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Franzosa JA, Bonzo JA, Jack J, Baker NC, Kothiya P, Witek RP, Hurban P, Siferd S, Hester S, Shah I, Ferguson SS, Houck KA, Wambaugh JF. High-throughput toxicogenomic screening of chemicals in the environment using metabolically competent hepatic cell cultures. NPJ Syst Biol Appl 2021; 7:7. [PMID: 33504769 PMCID: PMC7840683 DOI: 10.1038/s41540-020-00166-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 10/15/2020] [Indexed: 01/30/2023] Open
Abstract
The ToxCast in vitro screening program has provided concentration-response bioactivity data across more than a thousand assay endpoints for thousands of chemicals found in our environment and commerce. However, most ToxCast screening assays have evaluated individual biological targets in cancer cell lines lacking integrated physiological functionality (such as receptor signaling, metabolism). We evaluated differentiated HepaRGTM cells, a human liver-derived cell model understood to effectively model physiologically relevant hepatic signaling. Expression of 93 gene transcripts was measured by quantitative polymerase chain reaction using Fluidigm 96.96 dynamic arrays in response to 1060 chemicals tested in eight-point concentration-response. A Bayesian framework quantitatively modeled chemical-induced changes in gene expression via six transcription factors including: aryl hydrocarbon receptor, constitutive androstane receptor, pregnane X receptor, farnesoid X receptor, androgen receptor, and peroxisome proliferator-activated receptor alpha. For these chemicals the network model translates transcriptomic data into Bayesian inferences about molecular targets known to activate toxicological adverse outcome pathways. These data also provide new insights into the molecular signaling network of HepaRGTM cell cultures.
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Affiliation(s)
- Jill A Franzosa
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. EPA, Research Triangle Park, NC, 27711, USA
| | - Jessica A Bonzo
- Cell Biology, Biosciences Division, Thermo Fisher Scientific, Frederick, MD, 21703, USA
| | - John Jack
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. EPA, Research Triangle Park, NC, 27711, USA
| | | | - Parth Kothiya
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. EPA, Research Triangle Park, NC, 27711, USA
| | - Rafal P Witek
- Cell Biology, Biosciences Division, Thermo Fisher Scientific, Frederick, MD, 21703, USA
| | | | | | - Susan Hester
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. EPA, Research Triangle Park, NC, 27711, USA
| | - Imran Shah
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. EPA, Research Triangle Park, NC, 27711, USA
| | - Stephen S Ferguson
- Division of National Toxicology Program, National Institutes of Environmental Health Sciences of National Institutes of Health, Durham, NC, 27709, USA
| | - Keith A Houck
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. EPA, Research Triangle Park, NC, 27711, USA
| | - John F Wambaugh
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. EPA, Research Triangle Park, NC, 27711, USA.
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Garabed RB, Jolles A, Garira W, Lanzas C, Gutierrez J, Rempala G. Multi-scale dynamics of infectious diseases. Interface Focus 2019. [DOI: 10.1098/rsfs.2019.0118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
To address the challenge of multiscale dynamics of infectious diseases, the Mathematical Biosciences Institute organized a workshop at The Ohio State University to bring together scientists from a variety of disciplines to share expertise gained through looking at infectious diseases across different scales. The researchers at the workshop, held in April 2018, were specifically looking at three model systems: foot-and-mouth disease, vector-borne diseases and enteric diseases. Although every multiscale model must be necessarily derived from a multiscale system, not every multiscale system has to lead to multiscale models. These three model systems seem to have produced a variety of both multiscale and integrated single-scale mechanistic models that have developed their own strengths and particular challenges. Here, we present papers from some of the workshop participants to show the breadth of the field.
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Affiliation(s)
- Rebecca B. Garabed
- College of Veterinary Medicine–Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - Anna Jolles
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
- Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Winston Garira
- Mathematics and Applied Mathematics, University of Venda, Thohoyandou, Limpopo, South Africa
| | | | - Juan Gutierrez
- Department of Mathematics, University of Texas at San Antonio, San Antonio, TX, USA
| | - Grzegorz Rempala
- College of Public Health–Biostatistics, The Ohio State University, Columbus, OH, USA
- College of Arts and Sciences–Mathematics, The Ohio State University, Columbus, OH, USA
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