compounds via the controllable oxidation of aromatic amines, substantially expanding the chemical space of P450 enzymes.

AhR-mediated CYP1A1 and ROS overexpression are involved in hepatotoxicity of decabromodiphenyl ether (BDE-209)

Polybrominated diphenyl ethers (PBDEs) are persistent organic pollutants. They are constantly detected in terrestrial, ocean, and atmospheric systems, and it is of particular concern that these fat-soluble xenobiotics may have a negative impact on human health. This study aimed to evaluate the toxic effect and underlying mechanism of decabromodiphenyl ether (BDE-209) on human liver in a HepG2 cell model. The results showed that BDE-209 significantly induced HepG2 cells apoptosis, increased intracellular reactive oxygen species (ROS), disturbed [Ca ²⁺] homeostasis and mitochondrial membrane potential (MMP), and caused nuclear shrinkage and DNA double-strand breaks. BDE-209 also significantly decreased the activities of antioxidant parameters, superoxide dismutase (SOD), total antioxygenic capacity (T-AOC), glutathione (GSH), and total glutathione (T-GSH). The up-regulation of the Aryl hydrocarbon receptor (AhR)/cytochrome P4501A1 (CYP1A1) signaling pathway indicates that after long-term and high-dose exposure, BDE-209 may be a liver carcinogen. Interestingly, HepG2 cells attempt to metabolize BDE-209 through the Nrf2-mediated antioxidant pathway. These findings help elucidate the mechanisms of BDE-209-induced hepatotoxicity in humans.

Effects of Different Amine Activators on the Monomer Conversion, Biaxial Flexural Strength, and Color Stability of Experimental Provisional Dental Restorations

Objective  The aim was to assess the effect of different amine activators including N, N-dimethyl-p-toluidine (DMPT) or Na-N-tolyglycine glycidyl methacrylate (NTGGMA) on chemical-activated monomer conversion, biaxial flexural strength (BFS), and color stability of composites for provisional dental restorations.

Materials and Methods  Two formulations of composites containing either DMPT (D-temp) or NTGGMA (N-temp) were prepared. The degree of monomer conversion was assessed. The BFS of the materials was tested using the ball-on-ring testing jig. The color difference (∆E ₀₀ ) of the materials after immersion in water was also determined. The commercial comparisons were Unifast (UF), Protemp (PT), Luxacrown, and Luxatemp (LT).

Results  The monomer conversion of D-temp (57.4 ± 1.3%) was comparable to that of N-temp (59.0 ± 1.3%). The conversion of both D-temp and N-temp were higher than that of PT (48.1 ± 3.4%) and LT (48.0 ± 1.6%). BFS of both D-temp (164.2 ± 18.1 MPa) and N-temp (168.6 ± 8.9 MPa) were comparable but higher than that of UF (119.8 ± 13.6 MPa). ∆E ₀₀ of D-temp (2.7 ± 0.7) and N-temp (2.5 ± 0.8) were comparable but higher than that of other commercial materials (0.6–1.2).

Conclusion  The use of DMPT or NTGGMA showed negligible effect on monomer conversion, BFS, and color stability of the experimental provisional restorations. The conversion and BFS of the experimental materials were in the range of that obtained from commercial bis-acryl-based materials. However, the color stability of the experimental materials was lower than that of commercial materials.

The sensitivity of transcriptomics BMD modeling to the methods used for microarray data normalization

Whole-genome expression data generated by microarray studies have shown promise for quantitative human health risk assessment. While numerous approaches have been developed to determine benchmark doses (BMDs) from probeset-level dose responses, sensitivity of the results to methods used for normalization of the data has not yet been systematically investigated. Normalization of microarray data converts raw hybridization signals to expression estimates that are expected to be proportional to the amounts of transcripts in the profiled specimens. Different approaches to normalization have been shown to greatly influence the results of some downstream analyses, including biological interpretation. In this study we evaluate the influence of microarray normalization methods on the transcriptomic BMDs. We demonstrate using in vivo data that the use of alternative pipelines for normalization of Affymetrix microarray data can have a considerable impact on the number of detected differentially expressed genes and pathways (processes) determined to be treatment responsive, which may lead to alternative interpretations of the data. In addition, we found that normalization can have a considerable effect (as much as ~30-fold in this study) on estimation of the minimum biological potency (transcriptomic point of departure). We argue for consideration of alternative normalization methods and their data-informed selection to most effectively interpret microarray data for use in human health risk assessment.

BMDExpress 2: enhanced transcriptomic dose-response analysis workflow

SUMMARY

A new version (version 2) of the genomic dose-response analysis software, BMDExpress, has been created. The software addresses the increasing use of transcriptomic dose-response data in toxicology, drug design, risk assessment and translational research. In this new version, we have implemented additional statistical filtering options (e.g. Williams' trend test), curve fitting models, Linux and Macintosh compatibility and support for additional transcriptomic platforms with up-to-date gene annotations. Furthermore, we have implemented extensive data visualizations, on-the-fly data filtering, and a batch-wise analysis workflow. We have also significantly re-engineered the code base to reflect contemporary software engineering practices and streamline future development. The first version of BMDExpress was developed in 2007 to meet an unmet demand for easy-to-use transcriptomic dose-response analysis software. Since its original release, however, transcriptomic platforms, technologies, pathway annotations and quantitative methods for data analysis have undergone a large change necessitating a significant re-development of BMDExpress. To that end, as of 2016, the National Toxicology Program assumed stewardship of BMDExpress. The result is a modernized and updated BMDExpress 2 that addresses the needs of the growing toxicogenomics user community.

AVAILABILITY AND IMPLEMENTATION

BMDExpress 2 is available at https://github.com/auerbachs/BMDExpress-2/releases.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

PBDE-47 and PBDE mixture (DE-71) toxicities and liver transcriptomic changes at PND 22 after in utero/postnatal exposure in the rat

Pentabromodiphenyl ethers (PBDE) are found in human tissue, in household dust, and in the environment, and a particular concern is the potential for the induction of cancer pathways from these fat-soluble persistent organic pollutants. Only one PBDE cancer study has been conducted and that was for a PBDE mixture (DE-71). Because it is not feasible to test all PBDE congeners in the environment for cancer potential, it is important to develop a set of biological endpoints that can be used in short-term toxicity studies to predict disease outcome after long-term exposures. In this study, PBDE-47 was selected as the test PBDE congener to evaluate and compare toxicity to that of the carcinogenic PBDE mixture. The toxicities of PBDE-47 and the PBDE mixture were evaluated at PND 22 in Wistar Han rat (Crl: WI (Han)) pups after in utero/postnatal exposure (0, 0.1, 15, or 50 mg/kg; dams, GD6-21; pups, PND 12-PND 21; oral gavage daily dosing). By PND 22, PBDE-47 caused centrilobular hypertrophy and fatty change in liver, and reduced serum thyroxin (T4) levels; similar effects were also observed after PBDE mixture exposure. Transcriptomic changes in the liver included induction of cytochrome p450 transcripts and up-regulation of Nrf2 antioxidant pathway transcripts and ABC membrane transport transcripts. Decreases in other transport transcripts (ABCG5 & 8) provided a plausible mechanism for lipid accumulation, characterized by a treatment-related liver fatty change after PBDE-47 and PBDE mixture exposure. The benchmark dose calculation based on liver transcriptomic data was generally lower for PBDE-47 than for the PBDE mixture. The up-regulation of the Nrf2 antioxidant pathway and changes in metabolic transcripts after PBDE-47 and PBDE mixture exposure suggest that PBDE-47, like the PBDE mixture (NTP 2016, TR 589), could be a liver toxin/carcinogen after long-term exposure.