Characterization of diversity in toxicity mechanism using in vitro cytotoxicity assays in quantitative high throughput screening

Toxicity of lanthanide coagulants assessed using four in vitro bioassays

Rare earth element (REE) coagulants are prime contenders in wastewater treatment plants to remove phosphorus; unlike typical coagulants, they are not affected by pH. However, the use of REEs in wastewater treatment could mean increased human exposure to lanthanides (Ln) through wastewater effluent discharge to the environment or through water reuse. Information on the toxicity of lanthanides is scarce and, where available, there are conflicting views. Using in vitro bioassays, we assessed lanthanide toxicity by evaluating four relevant endpoints: the change in mitochondrial membrane potential (Δψm), intracellular adenosine triphosphate (I-ATP), genotoxicity, and cell viability. At less than 5000 μmol-Ln³⁺/L, lanthanides increased the Δψm, while above 5000 μmol-Ln³⁺/L, the Δψm level plummeted. The measure of I-ATP indicated constant levels of ATP up to 250 μmol-Ln³⁺/L, above which the I-ATP decreased steadily; the concentration of La, Ce, Gd, and Lu that triggered half of the cells to become ATP-inactive is 794, 1505, 1488, 1115 μmol-Ln³⁺/L, respectively. Although La and Lu accelerated cell death in shorter studies (24 h), chronic studies using three cell growth cycles showed cell recovery. Lanthanides exhibited antagonistic toxicity at less than 1000 μmol-Ln³⁺/L. However, the introduction of heavy REEs in a solution amplified lanthanide toxicity. Tested lanthanides appear to pose little risk, which could pave the way for lanthanide application in wastewater treatment.

Environmental Toxicology Assays Using Organ-on-Chip

Adverse effects of environmental toxicants to human health have traditionally been assayed using in vitro assays. Organ-on-chip (OOC) is a new platform that can bridge the gaps between in vitro assays (or 3D cell culture) and animal tests. Microenvironments, physical and biochemical stimuli, and adequate sensing and biosensing systems can be integrated into OOC devices to better recapitulate the in vivo tissue and organ behavior and metabolism. While OOCs have extensively been studied for drug toxicity screening, their implementation in environmental toxicology assays is minimal and has limitations. In this review, recent attempts of environmental toxicology assays using OOCs, including multiple-organs-on-chip, are summarized and compared with OOC-based drug toxicity screening. Requirements for further improvements are identified and potential solutions are suggested.

Massive-scale biological activity-based modeling identifies novel antiviral leads against SARS-CoV-2

The recent global pandemic caused by the new coronavirus SARS-CoV-2 presents an urgent need for new therapeutic candidates. While the importance of traditional in silico approaches such as QSAR in such efforts in unquestionable, these models fundamentally rely on structural similarity to infer biological activity and are thus prone to becoming trapped in the very nearby chemical spaces of already known ligands. For novel and unprecedented threats such as COVID-19 much faster and efficient paradigms must be devised to accelerate the identification of new chemical classes for rapid drug development. Here we report the development of a new biological activity-based modeling (BABM) approach that builds on the hypothesis that compounds with similar activity patterns tend to share similar targets or mechanisms of action. In BABM, compound activity profiles established on massive scale across multiple assays are used as signatures to predict compound activity in a new assay or against a new target. We first trained and validated this approach by identifying new antiviral lead candidates for Zika and Ebola based on data from ~0.5 million compounds screened against ~2,000 assays. BABM models were then applied to predict ~300 compounds not previously reported to have activity for SARS-CoV-2, which were then tested in a live virus assay with high (>30%) hit rates. The most potent compounds showed antiviral activities in the nanomolar range. These potent confirmed compounds have the potential to be further developed in novel chemical space into new anti-SARS-CoV-2 therapies. These results demonstrate unprecedented ability using BABM to predict novel structures as chemical leads significantly beyond traditional methods, and its application in rapid drug discovery response in a global public health crisis.

Beneficial Effects of Sideritis scardica and Cichorium spinosum against Amyloidogenic Pathway and Tau Misprocessing in Alzheimer's Disease Neuronal Cell Culture Models

BACKGROUND

Natural products are a significantly underutilized source of potential treatments against human disease. Alzheimer's disease (AD) is a prime example of conditions that could be amenable to such treatments as suggested by recent findings.

OBJECTIVE

Aiming to identify novel potentially therapeutic approaches against AD, we assessed the effects of Cichorium spinosum and Sideritis scardica extracts, both distinct components of the Mediterranean diet.

METHODS/RESULTS

After the detailed characterization of the extracts' composition using LC-HRMS methods, they were evaluated on two AD neuronal cell culture models, namely the AβPP overexpressing SH-SY5Y-AβPP and the hyperphosphorylated tau expressing PC12-htau. Initially their effect on cell viability of SH-SY5Y and PC12 cells was examined, and subsequently their downstream effects on AβPP and tau processing pathways were investigated in the SH-SY5Y-AβPP and PC12-htau cells. We found that the S. scardica and C. spinosum extracts have similar effects on tau, as they both significantly decrease total tau, the activation of the GSK3β, ERK1 and/or ERK2 kinases of tau, as well as tau hyperphosphorylation. Furthermore, both extracts appear to promote AβPP processing through the alpha, non-amyloidogenic pathway, albeit through partly different mechanisms.

CONCLUSIONS

These findings suggest that C. spinosum and S. scardica could have a notable potential in the prevention and/or treatment of AD, and merit further investigations at the in vivo level.

Assessment of the cytotoxicity and genotoxicity of homosalate in MCF-7

BACKGROUND

UV filters should be determined a strict toxicological safety prior to approval. Homosalate (HMS) is one of the most widely used organic UV filter. HMS accumulates in aquatic biota ecosystems and humans through the food chain; therefore, it is important to consider the effects on health and know its mechanisms of action.

AIMS

The study aimed to evaluate the cytotoxic and genotoxic effects of HMS in MCF-7 cell line.

METHODS

Cell viability was examined by the 3-(4,5-dimethylthiazol-2-yl)2,5-diphenyl tetrazolium bromide (MTT) and cell membrane integrity by the lactate dehydrogenase release assays (LDH), and genotoxicity by using the micronucleus test at 250, 500, 750, 1000, 1500, and 2000 µM concentrations with the human breast cell line MCF-7.

RESULTS

Homosalate affected the cell viability dose-dependently at a concentrations of above 1000 µM. Micronucleus formation was significantly induced at 750 and 1000 µM within 24 hours due to an increase in cytostatic effect, the cell viability of HMS decreased to 57% at a concentration of 2000 µM, and a sufficient number of binucleated cells could not be obtained to count. Homosalate was also clastogenic when the cells were incubated at cytotoxic concentrations.

CONCLUSION

These results suggest that homosalate can be considered as a cytotoxic and genotoxic substance.

Rationally designed hecogenin thiosemicarbazone analogs as novel MEK inhibitors for the control of breast malignancies

Natural products have documented oncology success history as valuable scaffolds for selective target modulation. Herein, the sapogenin hecogenin (1) was screened for its anti-breast cancer inhibitory capacity using in vitro assays, including proliferation, cytotoxicity, migration, invasion assays, and Western blotting. The results identified 1 as a propitious hit with modest activities attributed to the concurrent down-regulation of mitogen activated protein kinase kinase/extracellular signal-regulated kinase (MEK) distinctive downstream effectors. Guided by in silico 3D-structural insights of MAPK kinase domain, an extension strategy was adopted at 1's C-3 and C-12 aimed at the design of novel hecogenin-based analogs with improved target binding affinity. Thirty-three analogs were prepared and tested, among which hecogenin 12-(3'-methylphenyl thiosemicarbazone) (30) displayed the most potent selective anticancer effects. Analog 30 demonstrated antiproliferative, antimigratory and anti-invasive activities at low μM level, compared to the negligible effect on the non-tumorigenic MCF-10A mammary epithelial cells. Durable regression of breast tumor xenografts in athymic nude mice was observed after treatments with 30, compared to its parent hecogenin at the same dose regimen, confirmed the hit-to-lead promotion of this analog. Hecogenin-12-thiosemicarbazones, represented by 30, is a novel MEK inhibitory lead class to control breast neoplasms.

Characterization of three human cell line models for high-throughput neuronal cytotoxicity screening

More than 75 000 man-made chemicals contaminate the environment; many of these have not been tested for toxicities. These chemicals demand quantitative high-throughput screening assays to assess them for causative roles in neurotoxicities, including Parkinson's disease and other neurodegenerative disorders. To facilitate high throughput screening for cytotoxicity to neurons, three human neuronal cellular models were compared: SH-SY5Y neuroblastoma cells, LUHMES conditionally-immortalized dopaminergic neurons, and Neural Stem Cells (NSC) derived from human fetal brain. These three cell lines were evaluated for rapidity and degree of differentiation, and sensitivity to 32 known or candidate neurotoxicants. First, expression of neural differentiation genes was assayed during a 7-day differentiation period. Of the three cell lines, LUHMES showed the highest gene expression of neuronal markers after differentiation. Both in the undifferentiated state and after 7 days of neuronal differentiation, LUHMES cells exhibited greater cytotoxic sensitivity to most of 32 suspected or known neurotoxicants than SH-SY5Y or NSCs. LUHMES cells were also unique in being more susceptible to several compounds in the differentiating state than in the undifferentiated state; including known neurotoxicants colchicine, methyl-mercury (II), and vincristine. Gene expression results suggest that differentiating LUHMES cells may be susceptible to apoptosis because they express low levels of anti-apoptotic genes BCL2 and BIRC5/survivin, whereas SH-SY5Y cells may be resistant to apoptosis because they express high levels of BCL2, BIRC5/survivin, and BIRC3 genes. Thus, LUHMES cells exhibited favorable characteristics for neuro-cytotoxicity screening: rapid differentiation into neurons that exhibit high level expression neuronal marker genes, and marked sensitivity of LUHMES cells to known neurotoxicants. Copyright © 2016 John Wiley & Sons, Ltd.

Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization

Target-specific, mechanism-oriented in vitro assays post a promising alternative to traditional animal toxicology studies. Here we report the first comprehensive analysis of the Tox21 effort, a large-scale in vitro toxicity screening of chemicals. We test ∼ 10,000 chemicals in triplicates at 15 concentrations against a panel of nuclear receptor and stress response pathway assays, producing more than 50 million data points. Compound clustering by structure similarity and activity profile similarity across the assays reveals structure-activity relationships that are useful for the generation of mechanistic hypotheses. We apply structural information and activity data to build predictive models for 72 in vivo toxicity end points using a cluster-based approach. Models based on in vitro assay data perform better in predicting human toxicity end points than animal toxicity, while a combination of structural and activity data results in better models than using structure or activity data alone. Our results suggest that in vitro activity profiles can be applied as signatures of compound mechanism of toxicity and used in prioritization for more in-depth toxicological testing.

Screening for Chemical Contributions to Breast Cancer Risk: A Case Study for Chemical Safety Evaluation

BACKGROUND

Current approaches to chemical screening, prioritization, and assessment are being reenvisioned, driven by innovations in chemical safety testing, new chemical regulations, and demand for information on human and environmental impacts of chemicals. To conceptualize these changes through the lens of a prevalent disease, the Breast Cancer and Chemicals Policy project convened an interdisciplinary expert panel to investigate methods for identifying chemicals that may increase breast cancer risk.

METHODS

Based on a review of current evidence, the panel identified key biological processes whose perturbation may alter breast cancer risk. We identified corresponding assays to develop the Hazard Identification Approach for Breast Carcinogens (HIA-BC), a method for detecting chemicals that may raise breast cancer risk. Finally, we conducted a literature-based pilot test of the HIA-BC.

RESULTS

The HIA-BC identifies assays capable of detecting alterations to biological processes relevant to breast cancer, including cellular and molecular events, tissue changes, and factors that alter susceptibility. In the pilot test of the HIA-BC, chemicals associated with breast cancer all demonstrated genotoxic or endocrine activity, but not necessarily both. Significant data gaps persist.

CONCLUSIONS

This approach could inform the development of toxicity testing that targets mechanisms relevant to breast cancer, providing a basis for identifying safer chemicals. The study identified important end points not currently evaluated by federal testing programs, including altered mammary gland development, Her2 activation, progesterone receptor activity, prolactin effects, and aspects of estrogen receptor β activity. This approach could be extended to identify the biological processes and screening methods relevant for other common diseases.

Analysis of the ToxCast Chemical-Assay Space Using the Comparative Toxicogenomics Database

Many studies have attempted to predict in vivo hazards based on the ToxCast in vitro assay results with the goal of using these predictions to prioritize compounds for conventional toxicity testing. Most of these conventional studies rely on in vivo end points observed using preclinical species (e.g., mice and rats). Although the preclinical animal studies provide valuable insights, there can often be significant disconnects between these studies and safety concerns in humans. One way to address these concerns, for an admittedly more limited set of compounds, is to explore relationships between the in vitro data from human cell lines and observations from human related studies. The Comparative Toxicogenomics Database (CTD; http://ctdbase.org ) is a rich source of data linking chemicals to human diseases/adverse events and pathways. In this study we explored the relationships between ToxCast chemicals, their ToxCast in vitro test results, and their annotations of human disease/adverse event end points as captured in the CTD database. We mined these associations to identify potentially interesting, statistically significant in vitro assay and in vivo toxicity correlations. To the best of our knowledge, this is one of the first studies analyzing the relationships between the ToxCast in vitro assays results and the CTD disease/adverse event end point annotations. The in vitro profiles identified in this analysis may prove useful for prioritizing compounds for toxicity testing, suggesting mechanisms of toxicity, and forecasting potential in vivo human drug induced injury.

Population-based in vitro hazard and concentration-response assessment of chemicals: the 1000 genomes high-throughput screening study

BACKGROUND

Understanding of human variation in toxicity to environmental chemicals remains limited, so human health risk assessments still largely rely on a generic 10-fold factor (10½ each for toxicokinetics and toxicodynamics) to account for sensitive individuals or subpopulations.

OBJECTIVES

We tested a hypothesis that population-wide in vitro cytotoxicity screening can rapidly inform both the magnitude of and molecular causes for interindividual toxicodynamic variability.

METHODS

We used 1,086 lymphoblastoid cell lines from the 1000 Genomes Project, representing nine populations from five continents, to assess variation in cytotoxic response to 179 chemicals. Analysis included assessments of population variation and heritability, and genome-wide association mapping, with attention to phenotypic relevance to human exposures.

RESULTS

For about half the tested compounds, cytotoxic response in the 1% most "sensitive" individual occurred at concentrations within a factor of 10½ (i.e., approximately 3) of that in the median individual; however, for some compounds, this factor was > 10. Genetic mapping suggested important roles for variation in membrane and transmembrane genes, with a number of chemicals showing association with SNP rs13120371 in the solute carrier SLC7A11, previously implicated in chemoresistance.

CONCLUSIONS

This experimental approach fills critical gaps unaddressed by recent large-scale toxicity testing programs, providing quantitative, experimentally based estimates of human toxicodynamic variability, and also testable hypotheses about mechanisms contributing to interindividual variation.

Application of Titration-Based Screening for the Rapid Pilot Testing of High-Throughput Assays

Pilot testing of an assay intended for high-throughput screening (HTS) with small compound sets is a necessary but often time-consuming step in the validation of an assay protocol. When the initial testing concentration is less than optimal, this can involve iterative testing at different concentrations to further evaluate the pilot outcome, which can be even more time-consuming. Quantitative HTS (qHTS) enables flexible and rapid collection of assay performance statistics, hits at different concentrations, and concentration-response curves in a single experiment. Here we describe the qHTS process for pilot testing in which eight-point concentration-response curves are produced using an interplate asymmetric dilution protocol in which the first four concentrations are used to represent the range of typical HTS screening concentrations and the last four concentrations are added for robust curve fitting to determine potency/efficacy values. We also describe how these data can be analyzed to predict the frequency of false-positives, false-negatives, hit rates, and confirmation rates for the HTS process as a function of screening concentration. By taking into account the compound pharmacology, this pilot-testing paradigm enables rapid assessment of the assay performance and choosing the optimal concentration for the large-scale HTS in one experiment.

Improving the human hazard characterization of chemicals: a Tox21 update

BACKGROUND

In 2008, the National Institute of Environmental Health Sciences/National Toxicology Program, the U.S. Environmental Protection Agency's National Center for Computational Toxicology, and the National Human Genome Research Institute/National Institutes of Health Chemical Genomics Center entered into an agreement on "high throughput screening, toxicity pathway profiling, and biological interpretation of findings." In 2010, the U.S. Food and Drug Administration (FDA) joined the collaboration, known informally as Tox21.

OBJECTIVES

The Tox21 partners agreed to develop a vision and devise an implementation strategy to shift the assessment of chemical hazards away from traditional experimental animal toxicology studies to one based on target-specific, mechanism-based, biological observations largely obtained using in vitro assays.

DISCUSSION

Here we outline the efforts of the Tox21 partners up to the time the FDA joined the collaboration, describe the approaches taken to develop the science and technologies that are currently being used, assess the current status, and identify problems that could impede further progress as well as suggest approaches to address those problems.

CONCLUSION

Tox21 faces some very difficult issues. However, we are making progress in integrating data from diverse technologies and end points into what is effectively a systems-biology approach to toxicology. This can be accomplished only when comprehensive knowledge is obtained with broad coverage of chemical and biological/toxicological space. The efforts thus far reflect the initial stage of an exceedingly complicated program, one that will likely take decades to fully achieve its goals. However, even at this stage, the information obtained has attracted the attention of the international scientific community, and we believe these efforts foretell the future of toxicology.

Identification of repurposed small molecule drugs for chordoma therapy

Chordoma is a rare, slow growing malignant tumor arising from remnants of the fetal notochord. Surgery is the first choice for chordoma treatment, followed by radiotherapy, although postoperative complications remain significant. Recurrence of the disease occurs frequently due to the anatomy of the tumor location and violation of the tumor margins at the initial surgery. Currently, there are no effective drugs available for patients with chordoma. Due to the rarity of the disease, there is limited opportunity to test agents in clinical trials and no concerted effort to develop agents for chordoma in the pharmaceutical industry. To rapidly and efficiently identify small molecules that inhibit chordoma cell growth, we screened the NCGC Pharmaceutical Collection (NPC) containing approximately 2800 clinically approved and investigational drugs at 15 different concentrations in chordoma cell lines, U-CH1 and U-CH2. We identified a group of drugs including bortezomib, 17-AAG, digitoxin, staurosporine, digoxin, rubitecan, and trimetrexate that inhibited chordoma cell growth, with potencies from 10 to 370 nM in U-CH1 cells, but less potently in U-CH2 cells. Most of these drugs also induced caspase 3/7 activity with a similar rank order as the cytotoxic effect on U-CH1 cells. Cantharidin, digoxin, digitoxin, staurosporine, and bortezomib showed similar inhibitory effect on cell lines and 3 primary chordoma cell cultures. The combination treatment of bortezomib with topoisomerase I and II inhibitors increased the therapeutic potency in U-CH2 and patient-derived primary cultures. Our results provide information useful for repurposing currently approved drugs for chordoma and potential approach of combination therapy.

The multidimensional perturbation value: a single metric to measure similarity and activity of treatments in high-throughput multidimensional screens

Screens using high-throughput, information-rich technologies such as microarrays, high-content screening (HCS), and next-generation sequencing (NGS) have become increasingly widespread. Compared with single-readout assays, these methods produce a more comprehensive picture of the effects of screened treatments. However, interpreting such multidimensional readouts is challenging. Univariate statistics such as t-tests and Z-factors cannot easily be applied to multidimensional profiles, leaving no obvious way to answer common screening questions such as "Is treatment X active in this assay?" and "Is treatment X different from (or equivalent to) treatment Y?" We have developed a simple, straightforward metric, the multidimensional perturbation value (mp-value), which can be used to answer these questions. Here, we demonstrate application of the mp-value to three data sets: a multiplexed gene expression screen of compounds and genomic reagents, a microarray-based gene expression screen of compounds, and an HCS compound screen. In all data sets, active treatments were successfully identified using the mp-value, and simulations and follow-up analyses supported the mp-value's statistical and biological validity. We believe the mp-value represents a promising way to simplify the analysis of multidimensional data while taking full advantage of its richness.

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.

A three-stage algorithm to make toxicologically relevant activity calls from quantitative high throughput screening data

BACKGROUND

The ability of a substance to induce a toxicological response is better understood by analyzing the response profile over a broad range of concentrations than at a single concentration. In vitro quantitative high throughput screening (qHTS) assays are multiple-concentration experiments with an important role in the National Toxicology Program's (NTP) efforts to advance toxicology from a predominantly observational science at the level of disease-specific models to a more predictive science based on broad inclusion of biological observations.

OBJECTIVE

We developed a systematic approach to classify substances from large-scale concentration-​response data into statistically supported, toxicologically relevant activity categories.

METHODS

The first stage of the approach finds active substances with robust concentration-response profiles within the tested concentration range. The second stage finds substances with activity at the lowest tested concentration not captured in the first stage. The third and final stage separates statistically significant (but not robustly statistically significant) profiles from responses that lack statistically compelling support (i.e., "inactives"). The performance of the proposed algorithm was evaluated with simulated qHTS data sets.

RESULTS

The proposed approach performed well for 14-point-concentration-response curves with typical levels of residual error (σ ≤ 25%) or when maximal response (|RMAX|) was > 25% of the positive control response. The approach also worked well in most cases for smaller sample sizes when |RMAX| ≥ 50%, even with as few as four data points.

CONCLUSIONS

The three-stage classification algorithm performed better than one-stage classification approaches based on overall F-tests, t-tests, or linear regression.

Paradigm shift in toxicity testing and modeling

The limitations of traditional toxicity testing characterized by high-cost animal models with low-throughput readouts, inconsistent responses, ethical issues, and extrapolability to humans call for alternative strategies for chemical risk assessment. A new strategy using in vitro human cell-based assays has been designed to identify key toxicity pathways and molecular mechanisms leading to the prediction of an in vivo response. The emergence of quantitative high-throughput screening (qHTS) technology has proved to be an efficient way to decompose complex toxicological end points to specific pathways of targeted organs. In addition, qHTS has made a significant impact on computational toxicology in two aspects. First, the ease of mechanism of action identification brought about by in vitro assays has enhanced the simplicity and effectiveness of machine learning, and second, the high-throughput nature and high reproducibility of qHTS have greatly improved the data quality and increased the quantity of training datasets available for predictive model construction. In this review, the benefits of qHTS routinely used in the US Tox21 program will be highlighted. Quantitative structure-activity relationships models built on traditional in vivo data and new qHTS data will be compared and analyzed. In conjunction with the transition from the pilot phase to the production phase of the Tox21 program, more qHTS data will be made available that will enrich the data pool for predictive toxicology. It is perceivable that new in silico toxicity models based on high-quality qHTS data will achieve unprecedented reliability and robustness, thus becoming a valuable tool for risk assessment and drug discovery.

Genotoxicity of pesticide mixtures present in the diet of the French population

Consumers may be simultaneously exposed to several pesticide residues in their diet. A previous study identified the seven most common pesticide mixtures to which the French population was exposed through food consumption in 2006. The aim of this study was to investigate if the seven mixtures are potentially cytotoxic and genotoxic and if so, whether compounds in a same mixture have a combined effect. The cytotoxicity and genotoxicity of the seven mixtures were investigated with a new assay (γ-H2AX) using four human cell lines (ACHN, SH-SY5Y, LS-174T, and HepG2). Mixtures were tested at equimolar concentrations and also at concentrations reflecting their actual proportion in the diet. Irrespective of the cell line tested, parallel cytotoxicity of the seven mixtures was observed. Only one mixture was genotoxic for the HepG2 cells at concentrations = 3 μM in equimolar proportion and at 30 μM in actual proportion. Caspase 3/7 activity, the comet assay, and reactive oxygen species production were also investigated using the same mixture and HepG2 cells. Our results suggest that pesticide metabolites from the mixture generated by HepG2 cells were responsible for the observed damage to DNA. Among the five compounds in the genotoxic mixture, only fludioxonil and cyprodinil were genotoxic for HepG2 cells alone at concentrations = 4 and 20 μM, respectively. Our data suggest a combined genotoxic effect of the mixture at low concentrations with a significantly higher effect of the mixture of pesticides than would be expected from the response to the individual compounds. Environ. Mol. Mutagen. 2012. © 2012 Wiley Periodicals, Inc.

Automation of an in vitro cytotoxicity assay used to estimate starting doses in acute oral systemic toxicity tests

Application of High Throughput Screening (HTS) to the regulatory safety assessment of chemicals is still in its infancy but shows great promise in terms of facilitating better understanding of toxicological modes-of-action, reducing the reliance on animal testing, and allowing more data-poor chemicals to be assessed at a reasonable cost. To promote the uptake and acceptance of HTS approaches, we describe in a stepwise manner how a well known cytotoxicity assay can be automated to increase throughput while maintaining reliability. Results generated with selected reference chemicals compared very favourably with data obtained from a previous international validation study concerning the prediction of acute systemic toxicity in rodents. The automated assay was then included in a formal ECVAM validation study to determine if the assay could be used for binary classification of chemicals with respect to their acute oral toxicity, using a threshold equivalent to a dose of 2000 mg/kg b.w. in a rodent bioassay (LD50). This involved the blind-testing of 56 reference chemicals on the HTS platform to produce concentration-response and IC50 data. Finally, the assay was adapted to a format more suited to higher throughput testing without compromising the quality of the data obtained.

Quantitative high-throughput screening for chemical toxicity in a population-based in vitro model

A shift in toxicity testing from in vivo to in vitro may efficiently prioritize compounds, reveal new mechanisms, and enable predictive modeling. Quantitative high-throughput screening (qHTS) is a major source of data for computational toxicology, and our goal in this study was to aid in the development of predictive in vitro models of chemical-induced toxicity, anchored on interindividual genetic variability. Eighty-one human lymphoblast cell lines from 27 Centre d'Etude du Polymorphisme Humain trios were exposed to 240 chemical substances (12 concentrations, 0.26nM-46.0μM) and evaluated for cytotoxicity and apoptosis. qHTS screening in the genetically defined population produced robust and reproducible results, which allowed for cross-compound, cross-assay, and cross-individual comparisons. Some compounds were cytotoxic to all cell types at similar concentrations, whereas others exhibited interindividual differences in cytotoxicity. Specifically, the qHTS in a population-based human in vitro model system has several unique aspects that are of utility for toxicity testing, chemical prioritization, and high-throughput risk assessment. First, standardized and high-quality concentration-response profiling, with reproducibility confirmed by comparison with previous experiments, enables prioritization of chemicals for variability in interindividual range in cytotoxicity. Second, genome-wide association analysis of cytotoxicity phenotypes allows exploration of the potential genetic determinants of interindividual variability in toxicity. Furthermore, highly significant associations identified through the analysis of population-level correlations between basal gene expression variability and chemical-induced toxicity suggest plausible mode of action hypotheses for follow-up analyses. We conclude that as the improved resolution of genetic profiling can now be matched with high-quality in vitro screening data, the evaluation of the toxicity pathways and the effects of genetic diversity are now feasible through the use of human lymphoblast cell lines.

Assessment of compound hepatotoxicity using human plateable cryopreserved hepatocytes in a 1536-well-plate format

Hepatotoxicity is a major concern for both drug development and toxicological evaluation of environmental chemicals. The assessment of compound-induced hepatotoxicity has traditionally relied on in vivo testing; however, it is being replaced by human in vitro models due to an emphasis on the reduction of animal testing and species-specific differences. Since most cell lines and hybridomas lack the full complement of enzymes at physiological levels found in the liver, primary hepatocytes are the gold standard to study liver toxicities in vitro due to the retention of most of their in vivo activities. Here, we optimized a cell viability assay using plateable cryopreserved human hepatocytes in a 1536-well-plate format. The assay was validated by deriving inhibitory concentration at 50% values for 12 known compounds, including tamoxifen, staurosporine, and phenylmercuric acetate, with regard to hepatotoxicity and general cytotoxicity using multiple hepatocyte donors. The assay performed well, and the cytotoxicity of these compounds was confirmed in comparison to HepG2 cells. This is the first study to report the reliability of using plateable cryopreserved human hepatocytes for cytotoxicity studies in a 1536-well-plate format. These results suggest that plateable cryopreserved human hepatocytes can be scaled up for screening a large compound library and may be amenable to other hepatocytic assays such as metabolic or drug safety studies.

Chemical genomic profiling for antimalarial therapies, response signatures, and molecular targets

Malaria remains a devastating disease largely because of widespread drug resistance. New drugs and a better understanding of the mechanisms of drug action and resistance are essential for fulfilling the promise of eradicating malaria. Using high-throughput chemical screening and genome-wide association analysis, we identified 32 highly active compounds and genetic loci associated with differential chemical phenotypes (DCPs), defined as greater than or equal to fivefold differences in half-maximum inhibitor concentration (IC(50)) between parasite lines. Chromosomal loci associated with 49 DCPs were confirmed by linkage analysis and tests of genetically modified parasites, including three genes that were linked to 96% of the DCPs. Drugs whose responses mapped to wild-type or mutant pfcrt alleles were tested in combination in vitro and in vivo, which yielded promising new leads for antimalarial treatments.

Chemical genomics profiling of environmental chemical modulation of human nuclear receptors

BACKGROUND

The large and increasing number of chemicals released into the environment demands more efficient and cost-effective approaches for assessing environmental chemical toxicity. The U.S. Tox21 program has responded to this challenge by proposing alternative strategies for toxicity testing, among which the quantitative high-throughput screening (qHTS) paradigm has been adopted as the primary tool for generating data from screening large chemical libraries using a wide spectrum of assays.

OBJECTIVES

The goal of this study was to develop methods to evaluate the data generated from these assays to guide future assay selection and prioritization for the Tox21 program.

METHODS

We examined the data from the Tox21 pilot-phase collection of approximately 3,000 environmental chemicals profiled in qHTS format against a panel of 10 human nuclear receptors (AR, ERα, FXR, GR, LXRβ, PPARγ, PPARδ, RXRα, TRβ, and VDR) for reproducibility, concordance of biological activity profiles with sequence homology of the receptor ligand binding domains, and structure-activity relationships.

RESULTS

We determined the assays to be appropriate in terms of biological relevance. We found better concordance for replicate compounds for the agonist-mode than for the antagonist-mode assays, likely due to interference of cytotoxicity in the latter assays. This exercise also enabled us to formulate data-driven strategies for discriminating true signals from artifacts, and to prioritize assays based on data quality.

CONCLUSIONS

The results demonstrate the feasibility of qHTS to identify the potential for environmentally relevant chemicals to interact with key toxicity pathways related to human disease induction.

In vitro screening for population variability in chemical toxicity

Immortalized human lymphoblastoid cell lines have been used to demonstrate that it is possible to use an in vitro model system to identify genetic factors that affect responses to xenobiotics. To extend the application of such studies to investigative toxicology by assessing interindividual and population-wide variability and heritability of chemical-induced toxicity phenotypes, we have used cell lines from the Centre d'Etude du Polymorphisme Humain (CEPH) trios assembled by the HapMap Consortium. Our goal is to aid in the development of predictive in vitro genetics-anchored models of chemical-induced toxicity. Cell lines from the CEPH trios were exposed to three concentrations of 14 environmental chemicals. We assessed ATP production and caspase-3/7 activity 24 h after treatment. Replicate analyses were used to evaluate experimental variability and classify responses. We show that variability of response across the cell lines exists for some, but not all, chemicals, with perfluorooctanoic acid (PFOA) and phenobarbital eliciting the greatest degree of interindividual variability. Although the data for the chemicals used here do not show evidence for broad-sense heritability of toxicity response phenotypes, substantial cell line variation was found, and candidate genetic factors contributing to the variability in response to PFOA were investigated using genome-wide association analysis. The approach of screening chemicals for toxicity in a genetically defined yet diverse in vitro human cell-based system is potentially useful for identification of chemicals that may pose a highest risk, the extent of within-species variability in the population, and genetic loci of interest that potentially contribute to chemical susceptibility.

The pilot phase of the NIH Chemical Genomics Center

The NIH Chemical Genomics Center (NCGC) was the inaugural center of the Molecular Libraries and Screening Center Network (MLSCN). Along with the nine other research centers of the MLSCN, the NCGC was established with a primary goal of bringing industrial technology and experience to empower the scientific community with small molecule compounds for use in their research. We intend this review to serve as 1) an introduction to the NCGC standard operating procedures, 2) an overview of several of the lessons learned during the pilot phase and 3) a review of several of the innovative discoveries reported during the pilot phase of the MLSCN.

The future of toxicity testing: a focus on in vitro methods using a quantitative high-throughput screening platform

The US Tox21 collaborative program represents a paradigm shift in toxicity testing of chemical compounds from traditional in vivo tests to less expensive and higher throughput in vitro methods to prioritize compounds for further study, identify mechanisms of action and ultimately develop predictive models for adverse health effects in humans. The NIH Chemical Genomics Center (NCGC) is an integral component of the Tox21 collaboration owing to its quantitative high-throughput screening (qHTS) paradigm, in which titration-based screening is used to profile hundreds of thousands of compounds per week. Here, we describe the Tox21 collaboration, qHTS-based compound testing and the various Tox21 screening assays that have been validated and tested at the NCGC to date.

Coupling cytotoxicity biomarkers with DNA damage assessment in TK6 human lymphoblast cells

There is considerable discussion within the scientific community as to the appropriate measures of cytotoxicity to use when deciding on the maximum concentration of a substance to test in vitro for its ability to induce DNA damage using the Comet assay. Conventional cytotoxicity assessment methods, such as trypan blue dye exclusion or relative cell number (cell counts) may not be the most biologically relevant measurement for cytotoxicity in this assay. Thus, we evaluated for decreased levels of adenosine triphosphate (ATP) and activation of Caspase-3/7 as well as relative cell number and trypan blue exclusion in order to understand the correlation among test compound concentration, cytotoxicity and genotoxicity outcomes in the Comet assay. We tested two non-genotoxic and non-cytotoxic compounds (d-glucose and ethanol), two non-genotoxic but cytotoxic compounds (2,4-dichlorophenol and tunicamycin) and four genotoxic and cytotoxic compounds (methyl methanesulfonate, ethyl methanesulfonate, etoposide and 4-nitroquinoline-N-oxide) in TK6 human lymphoblast cells. Our data show that measuring ATP and Caspase-3/7 levels provides more rapid and perhaps more biologically relevant measures of cytotoxicity compared with trypan blue dye exclusion and relative cell number. Furthermore, incorporating these two assays into the Comet assay also provided insight on the cytotoxic mode of action of the chemicals tested. By extrapolation, such assays may also be useful in other in vitro genotoxicity assays.

Identification of known drugs that act as inhibitors of NF-kappaB signaling and their mechanism of action

Nuclear factor-kappa B (NF-kappaB) is a transcription factor that plays a critical role across many cellular processes including embryonic and neuronal development, cell proliferation, apoptosis, and immune responses to infection and inflammation. Dysregulation of NF-kappaB signaling is associated with inflammatory diseases and certain cancers. Constitutive activation of NF-kappaB signaling has been found in some types of tumors including breast, colon, prostate, skin and lymphoid, hence therapeutic blockade of NF-kappaB signaling in cancer cells provides an attractive strategy for the development of anticancer drugs. To identify small molecule inhibitors of NF-kappaB signaling, we screened approximately 2800 clinically approved drugs and bioactive compounds from the NIH Chemical Genomics Center Pharmaceutical Collection (NPC) in a NF-kappaB mediated beta-lactamase reporter gene assay. Each compound was tested at fifteen different concentrations in a quantitative high throughput screening format. We identified nineteen drugs that inhibited NF-kappaB signaling, with potencies as low as 20 nM. Many of these drugs, including emetine, fluorosalan, sunitinib malate, bithionol, narasin, tribromsalan, and lestaurtinib, inhibited NF-kappaB signaling via inhibition of IkappaBalpha phosphorylation. Others, such as ectinascidin 743, chromomycin A3 and bortezomib utilized other mechanisms. Furthermore, many of these drugs induced caspase 3/7 activity and had an inhibitory effect on cervical cancer cell growth. Our results indicate that many currently approved pharmaceuticals have previously unappreciated effects on NF-kappaB signaling, which may contribute to anticancer therapeutic effects. Comprehensive profiling of approved drugs provides insight into their molecular mechanisms, thus providing a basis for drug repurposing.

Weighted feature significance: a simple, interpretable model of compound toxicity based on the statistical enrichment of structural features

In support of the U.S. Tox21 program, we have developed a simple and chemically intuitive model we call weighted feature significance (WFS) to predict the toxicological activity of compounds, based on the statistical enrichment of structural features in toxic compounds. We trained and tested the model on the following: (1) data from quantitative high-throughput screening cytotoxicity and caspase activation assays conducted at the National Institutes of Health Chemical Genomics Center, (2) data from Salmonella typhimurium reverse mutagenicity assays conducted by the U.S. National Toxicology Program, and (3) hepatotoxicity data published in the Registry of Toxic Effects of Chemical Substances. Enrichments of structural features in toxic compounds are evaluated for their statistical significance and compiled into a simple additive model of toxicity and then used to score new compounds for potential toxicity. The predictive power of the model for cytotoxicity was validated using an independent set of compounds from the U.S. Environmental Protection Agency tested also at the National Institutes of Health Chemical Genomics Center. We compared the performance of our WFS approach with classical classification methods such as Naive Bayesian clustering and support vector machines. In most test cases, WFS showed similar or slightly better predictive power, especially in the prediction of hepatotoxic compounds, where WFS appeared to have the best performance among the three methods. The new algorithm has the important advantages of simplicity, power, interpretability, and ease of implementation.

Comprehensive characterization of cytochrome P450 isozyme selectivity across chemical libraries

The cytochrome P450 (CYP) gene family catalyzes drug metabolism and bioactivation and is therefore relevant to drug development. We determined potency values for 17,143 compounds against five recombinant CYP isozymes (1A2, 2C9, 2C19, 2D6 and 3A4) using an in vitro bioluminescent assay. The compounds included libraries of US Food and Drug Administration (FDA)-approved drugs and screening libraries. We observed cross-library isozyme inhibition (30-78%) with important differences between libraries. Whereas only 7% of the typical screening library was inactive against all five isozymes, 33% of FDA-approved drugs were inactive, reflecting the optimized pharmacological properties of the latter. Our results suggest that low CYP 2C isozyme activity is a common property of drugs, whereas other isozymes, such as CYP 2D6, show little discrimination between drugs and unoptimized compounds found in screening libraries. We also identified chemical substructures that differentiated between the five isozymes. The pharmacological compendium described here should further the understanding of CYP isozymes.

Cellular stress response pathway system as a sentinel ensemble in toxicological screening

High costs, long test times, and societal concerns related to animal use have required the development of in vitro assays for the rapid and cost-effective toxicological evaluation and characterization of compounds in both the pharmaceutical and environmental arenas. Although the pharmaceutical industry has developed very effective, high-throughput in vitro assays for determining the therapeutic potential of compounds, the application of this approach to toxicological screening has been limited. A primary reason for this is that while drug candidate screens are directed to a specific target/mechanism, xenobiotics can cause toxicity through any of a myriad of undefined interactions with cellular components and processes. Given that it is not practical to design assays that can interrogate each potential toxicological target, an integrative approach is required if there is to be a rapid and low-cost toxicological evaluation of chemicals. Cellular stress response pathways offer a viable solution to the creation of a set of integrative assays as there is a limited and hence manageable set (a small ensemble of 10 or less) of major cellular stress response pathways through which cells mount a homoeostatic response to toxicants and which also participate in cell fate/death decisions. Further, over the past decades, these pathways have been well characterized at a molecular level thereby enabling the development of high-throughput cell-based assays using the components of the pathways. Utilization of the set of cellular stress response pathway-based assays as indicators of toxic interactions of chemicals with basic cellular machinery will potentially permit the clustering of chemicals based on biological response profiles of common mode of action (MOA) and also the inference of the specific MOA of a toxicant. This article reviews the biochemical characteristics of the stress response pathways, their common architecture that enables rapid activation during stress, their participation in cell fate decisions, the essential nature of these pathways to the organism, and the biochemical basis of their cross-talk that permits an assay ensemble screening approach. Subsequent sections describe how the stress pathway ensemble assay approach could be applied to screening potentially toxic compounds and discuss how this approach may be used to derive toxicant MOA from the biological activity profiles that the ensemble strategy provides. The article concludes with a review of the application of the stress assay concept to noninvasive in vivo assessments of chemical toxicants.

High-content analysis in neuroscience

High-content analysis (HCA) combines automated microscopy and automated image analysis to quantify complex cellular anatomy and biochemistry objectively, accurately and quickly. High-content assays that are applicable to neuroscience include those that can quantify various aspects of dendritic trees, protein aggregation, transcription factor translocation, neurotransmitter receptor internalization, neuron and synapse number, cell migration, proliferation and apoptosis. The data that are generated by HCA are rich and multiplexed. HCA thus provides a powerful high-throughput tool for neuroscientists.