Incorporating ToxCast and Tox21 datasets to rank biological activity of chemicals at Superfund sites in North Carolina

Priority control sequence of 34 typical pollutants in effluents of Chinese wastewater treatment plants

The identification of the priority control sequence of pollutants in effluents of wastewater treatment plants (WWTPs) has important implications for the management of water quality. This study chose 34 typical pollutants based on their representativeness and detection rates in municipal wastewater. The occurrence frequency and concentration of these pollutants in 168 Chinese WWTP effluents were measured at the national level. The data on in vitro toxicity (67 assays) and in vivo toxicity (216 species) for target pollutants were obtained from the public toxicity database and our experimental data. An environmental health prioritization index (EHPi) method was proposed to integrate the occurrence frequency, concentration, removal rate, and in vitro and in vivo toxicity to determine the priority control sequence of target pollutants. Ethynyl estradiol, 17β-estradiol, estrone, diclofenac, and atrazine were the top 5 pollutants identified by the EHPi score. Several pollutants with high EHPi scores showed spatial differences. Besides the EHPi method which was from the single pollutant perspective, the combined toxicity of pollutants (300 pairs of binary combinations) was also measured based on in vitro toxicity assays to evaluate the key pollutants from the pollutant-pollutant interacting perspective. The pollutants (such as ofloxacin and acetaminophen) that could have significant synergetic effects with many other pollutants are worthy of prior attention. This study shed new light on the identification of the priority control sequence of pollutants in WWTP effluents. The results provide meaningful data for the effective management and control of wastewater water quality.

Toxicity prediction: An application of alternative testing and computational toxicology in contaminated groundwater sites in Taiwan

Groundwater contamination remains a global threat due to its toxic effects to humans and the environment. The remediation of contaminated groundwater sites can be costly, thus, identifying the priority areas of concern is important to reduce money spent on resources. In this study, we aimed to identify and rank the priority groundwater sites in a contaminated petrochemical district by combining alternative, non-animal approaches - chemical analysis, cell-based high throughput screening (HTS), and Toxicological Priority Index (ToxPi) computational toxicology tool. Groundwater samples collected from ten different sites in a contaminated district showed pollutant levels below the detection limit, however, hepatotoxic bioactivity was demonstrated in human hepatoma HepaRG cells. Integrating the pollutants information (i.e., pollutant characteristics and concentration data) with the bioactivity data of the groundwater samples, an evidence-based ranking of the groundwater sites for future remediation was established using ToxPi analysis. The currently presented combinatorial approach of screening groundwater sites for remediation purposes can further be refined by including relevant parameters, which can boost the utility of this approach for groundwater screening and future remediation.

Racial and social disparities in Ventura County, California related to agricultural pesticide applications and toxicity

Application of agricultural pesticides poses health concerns for farmworkers and for local communities due to pesticide drift from spraying or fumigation, pesticide volatilization into the air, contamination of household dust, as well as direct exposure for people who work in agriculture and their families. In this analysis of pesticide use records for Ventura County, California (USA) from 2016 to 2018, we identified the most prevalent toxicological effects of the pesticides applied. We also developed a cumulative toxicity index that incorporates specific toxicity endpoints for individual pesticides, the severity and strength of association for each endpoint, and the reliability of the data sources. Combining the toxicity index for each pesticide with the pounds applied within each square mile section in Ventura County, we calculated the total toxicity-weighted pesticide use and identified pesticides associated with higher potential risk to health. Analysis of U.S. Census data for Ventura County found a greater percentage of Hispanic/Latino, African American and Asian community members in township sections with a greater volume of pesticides applied and higher toxicity-weighted pesticide use. Similarly, areas with limited economic and social resources had elevated pesticide application overall and elevated toxicity-weighted pesticide use. The combination of toxicological and demographic analyses presented in this study provides information that can support the development of policies to protect public health from excessive exposure to pesticides and better environmental health protection for socially vulnerable populations.

Identification of emerging organic pollutants from solid waste incinerations by FT-ICR-MS and GC/Q-TOF-MS and their potential toxicities

Emissions from the incineration of solid waste are a global public health concern, but little attention has been paid to previously unrecognized chemical compounds that are generated by waste incineration and released into the atmosphere. We conducted nontarget analysis of organic chemicals formed during waste incineration by Fourier-transform ion cyclotron resonance mass spectrometry and gas chromatography-quadrupole time-of-flight mass spectrometry. Using toxicity data in the ToxCast library and predicted toxicity data for traditional priority polycyclic aromatic hydrocarbons and 2,3,7,8-tetrachlorodibenzo-p-dioxin, we prioritized 13 compounds including hexachloro-1,3-butadiene, 9 of which are reported here for the first time as constituents of emissions from the incineration of solid waste and hexachloro-1,3-butadiene was included in the Stockholm Convention in 2017. The predicted activity of these pollutants to androgen receptors and to the aryl hydrocarbon receptor were comparable to, or higher than, the 2,3,7,8-tetrachlorodibenzo-p-dioxin and benzo[a]pyrene. In addition, some alkylated polycyclic aromatic hydrocarbons and heteroatom polycyclic aromatic hydrocarbons were also identified in solid waste incineration processes, peak areas of which were 1-2 orders of magnitude higher than dioxins and 1-3 orders of magnitude lower than their parent polycyclic aromatic hydrocarbons. Our study can provide information for better recognizing and regulating the emissions of organic pollutants formed by the incineration of solid waste.

Implementing in vitro bioactivity data to modernize priority setting of chemical inventories

Internationally, there are thousands of existing and newly introduced chemicals in commerce, highlighting the ongoing importance of innovative approaches to identify emerging chemicals of concern. For many chemicals, there is a paucity of hazard and exposure data. Thus, there is a crucial need for efficient and robust approaches to address data gaps and support risk-based prioritization. Several studies have demonstrated the utility of in vitro bioactivity data from the ToxCast program in deriving points of departure (PODs). ToxCast contains data for nearly 1,400 endpoints per chemical, and the bioactivity concentrations, indicative of potential adverse outcomes, can be converted to human-equivalent PODs using high-throughput toxicokinetics (HTTK) modeling. However, data gaps need to be addressed for broader application: the limited chemical space of HTTK and quantitative high-throughput screening data. Here we explore the applicability of in silico models to address these data needs. Specifically, we used ADMET predictor for HTTK predictions and a generalized read-across approach to predict ToxCast bioactivity potency. We applied these models to profile 5,801 chemicals on Canada’s Domestic Substances List (DSL). To evaluate the approach’s performance, bioactivity PODs were compared with in vivo results from the EPA Toxicity Values database for 1,042 DSL chemicals. Comparisons demonstrated that the bioac­tivity PODs, based on ToxCast data or read-across, were conservative for 95% of the chemicals. Comparing bioactivity PODs to human exposure estimates supports the identification of chemicals of potential interest for further work. The bioac­tivity workflow shows promise as a powerful screening tool to support effective triaging of chemical inventories.

The Tox21 10K Compound Library: Collaborative Chemistry Advancing Toxicology

Since 2009, the Tox21 project has screened ∼8500 chemicals in more than 70 high-throughput assays, generating upward of 100 million data points, with all data publicly available through partner websites at the United States Environmental Protection Agency (EPA), National Center for Advancing Translational Sciences (NCATS), and National Toxicology Program (NTP). Underpinning this public effort is the largest compound library ever constructed specifically for improving understanding of the chemical basis of toxicity across research and regulatory domains. Each Tox21 federal partner brought specialized resources and capabilities to the partnership, including three approximately equal-sized compound libraries. All Tox21 data generated to date have resulted from a confluence of ideas, technologies, and expertise used to design, screen, and analyze the Tox21 10K library. The different programmatic objectives of the partners led to three distinct, overlapping compound libraries that, when combined, not only covered a diversity of chemical structures, use-categories, and properties but also incorporated many types of compound replicates. The history of development of the Tox21 "10K" chemical library and data workflows implemented to ensure quality chemical annotations and allow for various reproducibility assessments are described. Cheminformatics profiling demonstrates how the three partner libraries complement one another to expand the reach of each individual library, as reflected in coverage of regulatory lists, predicted toxicity end points, and physicochemical properties. ToxPrint chemotypes (CTs) and enrichment approaches further demonstrate how the combined partner libraries amplify structure-activity patterns that would otherwise not be detected. Finally, CT enrichments are used to probe global patterns of activity in combined ToxCast and Tox21 activity data sets relative to test-set size and chemical versus biological end point diversity, illustrating the power of CT approaches to discern patterns in chemical-activity data sets. These results support a central premise of the Tox21 program: A collaborative merging of programmatically distinct compound libraries would yield greater rewards than could be achieved separately.

The Tox21 10K Compound Library: Collaborative Chemistry Advancing Toxicology

Since 2009, the Tox21 project has screened ∼8500 chemicals in more than 70 high-throughput assays, generating upward of 100 million data points, with all data publicly available through partner websites at the United States Environmental Protection Agency (EPA), National Center for Advancing Translational Sciences (NCATS), and National Toxicology Program (NTP). Underpinning this public effort is the largest compound library ever constructed specifically for improving understanding of the chemical basis of toxicity across research and regulatory domains. Each Tox21 federal partner brought specialized resources and capabilities to the partnership, including three approximately equal-sized compound libraries. All Tox21 data generated to date have resulted from a confluence of ideas, technologies, and expertise used to design, screen, and analyze the Tox21 10K library. The different programmatic objectives of the partners led to three distinct, overlapping compound libraries that, when combined, not only covered a diversity of chemical structures, use-categories, and properties but also incorporated many types of compound replicates. The history of development of the Tox21 "10K" chemical library and data workflows implemented to ensure quality chemical annotations and allow for various reproducibility assessments are described. Cheminformatics profiling demonstrates how the three partner libraries complement one another to expand the reach of each individual library, as reflected in coverage of regulatory lists, predicted toxicity end points, and physicochemical properties. ToxPrint chemotypes (CTs) and enrichment approaches further demonstrate how the combined partner libraries amplify structure-activity patterns that would otherwise not be detected. Finally, CT enrichments are used to probe global patterns of activity in combined ToxCast and Tox21 activity data sets relative to test-set size and chemical versus biological end point diversity, illustrating the power of CT approaches to discern patterns in chemical-activity data sets. These results support a central premise of the Tox21 program: A collaborative merging of programmatically distinct compound libraries would yield greater rewards than could be achieved separately.

Evaluating consumer exposure to disinfecting chemicals against coronavirus disease 2019 (COVID-19) and associated health risks

Disinfection of surfaces has been recommended as one of the most effective ways to combat the spread of novel coronavirus (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19). However, overexposure to disinfecting chemicals may lead to unintended human health risks. Here, using an indoor fate and chemical exposure model, we estimate human exposure to 22 disinfecting chemicals on the lists recommended by various governmental agencies against COVID-19, resulting from contact with disinfected surfaces and handwashing. Three near-field exposure routes, i.e., mouthing-mediated oral ingestion, inhalation, and dermal absorption, are considered to calculate the whole-body uptake doses and blood concentrations caused by single use per day for three age groups (3, 14, and 24-year-old). We also assess the health risks by comparing the predicted whole-body uptake doses with in vivo toxicological data and the predicted blood concentrations with in vitro bioactivity data. Our results indicate that both the total exposure and relative contribution of each exposure route vary considerably among the disinfecting chemicals due to their diverse physicochemical properties. 3-year-old children have consistent higher exposure than other age groups, especially in the scenario of contact with disinfected surfaces, due to their more frequent hand contact and mouthing activities. Due to the short duration of handwashing, we do not expect any health risk from the use of disinfecting chemicals in handwashing. In contrast, exposure from contact with disinfected surfaces may result in health risks for certain age groups especially children, even the surfaces are disinfected once a day. Interestingly, risk assessments based on whole-body uptake doses and in vivo toxicological data tend to give higher risk estimates than do those based on blood concentrations and in vitro bioactivity data. Our results reveal the most important exposure routes for disinfecting chemicals used in the indoor environment; they also highlight the need for more accurate data for both chemical properties and toxicity to better understand the risks associated with the increased use of disinfecting chemicals in the pandemic.

A critical review of synthetic chemicals in surface waters of the US, the EU and China

There is a wide concern that emerging organic pollutants (EOPs) in surface water could adversely affect human health and wildlife. However, the geographic distribution, exposure pattern and ecological risk of emerging organic pollutants are poorly understood at a global scale. This paper provides a comprehensive survey on the exposure level of EOPs in China, the US and the EU based on the published literature. The hazard level of three categories of EOPs, namely pharmaceuticals and personal care products (PPCPs), pesticides and industrial chemicals was further evaluated by adopting a novel Aquatic HazPi index that jointly accounts for the persistence, bioaccumulation, toxicity and bioactivity. Furthermore, a correlation analysis of land use with the surface water exposure status regarding the synthetic chemicals was conducted. According to the published data reported between 2010 and 2016, the concentration of pesticides in the US was higher than in the EU and China. The concentration of PPCPs in the EU was generally lower than in both the US and China, while the concentration of industrial chemicals in China was higher than in the EU and the US. Among the chemicals whose median concentration in surface water was >10 ng/L, the antiretroviral Efavirenz, the pesticide Fipronil, and octocrylene, an industrial chemical and cosmetic ingredient, were found with the highest aquatic HazPi value. Lastly, the spatial distribution and concentration of hazardous EOPs was shown to depend on local landscape and land usages. Our study provides the first broad overview on the geographic distribution, exposure pattern of hazardous EOPs in the three major economic entities: China, the US and the EU.

Cadmium exposure and MEG3 methylation differences between Whites and African Americans in the NEST Cohort

Cadmium (Cd) is a ubiquitous environmental pollutant associated with a wide range of health outcomes including cancer. However, obscure exposure sources often hinder prevention efforts. Further, although epigenetic mechanisms are suspected to link these associations, gene sequence regions targeted by Cd are unclear. Aberrant methylation of a differentially methylated region (DMR) on the MEG3 gene that regulates the expression of a cluster of genes including MEG3, DLK1, MEG8, MEG9 and DIO3 has been associated with multiple cancers. In 287 infant-mother pairs, we used a combination of linear regression and the Getis-Ord Gi* statistic to determine if maternal blood Cd concentrations were associated with offspring CpG methylation of the sequence region regulating a cluster of imprinted genes including MEG3. Correlations were used to examine potential sources and routes. We observed a significant geographic co-clustering of elevated prenatal Cd levels and MEG3 DMR hypermethylation in cord blood (P = 0.01), and these findings were substantiated in our statistical models (β = 1.70, se = 0.80, P = 0.03). These associations were strongest in those born to African American women (β = 3.52, se = 1.32, P = 0.01) compared with those born to White women (β = 1.24, se = 2.11, P = 0.56) or Hispanic women (β = 1.18, se = 1.24, P = 0.34). Consistent with Cd bioaccumulation during the life course, blood Cd levels increased with age (β = 0.015 µg/dl/year, P = 0.003), and Cd concentrations were significantly correlated between blood and urine (ρ > 0.47, P < 0.01), but not hand wipe, soil or house dust concentrations (P > 0.05). Together, these data support that prenatal Cd exposure is associated with aberrant methylation of the imprint regulatory element for the MEG3 gene cluster at birth. However, neither house-dust nor water are likely exposure sources, and ingestion via contaminated hands is also unlikely to be a significant exposure route in this population. Larger studies are required to identify routes and sources of exposure.

Using Tox21 High-Throughput Screening Assays for the Evaluation of Botanical and Dietary Supplements

Introduction: Recent nationwide surveys found that natural products, including botanical dietary supplements, are used by ∼18% of adults. In many cases, there is a paucity of toxicological data available for these substances to allow for confident evaluations of product safety. The National Toxicology Program (NTP) has received numerous nominations from the public and federal agencies to study the toxicological effects of botanical dietary supplements. The NTP sought to evaluate the utility of in vitro quantitative high-throughput screening (qHTS) assays for toxicological assessment of botanical and dietary supplements.

Materials and Methods: In brief, concentration–response assessments of 90 test substances, including 13 distinct botanical species, and individual purported active constituents were evaluated using a subset of the Tox21 qHTS testing panel. The screen included 20 different endpoints that covered a broad range of biologically relevant signaling pathways to detect test article effects upon endocrine activity, nuclear receptor signaling, stress response signaling, genotoxicity, and cell death signaling.

Results and Discussion: Botanical dietary supplement extracts induced measurable and diverse activity. Elevated biological activity profiles were observed following treatments with individual chemical constituents relative to their associated botanical extract. The overall distribution of activity was comparable to activities exhibited by compounds present in the Tox21 10K chemical library.

Conclusion: Botanical supplements did not exhibit minimal or idiosyncratic activities that would preclude the use of qHTS platforms as a feasible method to screen this class of compounds. However, there are still many considerations and further development required when attempting to use in vitro qHTS methods to characterize the safety profile of botanical/dietary supplements.

Elucidating Gene-by-Environment Interactions Associated with Differential Susceptibility to Chemical Exposure

BACKGROUND

Modern societies are exposed to vast numbers of potentially hazardous chemicals. Despite demonstrated linkages between chemical exposure and severe health effects, there are limited, often conflicting, data on how adverse health effects of exposure differ across individuals.

OBJECTIVES

We tested the hypothesis that population variability in response to certain chemicals could elucidate a role for gene-environment interactions (GxE) in differential susceptibility.

METHODS

High-throughput screening (HTS) data on thousands of chemicals in genetically heterogeneous zebrafish were leveraged to identify a candidate chemical (Abamectin) with response patterns indicative of population susceptibility differences. We tested the prediction by generating genome-wide sequence data for 276 individual zebrafish displaying susceptible (Affected) vs. resistant (Unaffected) phenotypes following identical chemical exposure.

RESULTS

We found GxE associated with differential susceptibility in the sox7 promoter region and then confirmed gene expression differences between phenotypic response classes.

CONCLUSIONS

The results for Abamectin in zebrafish demonstrate that GxE associated with naturally occurring, population genetic variation play a significant role in mediating individual response to chemical exposure. https://doi.org/10.1289/EHP2662.

The US Federal Tox21 Program: A strategic and operational plan for continued leadership

The traditional approaches to toxicity testing have posed multiple challenges for evaluating the safety of commercial chemicals, pesticides, food additives/contaminants, and medical products.The challenges include number of chemicals that need to be tested, time and resource intensive nature of traditional toxicity tests, and unexpected adverse effects that occur in pharmaceutical clinical trials despite the extensive toxicological testing.Over a decade ago, the U.S. Environmental Protection Agency (EPA), National Toxicology Program (NTP), National Center for Advancing Translational Sciences (NCATS), and the Food and Drug Administration (FDA) formed a federal consortium for "Toxicology in the 21st Century" (Tox21) with a focus on developing and evaluating in vitro high-throughput screening (HTS) methods for hazard identification and providing mechanistic insights.The Tox21 consortium generated data on thousands of pharmaceuticals and datapoor chemicals, developed better understanding of the limits and applications of in vitro methods, and enabled incorporation of HTS data into regulatory decisions. To more broadly address the challenges in toxicology, Tox21 has developed a new strategic and operational plan that expands the focus of its research activities. The new focus areas include developing an expanded portfolio of alternative test systems, addressing technical limitations of in vitrotest systems, curating legacy in vivo toxicity testing data, establishing scientific confidence in the in vitrotest systems, and refining alternative methods for characterizing pharmacokinetics and in vitro assay disposition.The new Tox21 strategic and operational plan addresses key challenges to advance toxicology testing and will benefit both the organizations involved and the toxicology community.

ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models

Background

Drawing integrated conclusions from diverse source data requires synthesis across multiple types of information. The ToxPi (Toxicological Prioritization Index) is an analytical framework that was developed to enable integration of multiple sources of evidence by transforming data into integrated, visual profiles. Methodological improvements have advanced ToxPi and expanded its applicability, necessitating a new, consolidated software platform to provide functionality, while preserving flexibility for future updates.

Results

We detail the implementation of a new graphical user interface for ToxPi (Toxicological Prioritization Index) that provides interactive visualization, analysis, reporting, and portability. The interface is deployed as a stand-alone, platform-independent Java application, with a modular design to accommodate inclusion of future analytics. The new ToxPi interface introduces several features, from flexible data import formats (including legacy formats that permit backward compatibility) to similarity-based clustering to options for high-resolution graphical output.

Conclusions

We present the new ToxPi interface for dynamic exploration, visualization, and sharing of integrated data models. The ToxPi interface is freely-available as a single compressed download that includes the main Java executable, all libraries, example data files, and a complete user manual from http://toxpi.org.