Bioactivity screening of environmental chemicals using imaging-based high-throughput phenotypic profiling

Nyffeler, Johanna; Willis, Clinton; Lougee, Ryan; Richard, Ann M.; Friedman, Katie Paul; Harrill, Joshua

doi:10.1016/j.taap.2019.114876

Cited by 94 publications

(127 citation statements)

References 42 publications

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“…Two cytotoxic chemicals (staurosporine and ionomycin) were also included at a single concentration as cell viability positive controls. All 14 reference chemicals, negative controls, and cytotoxic chemicals can be found in Nyffeler et al 14 and the EPA chemical dashboard (https://comptox.epa.gov/dashboard/chemical_ lists/HTPP2019_REFSET).…”

Section: Materials and Test Chemicalsmentioning

confidence: 99%

“…Cell lines were detached from the flask via incubation with 1× TrypLE Select for 7 min (ARPE-19), 8 min (A549, HepG2, MCF7, and U-2 OS), or 10 min (HTB-9). Passaging and maintenance proceeded for each cell line as described in Nyffeler et al 14 Appropriate seeding densities for use during the expansion phase were determined for each cell line to keep a consistent passaging schedule [4 days in vitro (DIV4)] among all cell types. Each cell line was passaged and expanded individually with cryopreservation occurring at P4 (HepG2 and HTB-9), P5 (A549), P6 (MCF7 and U-2 OS), and P11 (ARPE-19) using the manufacturer's recommended cryopreservation media.…”

Section: Cell Culturementioning

confidence: 99%

“…All 14 phenotypic reference chemicals, along with the two negative controls and two cell viability positive controls, were solubilized in DMSO at concentrations ranging from 4 to 20 mM to create chemical stock solutions and stored at −20 °C. These chemical stocks were pipetted into an Echo Qualified 384PP plate and were used in dose plate preparation to make dilution series as described in Nyffeler et al 14 The 14 reference chemicals and two negative controls were tested at seven concentrations (approximate half-log spacing) with three technical replicates per plate. Concentration ranges are listed in Table 1.…”

Section: Chemical Treatmentmentioning

confidence: 99%

“…Assay plates were fluorescently labeled using the adapted Cell Painting procedure as described in Nyffeler et al 14 In the final wash step, 80 µL 1× PBS was dispensed into each well as a storage buffer. Plates were then sealed with optical adhesive tape and stored at 4 °C until image acquisition.…”

Section: Cell Painting (Cp) Assay and Image Processingmentioning

confidence: 99%

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Phenotypic Profiling of Reference Chemicals across Biologically Diverse Cell Types Using the Cell Painting Assay

2020

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Section: Materials and Test Chemicalsmentioning

confidence: 99%

Section: Cell Culturementioning

confidence: 99%

Section: Chemical Treatmentmentioning

confidence: 99%

Section: Cell Painting (Cp) Assay and Image Processingmentioning

confidence: 99%

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Phenotypic Profiling of Reference Chemicals across Biologically Diverse Cell Types Using the Cell Painting Assay

2020

Self Cite

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“…Cell Painting has been used to identify small-molecule mechanisms of action (MOA), study the impact of overexpressing cancer mutations, and discover new bioactive mechanisms, among many other applications (Caicedo et al, 2018;Christoforow et al, 2019;Hughes et al, 2020;Pahl and Sievers, 2019;Rohban et al, 2017;Simm et al, 2018;Wawer et al, 2014) . Additionally, Cell Painting can predict overall mammalian toxicity levels for environmental chemicals (Nyffeler et al, 2020) and some of its derived morphology measurements are readily interpreted by cell biologists and relate to cell health (Bray et al, 2016) . However, no single, inexpensive assay enables discovery of fine-grained cell health readouts that would provide researchers with a more complete understanding of perturbation mechanisms.…”

Section: Introductionmentioning

confidence: 99%

Predicting cell health phenotypes using image-based morphology profiling

Way

Kost‐Alimova

Shibue

et al. 2020

Preprint

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AbstractGenetic and chemical perturbations impact diverse cellular phenotypes, including multiple indicators of cell health. These readouts reveal toxicity and antitumorigenic effects relevant to drug discovery and personalized medicine. We developed two customized microscopy assays that use seven reagents to measure 70 specific cell health phenotypes including proliferation, apoptosis, reactive oxygen species (ROS), DNA damage, and aberrant cell cycle stage progression. We then tested an approach to predict multiple cell health phenotypes using Cell Painting, an inexpensive and scalable image-based morphology assay. In matched CRISPR perturbations of three cancer cell lines, we collected both Cell Painting and cell health data. We found that simple machine learning algorithms can predict many cell health readouts directly from Cell Painting images, at less than half the cost. We hypothesized that these trained models can be applied to accurately predict cell health assay outcomes for any future or existing Cell Painting dataset. For Cell Painting images from a set of 1,500+ compound perturbations across multiple doses, we validated predictions by orthogonal assay readouts, and by confirming mitotic arrest and ROS phenotypes via PLK and proteasome inhibition, respectively. We provide an intuitive web app to browse all predictions at http://broad.io/cell-health-app. Our approach can be used to add cell health annotations to Cell Painting perturbation datasets.

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Community‐Engaged Research and the Use of Open Access ToxVal/ToxRef In Vivo Databases and New Approach Methodologies (NAM) to Address Human Health Risks From Environmental Contaminants

Silva,

Capps,

London

2024

Birth Defects Research

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BackgroundThe paper analyzes opportunities for integrating Open access resources (Abstract Sifter, US EPA and NTP Toxicity Value and Toxicity Reference [ToxVal/ToxRefDB]) and New Approach Methodologies (NAM) integration into Community Engaged Research (CEnR).MethodsCompTox Chemicals Dashboard and Integrated Chemical Environment with in vivo ToxVal/ToxRef and NAMs (in vitro) databases are presented in three case studies to show how these resources could be used in Pilot Projects involving Community Engaged Research (CEnR) from the University of California, Davis, Environmental Health Sciences Center.ResultsCase #1 developed a novel assay methodology for testing pesticide toxicity. Case #2 involved detection of water contaminants from wildfire ash and Case #3 involved contaminants on Tribal Lands. Abstract Sifter/ToxVal/ToxRefDB regulatory data and NAMs could be used to screen/prioritize risks from exposure to metals, PAHs and PFAS from wildfire ash leached into water and to investigate activities of environmental toxins (e.g., pesticides) on Tribal lands. Open access NAMs and computational tools can apply to detection of sensitive biological activities in potential or known adverse outcome pathways to predict points of departure (POD) for comparison with regulatory values for hazard identification. Open access Systematic Empirical Evaluation of Models or biomonitoring exposures are available for human subpopulations and can be used to determine bioactivity (POD) to exposure ratio to facilitate mitigation.ConclusionsThese resources help prioritize chemical toxicity and facilitate regulatory decisions and health protective policies that can aid stakeholders in deciding on needed research. Insights into exposure risks can aid environmental justice and health equity advocates.

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Bioactivity screening of environmental chemicals using imaging-based high-throughput phenotypic profiling

Cited by 94 publications

References 42 publications

Phenotypic Profiling of Reference Chemicals across Biologically Diverse Cell Types Using the Cell Painting Assay

Phenotypic Profiling of Reference Chemicals across Biologically Diverse Cell Types Using the Cell Painting Assay

Predicting cell health phenotypes using image-based morphology profiling

Community‐Engaged Research and the Use of Open Access ToxVal/ToxRef In Vivo Databases and New Approach Methodologies (NAM) to Address Human Health Risks From Environmental Contaminants

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