Application of Cell Painting for chemical hazard evaluation in support of screening-level chemical assessments

Nyffeler, Jo; Willis, Clinton; Harris, Felix R.; Foster, M. J.; Chambers, Bryant; Culbreth, Megan; Brockway, Richard E.; Davidson-Fritz, Sarah; Dawson, Daniel; Shah, Imran; Friedman, Katie Paul; Chang, Dan; Everett, Logan J.; Wambaugh, John F.; Patlewicz, Grace; Harrill, Joshua A.

doi:10.1016/j.taap.2023.116513

Application of Cell Painting for chemical hazard evaluation in support of screening-level chemical assessments

Journal Article · Tue Apr 11 00:00:00 EDT 2023 · Toxicology and Applied Pharmacology

DOI:https://doi.org/10.1016/j.taap.2023.116513· OSTI ID:2425588

Nyffeler, Jo ^[1]; Willis, Clinton ^[2]; Harris, Felix R. ^[3]; Foster, M. J. ^[3]; Chambers, Bryant ^[2]; Culbreth, Megan ^[2]; Brockway, Richard E. ^[3]; Davidson-Fritz, Sarah ^[2]; Dawson, Daniel ^[2]; Shah, Imran ^[2]; Friedman, Katie Paul ^[2]; Chang, Dan ^[2]; Everett, Logan J. ^[2]; Wambaugh, John F. ^[2]; Patlewicz, Grace ^[2]; Harrill, Joshua A. ^[4]

US Environmental Protection Agency, Durham, NC (United States); Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)
US Environmental Protection Agency, Durham, NC (United States)
US Environmental Protection Agency, Durham, NC (United States); Oak Ridge Associated Universities (ORAU), Oak Ridge, TN (United States)
US Environmental Protection Agency, Durham, NC (United States); U.S. Environmental Protection Agency, Research Triangle Park, NC (United States)

‘Cell Painting’ is an imaging-based high-throughput phenotypic profiling (HTPP) method in which cultured cells are fluorescently labeled to visualize subcellular structures (i.e., nucleus, nucleoli, endoplasmic reticulum, cytoskeleton, Golgi apparatus / plasma membrane and mitochondria) and to quantify morphological changes in response to chemicals or other perturbagens. HTPP is a high-throughput and cost-effective bioactivity screening method that detects effects associated with many different molecular mechanisms in an untargeted manner, enabling rapid in vitro hazard assessment for thousands of chemicals. Here, 1201 chemicals from the ToxCast library were screened in concentration-response up to ~100 μM in human U-2 OS cells using HTPP. A phenotype altering concentration (PAC) was estimated for chemicals active in the tested range. PACs tended to be higher than lower bound potency values estimated from a broad collection of targeted high-throughput assays, but lower than the threshold for cytotoxicity. In vitro to in vivo extrapolation (IVIVE) was used to estimate administered equivalent doses (AEDs) based on PACs for comparison to human exposure predictions. AEDs for 18/412 chemicals overlapped with predicted human exposures. Phenotypic profile information was also leveraged to identify putative mechanisms of action and group chemicals. Of 58 known nuclear receptor modulators, only glucocorticoids and retinoids produced characteristic profiles; and both receptor types are expressed in U-2 OS cells. Thirteen chemicals with profile similarity to glucocorticoids were tested in a secondary screen and one chemical, pyrene, was confirmed by an orthogonal gene expression assay as a novel putative GR modulating chemical. Most active chemicals demonstrated profiles not associated with a known mechanism-of-action. However, many structurally related chemicals produced similar profiles, with exceptions such as diniconazole, whose profile differed from other active conazoles. Overall, the present study demonstrates how HTPP can be applied in screening-level chemical assessments through a series of examples and brief case studies.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC)

Grant/Contract Number:: SC0014664

OSTI ID:: 2425588

Alternate ID(s):: OSTI ID: 1999835

Journal Information:: Toxicology and Applied Pharmacology, Journal Name: Toxicology and Applied Pharmacology Journal Issue: C Vol. 468; ISSN 0041-008X

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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60 APPLIED LIFE SCIENCES
Cell Painting
Computational toxicology
Concentration-response
High-throughput phenotypic profiling
Pharmacology & Pharmacy
Toxicology

Application of Cell Painting for chemical hazard evaluation in support of screening-level chemical assessments

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