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Article ; Online: Adverse effects in traditional and alternative toxicity tests.

Browne, Patience / Paul Friedman, Katie / Boekelheide, Kim / Thomas, Russell S

Regulatory toxicology and pharmacology : RTP

2024 Volume 148, Page(s) 105579

Abstract: Chemical safety assessment begins with defining the lowest level of chemical that alters one or more measured endpoints. This critical effect level, along with factors to account for uncertainty, is used to derive limits for human exposure. In the ... ...

Abstract	Chemical safety assessment begins with defining the lowest level of chemical that alters one or more measured endpoints. This critical effect level, along with factors to account for uncertainty, is used to derive limits for human exposure. In the absence of data regarding the specific mechanisms or biological pathways affected, non-specific endpoints such as body weight and non-target organ weight changes are used to set critical effect levels. Specific apical endpoints such as impaired reproductive function or altered neurodevelopment have also been used to set chemical safety limits; however, in test guidelines designed for specific apical effect(s), concurrently measured non-specific endpoints may be equally or more sensitive than specific endpoints. This means that rather than predicting a specific toxicological response, animal data are often used to develop protective critical effect levels, without assuming the same change would be observed in humans. This manuscript is intended to encourage a rethinking of how adverse chemical effects are interpreted: non-specific endpoints from in vivo toxicological studies data are often used to derive points of departure for use with safety assessment factors to create recommended exposure levels that are broadly protective but not necessarily target-specific.
MeSH term(s)	Animals ; Humans ; Toxicity Tests ; Risk Assessment
Language	English
Publishing date	2024-02-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	604672-1
ISSN	1096-0295 ; 0273-2300
ISSN (online)	1096-0295
ISSN	0273-2300
DOI	10.1016/j.yrtph.2024.105579
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Article ; Online: Systematic Approaches for the Encoding of Chemical Groups: A Case Study.

Karamertzanis, Panagiotis G / Patlewicz, Grace / Sannicola, Marta / Paul-Friedman, Katie / Shah, Imran

Chemical research in toxicology

2024 Volume 37, Issue 4, Page(s) 600–619

Abstract: Regulatory authorities aim to organize substances into groups to facilitate prioritization within hazard and risk assessment processes. Often, such chemical groupings are not explicitly defined by structural rules or physicochemical property information. ...

Abstract	Regulatory authorities aim to organize substances into groups to facilitate prioritization within hazard and risk assessment processes. Often, such chemical groupings are not explicitly defined by structural rules or physicochemical property information. This is largely due to how these groupings are developed, namely, a manual expert curation process, which in turn makes updating and refining groupings, as new substances are evaluated, a practical challenge. Herein, machine learning methods were leveraged to build models that could preliminarily assign substances to predefined groups. A set of 86 groupings containing 2,184 substances as published on the European Chemicals Agency (ECHA) website were mapped to the U.S. Environmental Protection Agency (EPA) Distributed Toxicity Structure Database (DSSTox) content to extract chemical and structural information. Substances were represented using Morgan fingerprints, and two machine learning approaches were used to classify test substances into 56 groups containing at least 10 substances with a structural representation in the data set: k-nearest neighbor (kNN) and random forest (RF), that led to mean 5-fold cross-validation test accuracies (average F1 scores) of 0.781 and 0.853, respectively. With a 9% improvement, the RF classifier was significantly more accurate than KNN (
MeSH term(s)	United States ; Algorithms ; United States Environmental Protection Agency ; Machine Learning ; Databases, Factual
Language	English
Publishing date	2024-03-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	639353-6
ISSN	1520-5010 ; 0893-228X
ISSN (online)	1520-5010
ISSN	0893-228X
DOI	10.1021/acs.chemrestox.3c00411
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Zs.A 2320: Show issues

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Article ; Online: ToxRefDB v2.1: update to curated

Feshuk, Madison / Kolaczkowski, Lori / Watford, Sean / Paul Friedman, Katie

Frontiers in toxicology

2023 Volume 5, Page(s) 1260305

Abstract: The Toxicity Reference Database (ToxRefDB) ... ...

Abstract	The Toxicity Reference Database (ToxRefDB) contains
Language	English
Publishing date	2023-09-11
Publishing country	Switzerland
Document type	Journal Article ; Review
ISSN	2673-3080
ISSN (online)	2673-3080
DOI	10.3389/ftox.2023.1260305
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Article ; Online: Advances in computational methods along the exposure to toxicological response paradigm.

El-Masri, Hisham / Paul Friedman, Katie / Isaacs, Kristin / Wetmore, Barbara A

Toxicology and applied pharmacology

2022 Volume 450, Page(s) 116141

Abstract: Human health risk assessment is a function of chemical toxicity, bioavailability to reach target biological tissues, and potential environmental exposure. These factors are complicated by many physiological, biochemical, physical and lifestyle factors. ... ...

Abstract	Human health risk assessment is a function of chemical toxicity, bioavailability to reach target biological tissues, and potential environmental exposure. These factors are complicated by many physiological, biochemical, physical and lifestyle factors. Furthermore, chemical health risk assessment is challenging in view of the large, and continually increasing, number of chemicals found in the environment. These challenges highlight the need to prioritize resources for the efficient and timely assessment of those environmental chemicals that pose greatest health risks. Computational methods, either predictive or investigative, are designed to assist in this prioritization in view of the lack of cost prohibitive in vivo experimental data. Computational methods provide specific and focused toxicity information using in vitro high throughput screening (HTS) assays. Information from the HTS assays can be converted to in vivo estimates of chemical levels in blood or target tissue, which in turn are converted to in vivo dose estimates that can be compared to exposure levels of the screened chemicals. This manuscript provides a review for the landscape of computational methods developed and used at the U.S. Environmental Protection Agency (EPA) highlighting their potentials and challenges.
MeSH term(s)	Environmental Exposure/adverse effects ; Environmental Pollutants/toxicity ; High-Throughput Screening Assays ; Humans ; Risk Assessment/methods ; United States ; United States Environmental Protection Agency
Chemical Substances	Environmental Pollutants
Language	English
Publishing date	2022-06-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	204477-8
ISSN	1096-0333 ; 0041-008X
ISSN (online)	1096-0333
ISSN	0041-008X
DOI	10.1016/j.taap.2022.116141
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Article: Pervasive environmental chemicals impair oligodendrocyte development.

Cohn, Erin F / Clayton, Benjamin L L / Madhavan, Mayur / Yacoub, Sara / Federov, Yuriy / Paul-Friedman, Katie / Shafer, Timothy J / Tesar, Paul J

bioRxiv : the preprint server for biology

2023

Abstract: Exposure to environmental chemicals can impair ... ...

Abstract	Exposure to environmental chemicals can impair neurodevelopment
Language	English
Publishing date	2023-02-12
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.02.10.528042
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Article: Evaluating the utility of a high throughput thiol-containing fluorescent probe to screen for reactivity: A case study with the Tox21 library.

Patlewicz, Grace / Paul-Friedman, Katie / Houck, Keith / Zhang, Li / Huang, Ruili / Xia, Menghang / Brown, Jason / Simmons, Steven O

Computational toxicology (Amsterdam, Netherlands)

2023 Volume 26

Abstract: High-throughput screening (HTS) assays for bioactivity in the Tox21 program aim to evaluate an array of different biological targets and pathways, but a significant barrier to interpretation of these data is the lack of high-throughput screening (HTS) ... ...

Abstract	High-throughput screening (HTS) assays for bioactivity in the Tox21 program aim to evaluate an array of different biological targets and pathways, but a significant barrier to interpretation of these data is the lack of high-throughput screening (HTS) assays intended to identify non-specific reactive chemicals. This is an important aspect for prioritising chemicals to test in specific assays, identifying promiscuous chemicals based on their reactivity, as well as addressing hazards such as skin sensitisation which are not necessarily initiated by a receptor-mediated effect but act through a non-specific mechanism. Herein, a fluorescence-based HTS assay that allows the identification of thiol-reactive compounds was used to screen 7,872 unique chemicals in the Tox21 10K chemical library. Active chemicals were compared with profiling outcomes using structural alerts encoding electrophilic information. Random Forest classification models based on chemical fingerprints were developed to predict assay outcomes and evaluated through 10-fold stratified cross validation (CV). The mean CV Balanced Accuracy of the validation set was 0.648. The model developed shows promise as a tool to screen untested chemicals for their potential electrophilic reactivity based solely on chemical structural features.
Language	English
Publishing date	2023-06-30
Publishing country	Netherlands
Document type	Journal Article
ISSN	2468-1113
ISSN	2468-1113
DOI	10.1016/j.comtox.2023.100271
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Article ; Online: Pervasive environmental chemicals impair oligodendrocyte development.

Cohn, Erin F / Clayton, Benjamin L L / Madhavan, Mayur / Lee, Kristin A / Yacoub, Sara / Fedorov, Yuriy / Scavuzzo, Marissa A / Paul Friedman, Katie / Shafer, Timothy J / Tesar, Paul J

Nature neuroscience

2024

Abstract: Exposure to environmental chemicals can impair neurodevelopment, and oligodendrocytes may be particularly vulnerable, as their development extends from gestation into adulthood. However, few environmental chemicals have been assessed for potential risks ... ...

Abstract	Exposure to environmental chemicals can impair neurodevelopment, and oligodendrocytes may be particularly vulnerable, as their development extends from gestation into adulthood. However, few environmental chemicals have been assessed for potential risks to oligodendrocytes. Here, using a high-throughput developmental screen in cultured cells, we identified environmental chemicals in two classes that disrupt oligodendrocyte development through distinct mechanisms. Quaternary compounds, ubiquitous in disinfecting agents and personal care products, were potently and selectively cytotoxic to developing oligodendrocytes, whereas organophosphate flame retardants, commonly found in household items such as furniture and electronics, prematurely arrested oligodendrocyte maturation. Chemicals from each class impaired oligodendrocyte development postnatally in mice and in a human 3D organoid model of prenatal cortical development. Analysis of epidemiological data showed that adverse neurodevelopmental outcomes were associated with childhood exposure to the top organophosphate flame retardant identified by our screen. This work identifies toxicological vulnerabilities for oligodendrocyte development and highlights the need for deeper scrutiny of these compounds' impacts on human health.
Language	English
Publishing date	2024-03-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	1420596-8
ISSN	1546-1726 ; 1097-6256
ISSN (online)	1546-1726
ISSN	1097-6256
DOI	10.1038/s41593-024-01599-2
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Zs.A 4891: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 67: Show issues

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Article ; Online: High-Throughput Transcriptomics of Water Extracts Detects Reductions in Biological Activity with Water Treatment Processes.

Rogers, Jesse D / Leusch, Frederic D L / Chambers, Bryant / Daniels, Kevin D / Everett, Logan J / Judson, Richard / Maruya, Keith / Mehinto, Alvine C / Neale, Peta A / Paul-Friedman, Katie / Thomas, Russell / Snyder, Shane A / Harrill, Joshua

Environmental science & technology

2024 Volume 58, Issue 4, Page(s) 2027–2037

Abstract: The presence of numerous chemical contaminants from industrial, agricultural, and pharmaceutical sources in water supplies poses a potential risk to human and ecological health. Current chemical analyses suffer from limitations, including chemical ... ...

Abstract	The presence of numerous chemical contaminants from industrial, agricultural, and pharmaceutical sources in water supplies poses a potential risk to human and ecological health. Current chemical analyses suffer from limitations, including chemical coverage and high cost, and broad-coverage
MeSH term(s)	Humans ; Environmental Monitoring ; Water Pollutants, Chemical/analysis ; Water Quality ; Water Purification ; Gene Expression Profiling ; Biological Assay
Chemical Substances	Water Pollutants, Chemical
Language	English
Publishing date	2024-01-18
Publishing country	United States
Document type	Journal Article
ISSN	1520-5851
ISSN (online)	1520-5851
DOI	10.1021/acs.est.3c07525
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Article ; Online: Integrating Data From In Vitro New Approach Methodologies for Developmental Neurotoxicity.

Carstens, Kelly E / Carpenter, Amy F / Martin, Melissa M / Harrill, Joshua A / Shafer, Timothy J / Paul Friedman, Katie

Toxicological sciences : an official journal of the Society of Toxicology

2022 Volume 187, Issue 1, Page(s) 62–79

Abstract: In vivo developmental neurotoxicity (DNT) testing is resource intensive and lacks information on cellular processes affected by chemicals. To address this, DNT new approach methodologies (NAMs) are being evaluated, including: the microelectrode array ... ...

Abstract	In vivo developmental neurotoxicity (DNT) testing is resource intensive and lacks information on cellular processes affected by chemicals. To address this, DNT new approach methodologies (NAMs) are being evaluated, including: the microelectrode array neuronal network formation assay; and high-content imaging to evaluate proliferation, apoptosis, neurite outgrowth, and synaptogenesis. This work addresses 3 hypotheses: (1) a broad screening battery provides a sensitive marker of DNT bioactivity; (2) selective bioactivity (occurring at noncytotoxic concentrations) may indicate functional processes disrupted; and, (3) a subset of endpoints may optimally classify chemicals with in vivo evidence for DNT. The dataset was comprised of 92 chemicals screened in all 57 assay endpoints sourced from publicly available data, including a set of DNT NAM evaluation chemicals with putative positives (53) and negatives (13). The DNT NAM battery provides a sensitive marker of DNT bioactivity, particularly in cytotoxicity and network connectivity parameters. Hierarchical clustering suggested potency (including cytotoxicity) was important for classifying positive chemicals with high sensitivity (93%) but failed to distinguish patterns of disrupted functional processes. In contrast, clustering of selective values revealed informative patterns of differential activity but demonstrated lower sensitivity (74%). The false negatives were associated with several limitations, such as the maximal concentration tested or gaps in the biology captured by the current battery. This work demonstrates that this multi-dimensional assay suite provides a sensitive biomarker for DNT bioactivity, with selective activity providing possible insight into specific functional processes affected by chemical exposure and a basis for further research.
MeSH term(s)	Humans ; Neurogenesis ; Neuronal Outgrowth ; Neurons ; Neurotoxicity Syndromes/etiology ; Toxicity Tests/methods
Language	English
Publishing date	2022-02-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1420885-4
ISSN	1096-0929 ; 1096-6080
ISSN (online)	1096-0929
ISSN	1096-6080
DOI	10.1093/toxsci/kfac018
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Article ; Online: A Comparison of In Vitro Points of Departure with Human Blood Levels for Per- and Polyfluoroalkyl Substances (PFAS).

Judson, Richard S / Smith, Doris / DeVito, Michael / Wambaugh, John F / Wetmore, Barbara A / Paul Friedman, Katie / Patlewicz, Grace / Thomas, Russell S / Sayre, Risa R / Olker, Jennifer H / Degitz, Sigmund / Padilla, Stephanie / Harrill, Joshua A / Shafer, Timothy / Carstens, Kelly E

Toxics

2024 Volume 12, Issue 4

Abstract: Per- and polyfluoroalkyl substances (PFAS) are widely used, and their fluorinated state contributes to unique uses and stability but also long half-lives in the environment and humans. PFAS have been shown to be toxic, leading to immunosuppression, ... ...

Abstract	Per- and polyfluoroalkyl substances (PFAS) are widely used, and their fluorinated state contributes to unique uses and stability but also long half-lives in the environment and humans. PFAS have been shown to be toxic, leading to immunosuppression, cancer, and other adverse health outcomes. Only a small fraction of the PFAS in commerce have been evaluated for toxicity using in vivo tests, which leads to a need to prioritize which compounds to examine further. Here, we demonstrate a prioritization approach that combines human biomonitoring data (blood concentrations) with bioactivity data (concentrations at which bioactivity is observed in vitro) for 31 PFAS. The in vitro data are taken from a battery of cell-based assays, mostly run on human cells. The result is a Bioactive Concentration to Blood Concentration Ratio (BCBCR), similar to a margin of exposure (MoE). Chemicals with low BCBCR values could then be prioritized for further risk assessment. Using this method, two of the PFAS, PFOA (Perfluorooctanoic Acid) and PFOS (Perfluorooctane Sulfonic Acid), have BCBCR values < 1 for some populations. An additional 9 PFAS have BCBCR values < 100 for some populations. This study shows a promising approach to screening level risk assessments of compounds such as PFAS that are long-lived in humans and other species.
Language	English
Publishing date	2024-04-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2733883-6
ISSN	2305-6304 ; 2305-6304
ISSN (online)	2305-6304
ISSN	2305-6304
DOI	10.3390/toxics12040271
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