Prediction and classification of the modes of genotoxic actions using bacterial biosensors specific for DNA damages

Single and combined genotoxicity of metals and fluoroquinolones to zebrafish embryos at environmentally relevant concentrations

Fluoroquinolones (FQs) are known to have genotoxicity to aquatic organisms. However, their genotoxicity mechanisms, individually and in combination with heavy metals, are poorly understood. Here, we investigated the single and joint genotoxicity of FQs, ciprofloxacin (CIP) and enrofloxacin (ENR), and metals (Cd and Cu) at environmentally relevant concentrations (0.2 µM) to zebrafish embryos. We found that FQs or/and metals induced genotoxicity (i.e., DNA damage and cell apoptosis) to zebrafish embryos. Compared with their single exposure, the combined exposure of FQs and metals elicited less ROS overproduction but higher genotoxicity, suggesting other toxicity mechanisms may also act in addition to oxidation stress. The upregulation of nucleic acid metabolites and the dysregulation of proteins confirmed the occurrence of DNA damage and apoptosis, and further revealed the inhibition of DNA repair by Cd and binding of DNA or DNA topoisomerase by FQs. This study deepens the knowledge on the responses of zebrafish embryos to exposure of multiple pollutants, and highlights the genotoxicity of FQs and heavy metals to aquatic organisms.

Colorimetric Detection of DNase Type I 3'OH DNA Ends Using an Isothermal Amplification-Assisted Paper-Based Analytical Device

The generation of DNase type I 3'OH DNA ends is closely related to the harm of endogenous reactive oxygen species (ROS) and environmental genotoxic agents. The evaluation of this type of DNA damage plays an important role in clinical intervention and environmental toxicity assessment. Terminal deoxynucleotidyl transferase (TdT)-assisted isothermal amplification (TAIA) offers a facile and versatile way to detect DNase type I 3'OH DNA ends. Its ability of templated-independent isothermal amplification is one unique feature. Here, we reported a paper-based analytical device (PAD) coupled with a smartphone for the detection of DNase type I 3'OH DNA ends using TAIA and colorimetric signal readout. We achieved the integration of cell lysis, DNA extraction, TAIA, horseradish peroxidase (HRP)-enabled colorimetric reaction, and signal readout. This device could achieve a limit of detection of 264 cells with a total assay time of less than 45 min. By combining PAD with a smartphone, the integrated platform could be used for the visual and quantitative analysis of DNA damages with the advantages of ease-to-use, fast response, inexpensive, and instrument free. Furthermore, successful assessment of the genotoxicity in wastewater effluents suggested the great promise of the integrated platform for on-site testing in practical applications.

Machine learning-based biomarkers identification from toxicogenomics - Bridging to regulatory relevant phenotypic endpoints

One of the major challenges in realization and implementations of the Tox21 vision is the urgent need to establish quantitative link between in-vitro assay molecular endpoint and in-vivo regulatory-relevant phenotypic toxicity endpoint. Current toxicomics approach still mostly rely on large number of redundant markers without pre-selection or ranking, therefore, selection of relevant biomarkers with minimal redundancy would reduce the number of markers to be monitored and reduce the cost, time, and complexity of the toxicity screening and risk monitoring. Here, we demonstrated that, using time series toxicomics in-vitro assay along with machine learning-based feature selection (maximum relevance and minimum redundancy (MRMR)) and classification method (support vector machine (SVM)), an "optimal" number of biomarkers with minimum redundancy can be identified for prediction of phenotypic toxicity endpoints with good accuracy. We included two case studies for in-vivo carcinogenicity and Ames genotoxicity prediction, using 20 selected chemicals including model genotoxic chemicals and negative controls, respectively. The results suggested that, employing the adverse outcome pathway (AOP) concept, molecular endpoints based on a relatively small number of properly selected biomarker-ensemble involved in the conserved DNA-damage and repair pathways among eukaryotes, were able to predict both Ames genotoxicity endpoints and in-vivo carcinogenicity in rats. A prediction accuracy of 76% with AUC = 0.81 was achieved while predicting in-vivo carcinogenicity with the top-ranked five biomarkers. For Ames genotoxicity prediction, the top-ranked five biomarkers were able to achieve prediction accuracy of 70% with AUC = 0.75. However, the specific biomarkers identified as the top-ranked five biomarkers are different for the two different phenotypic genotoxicity assays. The top-ranked biomarkers for the in-vivo carcinogenicity prediction mainly focused on double strand break repair and DNA recombination, whereas the selected top-ranked biomarkers for Ames genotoxicity prediction are associated with base- and nucleotide-excision repair The method developed in this study will help to fill in the knowledge gap in phenotypic anchoring and predictive toxicology, and contribute to the progress in the implementation of tox 21 vision for environmental and health applications.

Chromogenic Escherichia coli reporter strain for screening DNA damaging agents

The presence of pollutants in soil and water has given rise to diverse analytical and biological approaches to detect and measure contaminants in the environment. Using bacterial cells as reporter strains represents an advantage for detecting pollutants present in soil or water samples. Here, an Escherichia coli reporter strain expressing a chromoprotein capable of interacting with soil or water samples and responding to DNA damaging compounds is validated. The reporter strain generates a qualitative signal and is based on the expression of the coral chromoprotein AmilCP under the control of the recA promoter. This strain can be used simply by applying soil or water samples directly and rendering activation upon DNA damage. This reporter strain responds to agents that damage DNA (with an apparent detection limit of 1 µg of mitomycin C) without observable response to membrane integrity damage, protein folding or oxidative stress generating agents, in the latter case, DNA damage was observed. The developed reporter strain reported here is effective for the detection of DNA damaging agents present in soils samples. In a proof-of-concept analysis using soil containing chromium, showing activation at 15.56 mg/L of Cr(VI) present in soil and leached samples and is consistent with Cr(III) toxicity at high concentrations (130 µg). Our findings suggest that chromogenic reporter strains can be applied for simple screening, thus reducing the number of samples requiring analytical techniques.

GFP-fused yeast cells as whole-cell biosensors for genotoxicity evaluation of nitrosamines

Nitrosamine compounds, represented by N-nitrosodimethylamine, are regarded as potentially genotoxic impurities (PGIs) due to their hazard warning structure, which has attracted great attention of pharmaceutical companies and regulatory authorities. At present, great research gaps exist in genotoxicity assessment and carcinogenicity comparison of nitrosamine compounds. In this work, a collection of GFP-fused yeast cells representing DNA damage repair pathways were used to evaluate the genotoxicity of eight nitrosamine compounds (10^-6-10⁵ μg/mL). The high-resolution expression profiles of GFP-fused protein revealed the details of the DNA damage repair of nitrosamines. Studies have shown that nitrosamine compounds can cause extensive DNA damage and activate multiple repair pathways. The evaluation criteria based on the total expression level of protein show a good correlation with the mammalian carcinogenicity data TD₅₀, and the yeast cell collection can be used as a potential reliable criterion for evaluating the carcinogenicity of compounds. The assay based on DNA damage pathway integration has high sensitivity and can be used as a supplementary method for the evaluation of trace PGIs in actual production. KEY POINTS: • The genotoxicity mechanism of nitrosamines was systematically studied. • The influence of compound structure on the efficacy of genotoxicity was explored. • GFP-fused yeast cells have the potential to evaluate impurities in production.

Mathematical Modeling Approaches for Assessing the Joint Toxicity of Chemical Mixtures Based on Luminescent Bacteria: A Systematic Review

Developments in industrial applications inevitably accelerate the discharge of enormous substances into the environment, whereas multi-component mixtures commonly cause joint toxicity which is distinct from the simple sum of independent effect. Thus, ecotoxicological assessment, by luminescent bioassays has recently brought increasing attention to overcome the environmental risks. Based on the above viewpoint, this review included a brief introduction to the occurrence and characteristics of toxic bioassay based on the luminescent bacteria. In order to assess the environmental risk of mixtures, a series of models for the prediction of the joint effect of multi-component mixtures have been summarized and discussed in-depth. Among them, Quantitative Structure-Activity Relationship (QSAR) method which was widely applied in silico has been described in detail. Furthermore, the reported potential mechanisms of joint toxicity on the luminescent bacteria were also overviewed, including the Trojan-horse type mechanism, funnel hypothesis, and fishing hypothesis. The future perspectives toward the development and application of toxicity assessment based on luminescent bacteria were proposed.

2,4-Dichlorophenol induces DNA damage through ROS accumulation and GSH depletion in goldfish Carassius auratus

2,4-Dichlorophenol (2,4-DCP) is one of the most abundant chlorophenols in the aquatic environment and has been frequently detected in surface waters. Although ecological and cellular toxicity of 2,4-DCP has aroused the public concern, few reports focus on the genotoxicity, especially on DNA double strand breaks (DSBs), of 2,4-DCP in fish. The present study aims to explore the genotoxic effect of 2,4-DCP on DSBs in goldfish Carassius auratus and to further elucidate its potential mechanism. The results showed that 2,4-DCP significantly induced DSBs (detected by neutral comet assay) in erythrocytes and hepatocytes of goldfish in a dose-dependent manner, indicating a genotoxicity of 2,4-DCP on fish. The total antioxidant capability and the content of reduced glutathione (GSH) were significantly decreased, while the level of reactive oxygen species (ROS) was significantly increased in a dose-dependent manner in erythrocytes and hepatocytes, suggesting an oxidative stress caused by 2,4-DCP in fish. N-acetyl-l-cysteine, a precursor of GSH and a ROS scavenger, significantly impaired 2,4-DCP-induced ROS overproduction and DSBs, which proves that ROS accumulation and GSH depletion are involved in 2,4-DCP-induced DNA damage in fish. Environ. Mol. Mutagen. 59:798-9, 2018. © 2018 Wiley Periodicals, Inc.

Genotoxicity Assessment of Drinking Water Disinfection Byproducts by DNA Damage and Repair Pathway Profiling Analysis

Genotoxicity is considered a major concern for drinking water disinfection byproducts (DBPs). Of over 700 DBPs identified to date, only a small number has been assessed with limited information for DBP genotoxicity mechanism(s). In this study, we evaluated genotoxicity of 20 regulated and unregulated DBPs applying a quantitative toxicogenomics approach. We used GFP-fused yeast strains that examine protein expression profiling of 38 proteins indicative of all known DNA damage and repair pathways. The toxicogenomics assay detected genotoxicity potential of these DBPs that is consistent with conventional genotoxicity assays end points. Furthermore, the high-resolution, real-time pathway activation and protein expression profiling, in combination with clustering analysis, revealed molecular level details in the genotoxicity mechanisms among different DBPs and enabled classification of DBPs based on their distinct DNA damage effects and repair mechanisms. Oxidative DNA damage and base alkylation were confirmed to be the main molecular mechanisms of DBP genotoxicity. Initial exploration of QSAR modeling using moleular genotoxicity end points (PELI) suggested that genotoxicity of DBPs in this study was correlated with topological and quantum chemical descriptors. This study presents a toxicogenomics-based assay for fast and efficient mechanistic genotoxicity screening and assessment of a large number of DBPs. The results help to fill in the knowledge gap in the understanding of the molecular mechanisms of DBP genotoxicity.

Reporter Gene Assays in Ecotoxicology

The need for simple and rapid means for evaluating the potential toxic effects of environmental samples has prompted the development of reporter gene assays, based on tester cells (bioreporters) genetically engineered to report on sample toxicity by producing a readily quantifiable signal. Bacteria are especially suitable to serve as bioreporters owing to their fast responses, low cost, convenient preservation, ease of handling, and amenability to genetic manipulations. Various bacterial bioreporters have been introduced for general toxicity and genotoxicity assessment, and the monitoring of endocrine disrupting and dioxin-like compounds has been mostly covered by similarly engineered eukaryotic cells. Some reporter gene assays have been validated, standardized, and accredited, and many others are under constant development. Efforts are aimed at broadening detection spectra, lowering detection thresholds, and combining toxicity identification capabilities with characterization of the toxic effects. Taking advantage of bacterial robustness, attempts are also being made to incorporate bacterial bioreporters into field instrumentation for online continuous monitoring or on-site spot checks. However, key hurdles concerning test validation, cell preservation, and regulatory issues related to the use of genetically modified organisms still remain to be overcome.

A Quantitative Toxicogenomics Assay for High-throughput and Mechanistic Genotoxicity Assessment and Screening of Environmental Pollutants

The ecological and health concern of mutagenicity and carcinogenicity potentially associated with an overwhelmingly large and ever-increasing number of chemicals demands for cost-effective and feasible method for genotoxicity screening and risk assessment. This study proposed a genotoxicity assay using GFP-tagged yeast reporter strains, covering 38 selected protein biomarkers indicative of all the seven known DNA damage repair pathways. The assay was applied to assess four model genotoxic chemicals, eight environmental pollutants and four negative controls across six concentrations. Quantitative molecular genotoxicity end points were derived based on dose response modeling of a newly developed integrated molecular effect quantifier, Protein Effect Level Index (PELI). The molecular genotoxicity end points were consistent with multiple conventional in vitro genotoxicity assays, as well as with in vivo carcinogenicity assay results. Further more, the proposed genotoxicity end point PELI values quantitatively correlated with both comet assay in human cell and carcinogenicity potency assay in mice, providing promising evidence for linking the molecular disturbance measurements to adverse outcomes at a biological relevant level. In addition, the high-resolution DNA damaging repair pathway alternated protein expression profiles allowed for chemical clustering and classification. This toxicogenomics-based assay presents a promising alternative for fast, efficient and mechanistic genotoxicity screening and assessment of drugs, foods, and environmental contaminants.

Comparative and mechanistic genotoxicity assessment of nanomaterials via a quantitative toxicogenomics approach across multiple species

This study reports a comparative and mechanistic genotoxicity assessment of four engineered nanomaterials (ENMs) across three species, including E. coli, yeast, and human cells, with the aim to reveal the distinct potential genotoxicity mechanisms among the different nanomaterials and their association with physiochemical features. Both the conventional phenotypic alkaline comet test and the newly developed quantitative toxicogenomics assay, that detects and quantifies molecular level changes in the regulation of six DNA damage repair pathways, were employed. The proposed molecular endpoints derived from the toxicogenomics assays, namely TELI (Transcriptional Effect Level Index) and PELI (Protein Effect Level Index), correlated well with the phenotypic DNA damage endpoints from comet tests, suggesting that the molecular genotoxicity assay is suitable for genotoxicity detection. Temporal altered gene or protein expression profiles revealed various potential DNA damage types and relevant genotoxic mechanisms induced by the tested ENMs. nTiO2_a induced a wide spectrum of DNA damage consistently across three species. Three carbon-based ENMs, namely carbon black, single wall carbon nanotube (SWCNT) and fullerene, exhibited distinct, species and ENM property-dependent DNA damage mechanisms. All carbon based ENMs induced relatively weak DNA damage repair response in E. coli, but more severe DNA double strand break in eukaryotes. The differences in cellular structure and defense systems among prokaryotic and eukaryotic species lead to distinct susceptibility and mechanisms for ENM uptake and, thus, varying DNA damages and repair responses. The observation suggested that eukaryotes, especially mammalian cells, are likely more susceptible to genotoxicity than prokaryotes in the ecosystem when exposed to these ENMs.

A dip-stick type biosensor using bioluminescent bacteria encapsulated in color-coded alginate microbeads for detection of water toxicity

The use of genetically engineered bioluminescent bacteria, in which bioluminescence is induced by different modes of toxic action, represents an alternative to acute toxicity tests using living aquatic organisms (plants, vertebrates, or invertebrates) in an aqueous environment.

Serum complement enhances the responses of genotoxin- and oxidative stress-sensitive Escherichia coli bioreporters

Bacterial bioreporters are limited in their abilities to detect large polar molecules due to their membrane selectivity. In this study, the activity of serum complement was used to bypass this undesired selectivity. Initially, the serum complement activity was assessed using the responses of a bacterial bioreporter harboring a recA::luxCDABE transcriptional fusion when exposed to the chemotherapy drug, mitomycin C (MMC). Using 50 °C-treated serum, the limit of detection for this bacterial sensor was lowered by nearly 450-fold, from 31 μg/L to 0.07 μg/L MMC. Real-time quantitative PCR demonstrated that serum-treated cultures responded more strongly to 100 μg/L MMC, with 3.1-fold higher recA expression levels. Subsequent experiments with other bioreporter strains also found enhanced sensitivities and responses. Finally, combining each of the above findings, tests were performed to demonstrate the potential application of the recA::luxCDABE bioreporter within a lab-on-a-CD platform as a point-of-care diagnostic to measure chemotherapeutic drug concentrations within blood.

Analyzing high dimensional toxicogenomic data using consensus clustering

Rapid development of high-throughput toxicogenomics technologies has created new approaches to screen environmental samples for mechanistic toxicity assessment. However, challenges remain in the analysis, especially clustering of the resulting high-dimensional data. Because of the lack of commonly accepted validation methods, it is difficult to compare clustering results between studies or to identify the key experimental or data features that impact the clustering results. We applied consensus clustering (CC), an approach that clusters the input data repeatedly through iterative resampling, and identifies frequently occurring high-confidence clusters. We used CC to analyze a set of high dimensional transcriptomics data with temporal resolution, which were generated using our E. coli whole-cell array system for a diverse variety of toxicants at different dose concentrations. The CC analysis allowed us to evaluate the clustering results' robustness and sensitivity against a number of conditions that represent the common variations in high-throughput experiments, including noisy data, subsets of treatments, subsets of reporter genes, and subsets of time points. We demonstrated the value of utilizing rich time-series data and underscored the importance of careful selection of sampling times for a given experimental system. The results also indicated that temporal data compression using our proposed Transcriptional Effect Level Index (TELI) concept followed by CC largely conserved the cluster resolution. We also found that for our cellular stress response ensemble-based high-throughput transcriptomics assay platform, the size and composition of the reporter gene set are critical factors that affect the resulting coherency of clusters. Taken together, these results demonstrated that more robust consensus clustering such as CC may be valuable in analyzing high-dimensional toxicogenomic data sets.

Randomly distributed arrays of optically coded functional microbeads for toxicity screening and monitoring

We have successfully developed optically coded functional microbeads by co-encapsulating both bioluminescent reporter bacterial cells and fluorescent microspheres within a common alginate microbead. These microbeads harboring an individual self-identification code using fluorescent microspheres could be randomly scattered on any multi-well chip plate as long as the size of the microbeads are made to fit on it with the result that, since cell types are identified on the basis of fluorescent color, microbead arrays were fabricated without pre-designation of an individual well. As an example of this method, five different stress specific bioluminescent bacterial strains, each with a different optical code, were successfully implemented to make five different types of optically coded functional microbeads, with a speed of about 30 microbeads/min. Each functional microbead has a specific stress-specific bacterial strain and, as an identification optical code, one of five optical codes generated from fluorescence microspheres such as yellow, green, red, yellow + green, or no fluorescence. This final randomly scattered functional microbeads array biochip, with a fast fabrication of each chip at every 2 min, successfully demonstrated its ability in toxicity screening and monitoring for samples with a few examples for five different stress chemicals. This simple and fast, but not tedious and complicated procedure should be widely and practically used in making cell array chips for the monitoring of environmental toxicity, new-borne chemicals, pharmaceutical drugs and cosmic rays in the space station or spaceships in future.