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Colvin VC, Bramer LM, Rivera BN, Pennington JM, Waters KM, Tilton SC. Modeling PAH Mixture Interactions in a Human In Vitro Organotypic Respiratory Model. Int J Mol Sci 2024; 25:4326. [PMID: 38673911 PMCID: PMC11050152 DOI: 10.3390/ijms25084326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
One of the most significant challenges in human health risk assessment is to evaluate hazards from exposure to environmental chemical mixtures. Polycyclic aromatic hydrocarbons (PAHs) are a class of ubiquitous contaminants typically found as mixtures in gaseous and particulate phases in ambient air pollution associated with petrochemicals from Superfund sites and the burning of fossil fuels. However, little is understood about how PAHs in mixtures contribute to toxicity in lung cells. To investigate mixture interactions and component additivity from environmentally relevant PAHs, two synthetic mixtures were created from PAHs identified in passive air samplers at a legacy creosote site impacted by wildfires. The primary human bronchial epithelial cells differentiated at the air-liquid interface were treated with PAH mixtures at environmentally relevant proportions and evaluated for the differential expression of transcriptional biomarkers related to xenobiotic metabolism, oxidative stress response, barrier integrity, and DNA damage response. Component additivity was evaluated across all endpoints using two independent action (IA) models with and without the scaling of components by toxic equivalence factors. Both IA models exhibited trends that were unlike the observed mixture response and generally underestimated the toxicity across dose suggesting the potential for non-additive interactions of components. Overall, this study provides an example of the usefulness of mixture toxicity assessment with the currently available methods while demonstrating the need for more complex yet interpretable mixture response evaluation methods for environmental samples.
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Affiliation(s)
- Victoria C. Colvin
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
- OSU/PNNL Superfund Research Program, Oregon State University, Corvallis, OR 97331, USA
| | - Lisa M. Bramer
- OSU/PNNL Superfund Research Program, Oregon State University, Corvallis, OR 97331, USA
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Brianna N. Rivera
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
- OSU/PNNL Superfund Research Program, Oregon State University, Corvallis, OR 97331, USA
| | - Jamie M. Pennington
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Katrina M. Waters
- OSU/PNNL Superfund Research Program, Oregon State University, Corvallis, OR 97331, USA
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Susan C. Tilton
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
- OSU/PNNL Superfund Research Program, Oregon State University, Corvallis, OR 97331, USA
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2
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Eisfeld AJ, Anderson LN, Fan S, Walters KB, Halfmann PJ, Westhoff Smith D, Thackray LB, Tan Q, Sims AC, Menachery VD, Schäfer A, Sheahan TP, Cockrell AS, Stratton KG, Webb-Robertson BJM, Kyle JE, Burnum-Johnson KE, Kim YM, Nicora CD, Peralta Z, N'jai AU, Sahr F, van Bakel H, Diamond MS, Baric RS, Metz TO, Smith RD, Kawaoka Y, Waters KM. A compendium of multi-omics data illuminating host responses to lethal human virus infections. Sci Data 2024; 11:328. [PMID: 38565538 PMCID: PMC10987564 DOI: 10.1038/s41597-024-03124-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host response to infection generated from 45 individual experiments involving human viruses from the Orthomyxoviridae, Filoviridae, Flaviviridae, and Coronaviridae families. Analogous experimental designs were implemented across human or mouse host model systems, longitudinal samples were collected over defined time courses, and global multi-omics data (transcriptomics, proteomics, metabolomics, and lipidomics) were acquired by microarray, RNA sequencing, or mass spectrometry analyses. For comparison, we have included transcriptomics datasets from cells treated with type I and type II human interferon. Raw multi-omics data and metadata were deposited in public repositories, and we provide a central location linking the raw data with experimental metadata and ready-to-use, quality-controlled, statistically processed multi-omics datasets not previously available in any public repository. This compendium of infection-induced host response data for reuse will be useful for those endeavouring to understand viral disease pathophysiology and network biology.
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Affiliation(s)
- Amie J Eisfeld
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Lindsey N Anderson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Shufang Fan
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Coronavirus and Other Respiratory Viruses Laboratory Branch (CRVLB), Coronavirus and Other Respiratory Viruses Division (CORVD), National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, GA, 30329, USA
| | - Kevin B Walters
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, 21702, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Danielle Westhoff Smith
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Surgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Qing Tan
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Amy C Sims
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
- Nuclear, Chemistry, and Biosciences Division; National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Vineet D Menachery
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Adam S Cockrell
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
- Solid Biosciences, Charlston, MA, 02139, USA
| | - Kelly G Stratton
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Bobbie-Jo M Webb-Robertson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kristin E Burnum-Johnson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Young-Mo Kim
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Carrie D Nicora
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Zuleyma Peralta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, USA
- Partillion Bioscience, Los Angeles, CA, 90064, USA
| | - Alhaji U N'jai
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biological Sciences, Fourah Bay College, Freetown, Sierra Leone
- Department of Microbiology, College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- Department of Medical Education, California University of Science and Medicine, Colton, CA, 92324, USA
| | - Foday Sahr
- Department of Microbiology, College of Medicine and Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, North Carolina, 27599, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Thomas O Metz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Richard D Smith
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 108-8639, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 108-8639, Japan
| | - Katrina M Waters
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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3
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McLarnan SM, Bramer LM, Dixon HM, Scott RP, Calero L, Holmes D, Gibson EA, Cavalier HM, Rohlman D, Miller RL, Kincl L, Waters KM, Anderson KA, Herbstman JB. Predicting personal PAH exposure using high dimensional questionnaire and wristband data. J Expo Sci Environ Epidemiol 2024:10.1038/s41370-023-00617-y. [PMID: 38177333 DOI: 10.1038/s41370-023-00617-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND Polycyclic aromatic hydrocarbons (PAHs) are a class of pervasive environmental pollutants with a variety of known health effects. While significant work has been completed to estimate personal exposure to PAHs, less has been done to identify sources of these exposures. Comprehensive characterization of reported sources of personal PAH exposure is a critical step to more easily identify individuals at risk of high levels of exposure and for developing targeted interventions based on source of exposure. OBJECTIVE In this study, we leverage data from a New York (NY)-based birth cohort to identify personal characteristics or behaviors associated with personal PAH exposure and develop models for the prediction of PAH exposure. METHODS We quantified 61 PAHs measured using silicone wristband samplers in association with 75 questionnaire variables from 177 pregnant individuals. We evaluated univariate associations between each compound and questionnaire variable, conducted regression tree analysis for each PAH compound and completed a principal component analysis of for each participant's entire PAH exposure profile to determine the predictors of PAH levels. RESULTS Regression tree analyses of individual compounds and exposure mixture identified income, time spent outdoors, maternal age, country of birth, transportation type, and season as the variables most frequently predictive of exposure.
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Affiliation(s)
- Sarah M McLarnan
- Department of Environmental Health Sciences, Columbia University, Columbia Center for Children's Environmental Health, Mailman School of Public Health, New York City, NY, USA.
| | - Lisa M Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Holly M Dixon
- Environmental and Molecular Toxicology, Food Safety and Environmental Stewardship Program, Oregon State University, Corvallis, OR, USA
| | - Richard P Scott
- Environmental and Molecular Toxicology, Food Safety and Environmental Stewardship Program, Oregon State University, Corvallis, OR, USA
| | - Lehyla Calero
- Department of Environmental Health Sciences, Columbia University, Columbia Center for Children's Environmental Health, Mailman School of Public Health, New York City, NY, USA
| | - Darrell Holmes
- Department of Environmental Health Sciences, Columbia University, Columbia Center for Children's Environmental Health, Mailman School of Public Health, New York City, NY, USA
| | - Elizabeth A Gibson
- Department of Environmental Health Sciences, Columbia University, Columbia Center for Children's Environmental Health, Mailman School of Public Health, New York City, NY, USA
| | - Haleigh M Cavalier
- Department of Environmental Health Sciences, Columbia University, Columbia Center for Children's Environmental Health, Mailman School of Public Health, New York City, NY, USA
| | - Diana Rohlman
- Oregon State University, College of Public Health and Human Sciences, Corvallis, OR, USA
| | - Rachel L Miller
- Division of Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Laurel Kincl
- Oregon State University, College of Public Health and Human Sciences, Corvallis, OR, USA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Environmental and Molecular Toxicology, Food Safety and Environmental Stewardship Program, Oregon State University, Corvallis, OR, USA
| | - Kim A Anderson
- Environmental and Molecular Toxicology, Food Safety and Environmental Stewardship Program, Oregon State University, Corvallis, OR, USA
| | - Julie B Herbstman
- Department of Environmental Health Sciences, Columbia University, Columbia Center for Children's Environmental Health, Mailman School of Public Health, New York City, NY, USA
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4
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Bramer LM, Dixon HM, Degnan DJ, Rohlman D, Herbstman JB, Anderson KA, Waters KM. Expanding the access of wearable silicone wristbands in community-engaged research through best practices in data analysis and integration. Pac Symp Biocomput 2024; 29:170-186. [PMID: 38160278 PMCID: PMC10766083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Wearable silicone wristbands are a rapidly growing exposure assessment technology that offer researchers the ability to study previously inaccessible cohorts and have the potential to provide a more comprehensive picture of chemical exposure within diverse communities. However, there are no established best practices for analyzing the data within a study or across multiple studies, thereby limiting impact and access of these data for larger meta-analyses. We utilize data from three studies, from over 600 wristbands worn by participants in New York City and Eugene, Oregon, to present a first-of-its-kind manuscript detailing wristband data properties. We further discuss and provide concrete examples of key areas and considerations in common statistical modeling methods where best practices must be established to enable meta-analyses and integration of data from multiple studies. Finally, we detail important and challenging aspects of machine learning, meta-analysis, and data integration that researchers will face in order to extend beyond the limited scope of individual studies focused on specific populations.
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Affiliation(s)
- Lisa M Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd Richland, WA 99354, United States,
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5
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Bramer LM, Dixon HM, Degnan DJ, Rohlman D, Herbstman JB, Anderson KA, Waters KM. Expanding the access of wearable silicone wristbands in community-engaged research through best practices in data analysis and integration. bioRxiv 2023:2023.09.29.560217. [PMID: 37873084 PMCID: PMC10592864 DOI: 10.1101/2023.09.29.560217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Wearable silicone wristbands are a rapidly growing exposure assessment technology that offer researchers the ability to study previously inaccessible cohorts and have the potential to provide a more comprehensive picture of chemical exposure within diverse communities. However, there are no established best practices for analyzing the data within a study or across multiple studies, thereby limiting impact and access of these data for larger meta-analyses. We utilize data from three studies, from over 600 wristbands worn by participants in New York City and Eugene, Oregon, to present a first-of-its-kind manuscript detailing wristband data properties. We further discuss and provide concrete examples of key areas and considerations in common statistical modeling methods where best practices must be established to enable meta-analyses and integration of data from multiple studies. Finally, we detail important and challenging aspects of machine learning, meta-analysis, and data integration that researchers will face in order to extend beyond the limited scope of individual studies focused on specific populations.
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Affiliation(s)
- Lisa M Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd Richland, WA 99354, United States
| | - Holly M Dixon
- Environmental and Molecular Toxicology, Oregon State University, 1007 Agriculture & Life Sciences Building, Corvallis, OR 97331, United States
| | - David J Degnan
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd Richland, WA 99354, United States
| | - Diana Rohlman
- College of Health, Oregon State University, 103 SW Memorial Place, Corvallis, OR 97331, United States
| | - Julie B Herbstman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York City, NY 10032, United States
| | - Kim A Anderson
- Environmental and Molecular Toxicology, Oregon State University, 1007 Agriculture & Life Sciences Building, Corvallis, OR 97331, United States
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd Richland, WA 99354, United States
- Environmental and Molecular Toxicology, Oregon State University, 1007 Agriculture & Life Sciences Building, Corvallis, OR 97331, United States
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6
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McClure RS, Rericha Y, Waters KM, Tanguay RL. 3' RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism. Front Bioinform 2023; 3:1234218. [PMID: 37576716 PMCID: PMC10414111 DOI: 10.3389/fbinf.2023.1234218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction: The application of RNA-sequencing has led to numerous breakthroughs related to investigating gene expression levels in complex biological systems. Among these are knowledge of how organisms, such as the vertebrate model organism zebrafish (Danio rerio), respond to toxicant exposure. Recently, the development of 3' RNA-seq has allowed for the determination of gene expression levels with a fraction of the required reads compared to standard RNA-seq. While 3' RNA-seq has many advantages, a comparison to standard RNA-seq has not been performed in the context of whole organism toxicity and sparse data. Methods and results: Here, we examined samples from zebrafish exposed to perfluorobutane sulfonamide (FBSA) with either 3' or standard RNA-seq to determine the advantages of each with regards to the identification of functionally enriched pathways. We found that 3' and standard RNA-seq showed specific advantages when focusing on annotated or unannotated regions of the genome. We also found that standard RNA-seq identified more differentially expressed genes (DEGs), but that this advantage disappeared under conditions of sparse data. We also found that standard RNA-seq had a significant advantage in identifying functionally enriched pathways via analysis of DEG lists but that this advantage was minimal when identifying pathways via gene set enrichment analysis of all genes. Conclusions: These results show that each approach has experimental conditions where they may be advantageous. Our observations can help guide others in the choice of 3' RNA-seq vs standard RNA sequencing to query gene expression levels in a range of biological systems.
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Affiliation(s)
- Ryan S. McClure
- Biological Sciences Division, Pacific Northwest Laboratory, Richland, WA, United States
| | - Yvonne Rericha
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Katrina M. Waters
- Biological Sciences Division, Pacific Northwest Laboratory, Richland, WA, United States
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Robyn L. Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
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7
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Fritch EJ, Sanders W, Sims AC, Herring LE, Barker NK, Schepmoes AA, Weitz KK, Texier JR, Dittmer DP, Graves LM, Smith RD, Waters KM, Moorman NJ, Baric RS, Graham RL. Metatranscriptomics analysis reveals a novel transcriptional and translational landscape during Middle East respiratory syndrome coronavirus infection. iScience 2023; 26:106780. [PMID: 37193127 PMCID: PMC10152751 DOI: 10.1016/j.isci.2023.106780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 01/31/2023] [Accepted: 04/25/2023] [Indexed: 05/18/2023] Open
Abstract
Among all RNA viruses, coronavirus RNA transcription is the most complex and involves a process termed "discontinuous transcription" that results in the production of a set of 3'-nested, co-terminal genomic and subgenomic RNAs during infection. While the expression of the classic canonical set of subgenomic RNAs depends on the recognition of a 6- to 7-nt transcription regulatory core sequence (TRS), here, we use deep sequence and metagenomics analysis strategies and show that the coronavirus transcriptome is even more vast and more complex than previously appreciated and involves the production of leader-containing transcripts that have canonical and noncanonical leader-body junctions. Moreover, by ribosome protection and proteomics analyses, we show that both positive- and negative-sense transcripts are translationally active. The data support the hypothesis that the coronavirus proteome is much vaster than previously noted in the literature.
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Affiliation(s)
- Ethan J Fritch
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Wes Sanders
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Amy C Sims
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura E Herring
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Michael Hooker Proteomics Core Facility, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie K Barker
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Michael Hooker Proteomics Core Facility, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99394, USA
| | - Karl K Weitz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99394, USA
| | - Jordan R Texier
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dirk P Dittmer
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lee M Graves
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Michael Hooker Proteomics Core Facility, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Richard D Smith
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99394, USA
| | - Katrina M Waters
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99394, USA
| | - Nathaniel J Moorman
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ralph S Baric
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rachel L Graham
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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8
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Gosline SJC, Kim DN, Pande P, Thomas DG, Truong L, Hoffman P, Barton M, Loftus J, Moran A, Hampton S, Dowson S, Franklin L, Degnan D, Anderson L, Thessen A, Tanguay RL, Anderson KA, Waters KM. The Superfund Research Program Analytics Portal: linking environmental chemical exposure to biological phenotypes. Sci Data 2023; 10:151. [PMID: 36944655 PMCID: PMC10030892 DOI: 10.1038/s41597-023-02021-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/14/2023] [Indexed: 03/23/2023] Open
Abstract
The OSU/PNNL Superfund Research Program (SRP) represents a longstanding collaboration to quantify Polycyclic Aromatic Hydrocarbons (PAHs) at various superfund sites in the Pacific Northwest and assess their potential impact on human health. To link the chemical measurements to biological activity, we describe the use of the zebrafish as a high-throughput developmental toxicity model that provides quantitative measurements of the exposure to chemicals. Toward this end, we have linked over 150 PAHs found at Superfund sites to the effect of these same chemicals in zebrafish, creating a rich dataset that links environmental exposure to biological response. To quantify this response, we have implemented a dose-response modelling pipeline to calculate benchmark dose parameters which enable potency comparison across over 500 chemicals and 12 of the phenotypes measured in zebrafish. We provide a rich dataset for download and analysis as well as a web portal that provides public access to this dataset via an interactive web site designed to support exploration and re-use of these data by the scientific community at http://srp.pnnl.gov .
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Affiliation(s)
| | - Doo Nam Kim
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Paritosh Pande
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | | | | | - Joseph Loftus
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Addy Moran
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Shawn Hampton
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Scott Dowson
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - David Degnan
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Anne Thessen
- University of Colorado Anschutz Medical School, Denver, CO, USA
| | | | | | - Katrina M Waters
- Pacific Northwest National Laboratory, Richland, WA, USA.
- Oregon State University, Corvallis, WA, USA.
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9
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Bramer LM, Hontz RD, Eisfeld AJ, Sims AC, Kim YM, Stratton KG, Nicora CD, Gritsenko MA, Schepmoes AA, Akasaka O, Koga M, Tsutsumi T, Nakamura M, Nakachi I, Baba R, Tateno H, Suzuki S, Nakajima H, Kato H, Ishida K, Ishii M, Uwamino Y, Mitamura K, Paurus VL, Nakayasu ES, Attah IK, Letizia AG, Waters KM, Metz TO, Corson K, Kawaoka Y, Gerbasi VR, Yotsuyanagi H, Iwatsuki-Horimoto K. Multi-omics of NET formation and correlations with CNDP1, PSPB, and L-cystine levels in severe and mild COVID-19 infections. Heliyon 2023; 9:e13795. [PMID: 36915486 PMCID: PMC9988701 DOI: 10.1016/j.heliyon.2023.e13795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
The detailed mechanisms of COVID-19 infection pathology remain poorly understood. To improve our understanding of SARS-CoV-2 pathology, we performed a multi-omics and correlative analysis of an immunologically naïve SARS-CoV-2 clinical cohort from blood plasma of uninfected controls, mild, and severe infections. Consistent with previous observations, severe patient populations showed an elevation of pulmonary surfactant levels. Intriguingly, mild patients showed a statistically significant elevation in the carnosine dipeptidase modifying enzyme (CNDP1). Mild and severe patient populations showed a strong elevation in the metabolite L-cystine (oxidized form of the amino acid cysteine) and enzymes with roles in glutathione metabolism. Neutrophil extracellular traps (NETs) were observed in both mild and severe populations, and NET formation was higher in severe vs. mild samples. Our correlative analysis suggests a potential protective role for CNDP1 in suppressing PSPB release from the pulmonary space whereas NET formation correlates with increased PSPB levels and disease severity. In our discussion we put forward a possible model where NET formation drives pulmonary occlusions and CNDP1 promotes antioxidation, pleiotropic immune responses, and vasodilation by accelerating histamine synthesis.
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Affiliation(s)
- Lisa M Bramer
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert D Hontz
- U.S. Naval Medical Research Unit No. TWO (NAMRU-2), Singapore, Singapore
| | - Amie J Eisfeld
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Amy C Sims
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Young-Mo Kim
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | | | | | - Osamu Akasaka
- Emergency Medical Center, Fujisawa City Hospital 2-6-1 Fujisawa, Fujisawa, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Morio Nakamura
- Department of Pulmonary Medicine, Tokyo Saiseikai Central, Tokyo, Japan
| | - Ichiro Nakachi
- Pulmonary Division, Department of Internal Medicine, Utsunomiya Hospital, Utsunomiya, Japan
| | - Rie Baba
- Pulmonary Division, Department of Internal Medicine, Utsunomiya Hospital, Utsunomiya, Japan
| | - Hiroki Tateno
- Department of Pulmonary Medicine, Saitama City Hospital, Saitama, Japan
| | - Shoji Suzuki
- Department of Pulmonary Medicine, Saitama City Hospital, Saitama, Japan
| | - Hideaki Nakajima
- Department of Hematology and Clinical Immunology, University School of Medicine, Yokohama, Japan
| | - Hideaki Kato
- Department of Hematology and Clinical Immunology, University School of Medicine, Yokohama, Japan
| | | | - Makoto Ishii
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yoshifumi Uwamino
- Department of Laboratory Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Keiko Mitamura
- Division of Infection Control, Eiju General Hospital, Tokyo, Japan
| | | | | | - Isaac K Attah
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Andrew G Letizia
- U.S. Naval Medical Research Unit No. TWO (NAMRU-2), Singapore, Singapore
| | | | - Thomas O Metz
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karen Corson
- U.S. Naval Medical Research Unit No. TWO (NAMRU-2), Singapore, Singapore
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.,Department of Microbiology and Immunology, Japan.,International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | | | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo
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10
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Rude CI, Tidwell LG, Tilton SC, Waters KM, Anderson KA, Tanguay RL. Coupling Environmental Whole Mixture Toxicity Screening with Unbiased RNA-Seq Reveals Site-Specific Biological Responses in Zebrafish. Toxics 2023; 11:201. [PMID: 36976966 PMCID: PMC10053777 DOI: 10.3390/toxics11030201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Passive sampling device (PSD) extracts paired with developmental toxicity assays in Danio Rerio (zebrafish) are excellent sensors for whole mixture toxicity associated with the bioavailable non-polar organics at environmental sites. We expand this concept by incorporating RNA-Seq in 48-h post fertilization zebrafish statically exposed to PSD extracts from two Portland Harbor Superfund Site locations: river mile 6.5W (RM 6.5W) and river mile 7W (RM 7W). RM 6.5W contained higher concentrations of polycyclic aromatic hydrocarbons (PAHs), but the diagnostic ratios of both extracts indicated similar PAH sourcing and composition. Developmental screens determined RM 6.5W to be more toxic with the most sensitive endpoint being a "wavy" notochord malformation. Differential gene expression from exposure to both extracts was largely parallel, although more pronounced for RM 6.5W. When compared to the gene expression associated with individual chemical exposures, PSD extracts produced some gene signatures parallel to PAHs but were more closely matched by oxygenated-PAHs. Additionally, differential expression, reminiscent of the wavy notochord phenotype, was not accounted for by either class of chemical, indicating the potential of other contaminants driving mixture toxicity. These techniques offer a compelling method for non-targeted hazard characterization of whole mixtures in an in vivo vertebrate system without requiring complete chemical characterization.
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Affiliation(s)
- Christian I. Rude
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Lane G. Tidwell
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Susan C. Tilton
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Katrina M. Waters
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA 99354, USA
| | - Kim A. Anderson
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Robyn L. Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
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11
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Flores JE, Claborne DM, Weller ZD, Webb-Robertson BJM, Waters KM, Bramer LM. Missing data in multi-omics integration: Recent advances through artificial intelligence. Front Artif Intell 2023; 6:1098308. [PMID: 36844425 PMCID: PMC9949722 DOI: 10.3389/frai.2023.1098308] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Biological systems function through complex interactions between various 'omics (biomolecules), and a more complete understanding of these systems is only possible through an integrated, multi-omic perspective. This has presented the need for the development of integration approaches that are able to capture the complex, often non-linear, interactions that define these biological systems and are adapted to the challenges of combining the heterogenous data across 'omic views. A principal challenge to multi-omic integration is missing data because all biomolecules are not measured in all samples. Due to either cost, instrument sensitivity, or other experimental factors, data for a biological sample may be missing for one or more 'omic techologies. Recent methodological developments in artificial intelligence and statistical learning have greatly facilitated the analyses of multi-omics data, however many of these techniques assume access to completely observed data. A subset of these methods incorporate mechanisms for handling partially observed samples, and these methods are the focus of this review. We describe recently developed approaches, noting their primary use cases and highlighting each method's approach to handling missing data. We additionally provide an overview of the more traditional missing data workflows and their limitations; and we discuss potential avenues for further developments as well as how the missing data issue and its current solutions may generalize beyond the multi-omics context.
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Affiliation(s)
- Javier E. Flores
- Pacific Northwest National Laboratory, Biological Sciences Division, Earth and Biological Sciences Directorate, Richland, WA, United States
| | - Daniel M. Claborne
- Pacific Northwest National Laboratory, Artificial Intelligence and Data Analytics Division, National Security Directorate, Richland, WA, United States
| | - Zachary D. Weller
- Pacific Northwest National Laboratory, Artificial Intelligence and Data Analytics Division, National Security Directorate, Richland, WA, United States
| | - Bobbie-Jo M. Webb-Robertson
- Pacific Northwest National Laboratory, Biological Sciences Division, Earth and Biological Sciences Directorate, Richland, WA, United States
| | - Katrina M. Waters
- Pacific Northwest National Laboratory, Biological Sciences Division, Earth and Biological Sciences Directorate, Richland, WA, United States
| | - Lisa M. Bramer
- Pacific Northwest National Laboratory, Biological Sciences Division, Earth and Biological Sciences Directorate, Richland, WA, United States,*Correspondence: Lisa M. Bramer ✉
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12
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Wilson LB, McClure RS, Waters KM, Simonich MT, Tanguay RL. Concentration-response gene expression analysis in zebrafish reveals phenotypically-anchored transcriptional responses to retene. Front Toxicol 2022; 4:950503. [PMID: 36093370 PMCID: PMC9453431 DOI: 10.3389/ftox.2022.950503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental contaminants and are associated with human disease. Canonically, many PAHs induce toxicity via activation of the aryl hydrocarbon receptor (AHR) pathway. While the interaction between PAHs and the AHR is well-established, understanding which AHR-regulated transcriptional effects directly result in observable phenotypes and which are adaptive or benign is important to better understand PAH toxicity. Retene is a frequently detected PAH in environmental sampling and has been associated with AHR2-dependent developmental toxicity in zebrafish, though its mechanism of toxicity has not been fully elucidated. To interrogate transcriptional changes causally associated with retene toxicity, we conducted whole-animal RNA sequencing at 48 h post-fertilization after exposure to eight retene concentrations. We aimed to identify the most sensitive transcriptomic responses and to determine whether this approach could uncover gene sets uniquely differentially expressed at concentrations which induce a phenotype. We identified a concentration-response relationship for differential gene expression in both number of differentially expressed genes (DEGs) and magnitude of expression change. Elevated expression of cyp1a at retene concentrations below the threshold for teratogenicity suggested that while cyp1a expression is a sensitive biomarker of AHR activation, it may be too sensitive to serve as a biomarker of teratogenicity. Genes differentially expressed at only non-teratogenic concentrations were enriched for transforming growth factor-β (TGF-β) signaling pathway disruption while DEGs identified at only teratogenic concentrations were significantly enriched for response to xenobiotic stimulus and reduction-oxidation reaction activity. DEGs which spanned both non-teratogenic and teratogenic concentrations showed similar disrupted biological processes to those unique to teratogenic concentrations, indicating these processes were disrupted at low exposure concentrations. Gene co-expression network analysis identified several gene modules, including those associated with PAHs and AHR2 activation. One, Module 7, was strongly enriched for AHR2-associated genes and contained the strongest responses to retene. Benchmark concentration (BMC) of Module seven genes identified a median BMC of 7.5 µM, nearly the highest retene concentration with no associated teratogenicity, supporting the hypothesis that Module seven genes are largely responsible for retene toxicity.
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Affiliation(s)
- Lindsay B. Wilson
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States
| | - Ryan S. McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Katrina M. Waters
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Michael T. Simonich
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States
| | - Robyn L. Tanguay
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Oregon State University, Corvallis, OR, United States
- *Correspondence: Robyn L. Tanguay,
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13
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Evoy R, Kincl L, Rohlman D, Bramer LM, Dixon HM, Hystad P, Bae H, Barton M, Phillips A, Miller RL, Waters KM, Herbstman JB, Anderson KA. Impact of acute temperature and air pollution exposures on adult lung function: A panel study of asthmatics. PLoS One 2022; 17:e0270412. [PMID: 35763502 PMCID: PMC9239441 DOI: 10.1371/journal.pone.0270412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 06/09/2022] [Indexed: 11/25/2022] Open
Abstract
Background Individuals with respiratory conditions, such as asthma, are particularly susceptible to adverse health effects associated with higher levels of ambient air pollution and temperature. This study evaluates whether hourly levels of fine particulate matter (PM2.5) and dry bulb globe temperature (DBGT) are associated with the lung function of adult participants with asthma. Methods and findings Global positioning system (GPS) location, respiratory function (measured as forced expiratory volume at 1 second (FEV1)), and self-reports of asthma medication usage and symptoms were collected as part of the Exposure, Location, and Lung Function (ELF) study. Hourly ambient PM2.5 and DBGT exposures were estimated by integrating air quality and temperature public records with time-activity patterns using GPS coordinates for each participant (n = 35). The relationships between acute PM2.5, DBGT, rescue bronchodilator use, and lung function collected in one week periods and over two seasons (summer/winter) were analyzed by multivariate regression, using different exposure time frames. In separate models, increasing levels in PM2.5, but not DBGT, were associated with rescue bronchodilator use. Conversely DBGT, but not PM2.5, had a significant association with FEV1. When DBGT and PM2.5 exposures were placed in the same model, the strongest association between cumulative PM2.5 exposures and the use of rescue bronchodilator was identified at the 0–24 hours (OR = 1.030; 95% CI = 1.012–1.049; p-value = 0.001) and 0–48 hours (OR = 1.030; 95% CI = 1.013–1.057; p-value = 0.001) prior to lung function measure. Conversely, DBGT exposure at 0 hours (β = 3.257; SE = 0.879; p-value>0.001) and 0–6 hours (β = 2.885; SE = 0.903; p-value = 0.001) hours before a reading were associated with FEV1. No significant interactions between DBGT and PM2.5 were observed for rescue bronchodilator use or FEV1. Conclusions Short-term increases in PM2.5 were associated with increased rescue bronchodilator use, while DBGT was associated with higher lung function (i.e. FEV1). Further studies are needed to continue to elucidate the mechanisms of acute exposure to PM2.5 and DBGT on lung function in asthmatics.
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Affiliation(s)
- Richard Evoy
- College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| | - Laurel Kincl
- College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon, United States of America
| | - Diana Rohlman
- College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon, United States of America
- Superfund Research Program, Oregon State University, Corvallis, Oregon, United States of America
| | - Lisa M. Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Holly M. Dixon
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, United States of America
| | - Perry Hystad
- College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon, United States of America
| | - Harold Bae
- College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon, United States of America
| | - Michael Barton
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, United States of America
| | - Aaron Phillips
- Computing & Analytics Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Rachel L. Miller
- Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Katrina M. Waters
- Superfund Research Program, Oregon State University, Corvallis, Oregon, United States of America
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
- Computing & Analytics Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Julie B. Herbstman
- Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York City, New York, United States of America
| | - Kim A. Anderson
- Superfund Research Program, Oregon State University, Corvallis, Oregon, United States of America
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, Oregon, United States of America
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14
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Dixon HM, Bramer LM, Scott RP, Calero L, Holmes D, Gibson EA, Cavalier HM, Rohlman D, Miller RL, Calafat AM, Kincl L, Waters KM, Herbstman JB, Anderson KA. Evaluating predictive relationships between wristbands and urine for assessment of personal PAH exposure. Environ Int 2022; 163:107226. [PMID: 35405507 PMCID: PMC8978533 DOI: 10.1016/j.envint.2022.107226] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
During events like the COVID-19 pandemic or a disaster, researchers may need to switch from collecting biological samples to personal exposure samplers that are easy and safe to transport and wear, such as silicone wristbands. Previous studies have demonstrated significant correlations between urine biomarker concentrations and chemical levels in wristbands. We build upon those studies and use a novel combination of descriptive statistics and supervised statistical learning to evaluate the relationship between polycyclic aromatic hydrocarbon (PAH) concentrations in silicone wristbands and hydroxy-PAH (OH-PAH) concentrations in urine. In New York City, 109 participants in a longitudinal birth cohort wore one wristband for 48 h and provided a spot urine sample at the end of the 48-hour period during their third trimester of pregnancy. We compared four PAHs with the corresponding seven OH-PAHs using descriptive statistics, a linear regression model, and a linear discriminant analysis model. Five of the seven PAH and OH-PAH pairs had significant correlations (Pearson's r = 0.35-0.64, p ≤ 0.003) and significant chi-square tests of independence for exposure categories (p ≤ 0.009). For these five comparisons, the observed PAH or OH-PAH concentration could predict the other concentration within a factor of 1.47 for 50-80% of the measurements (depending on the pair). Prediction accuracies for high exposure categories were at least 1.5 times higher compared to accuracies based on random chance. These results demonstrate that wristbands and urine provide similar PAH exposure assessment information, which is critical for environmental health researchers looking for the flexibility to switch between biological sample and wristband collection.
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Affiliation(s)
- Holly M Dixon
- Oregon State University, Environmental and Molecular Toxicology, Food Safety and Environmental Stewardship Program, Corvallis, OR, USA
| | - Lisa M Bramer
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, USA
| | - Richard P Scott
- Oregon State University, Environmental and Molecular Toxicology, Food Safety and Environmental Stewardship Program, Corvallis, OR, USA
| | - Lehyla Calero
- Columbia University, Columbia Center for Children's Environmental Health, Department of Environmental Health Sciences, Mailman School of Public Health, New York City, NY, USA
| | - Darrell Holmes
- Columbia University, Columbia Center for Children's Environmental Health, Department of Environmental Health Sciences, Mailman School of Public Health, New York City, NY, USA
| | - Elizabeth A Gibson
- Columbia University, Columbia Center for Children's Environmental Health, Department of Environmental Health Sciences, Mailman School of Public Health, New York City, NY, USA
| | - Haleigh M Cavalier
- Columbia University, Columbia Center for Children's Environmental Health, Department of Environmental Health Sciences, Mailman School of Public Health, New York City, NY, USA
| | - Diana Rohlman
- Oregon State University, College of Public Health and Human Sciences, Corvallis, OR, USA
| | - Rachel L Miller
- Icahn School of Medicine at Mount Sinai, Division of Clinical Immunology, New York City, NY, USA
| | - Antonia M Calafat
- Centers for Disease Control and Prevention, National Center for Environmental Health, Division of Laboratory Sciences, Atlanta, GA, USA
| | - Laurel Kincl
- Oregon State University, College of Public Health and Human Sciences, Corvallis, OR, USA
| | - Katrina M Waters
- Oregon State University, Environmental and Molecular Toxicology, Food Safety and Environmental Stewardship Program, Corvallis, OR, USA; Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, USA
| | - Julie B Herbstman
- Columbia University, Columbia Center for Children's Environmental Health, Department of Environmental Health Sciences, Mailman School of Public Health, New York City, NY, USA
| | - Kim A Anderson
- Oregon State University, Environmental and Molecular Toxicology, Food Safety and Environmental Stewardship Program, Corvallis, OR, USA.
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15
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Shankar P, Garcia GR, LaDu JK, Sullivan CM, Dunham CL, Goodale BC, Waters KM, Stanisheuski S, Maier CS, Thunga P, Reif DM, Tanguay RL. The Ahr2-Dependent wfikkn1 Gene Influences Zebrafish Transcriptome, Proteome, and Behavior. Toxicol Sci 2022; 187:325-344. [PMID: 35377459 DOI: 10.1093/toxsci/kfac037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is required for vertebrate development and is also activated by exogenous chemicals, including polycyclic aromatic hydrocarbons (PAHs) and TCDD. AHR activation is well-understood, but roles of downstream molecular signaling events are largely unknown. From previous transcriptomics in 48-hours post fertilization (hpf) zebrafish exposed to several PAHs and TCDD, we found wfikkn1 was highly co-expressed with cyp1a (marker for AHR activation). Thus, we hypothesized wfikkn1's role in AHR signaling, and showed that wfikkn1 expression was Ahr2 (zebrafish ortholog of human AHR)-dependent in developing zebrafish exposed to TCDD. To functionally characterize wfikkn1, we made a CRISPR-Cas9 mutant line with a 16-bp deletion in wfikkn1's exon, and exposed wildtype and mutants to DMSO or TCDD. 48-hpf mRNA sequencing revealed over 700 genes that were differentially expressed (p < 0.05, log2FC > 1) between each pair of treatment combinations, suggesting an important role for wfikkn1 in altering both the 48-hpf transcriptome and TCDD-induced expression changes. Mass spectrometry-based proteomics of 48-hpf wildtype and mutants revealed 325 significant differentially expressed proteins. Functional enrichment demonstrated wfikkn1 was involved in skeletal muscle development and played a role in neurological pathways after TCDD exposure. Mutant zebrafish appeared morphologically normal but had significant behavior deficiencies at all life stages, and absence of Wfikkn1 did not significantly alter TCDD-induced behavior effects at all life stages. In conclusion, wfikkn1 did not appear to be significantly involved in TCDD's overt toxicity but is likely a necessary functional member of the AHR signaling cascade.
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Affiliation(s)
- Prarthana Shankar
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| | - Gloria R Garcia
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| | - Jane K LaDu
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| | - Christopher M Sullivan
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| | - Cheryl L Dunham
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
| | - Britton C Goodale
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756 USA
| | - Katrina M Waters
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331.,Biological Sciences Division, Pacific Northwest Laboratory, 902 Battelle Boulevard, Richland, P.O. Box 999, USA WA 99352
| | | | - Claudia S Maier
- Department of Chemistry, Oregon State University, Corvallis, OR, 97330, USA
| | - Preethi Thunga
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - David M Reif
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Robyn L Tanguay
- The Sinnhuber Aquatic Research Laboratory Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, USA OR 97331
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16
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O’Callahan B, Qafoku O, Balema V, Negrete OA, Passian A, Engelhard MH, Waters KM. Atomic Force Microscopy and Infrared Nanospectroscopy of COVID-19 Spike Protein for the Quantification of Adhesion to Common Surfaces. Langmuir 2021; 37:12089-12097. [PMID: 34609882 PMCID: PMC8507151 DOI: 10.1021/acs.langmuir.1c01910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/13/2021] [Indexed: 06/13/2023]
Abstract
The COVID-19 pandemic has claimed millions of lives worldwide, sickened many more, and has resulted in severe socioeconomic consequences. As society returns to normal, understanding the spread and persistence of SARS CoV-2 on commonplace surfaces can help to mitigate future outbreaks of coronaviruses and other pathogens. We hypothesize that such an understanding can be aided by studying the binding and interaction of viral proteins with nonbiological surfaces. Here, we propose a methodology for investigating the adhesion of the SARS CoV-2 spike glycoprotein on common inorganic surfaces such as aluminum, copper, iron, silica, and ceria oxides as well as metallic gold. Quantitative adhesion was obtained from the analysis of measured forces at the nanoscale using an atomic force microscope operated under ambient conditions. Without imposing further constraints on the measurement conditions, our preliminary findings suggest that spike glycoproteins interact with similar adhesion forces across the majority of the metal oxides tested with the exception to gold, for which attraction forces ∼10 times stronger than all other materials studied were observed. Ferritin, which was used as a reference protein, was found to exhibit similar adhesion forces as SARS CoV-2 spike protein. This study results show that glycoprotein adhesion forces for similar ambient humidity, tip shape, and contact surface are nonspecific to the properties of metal oxide surfaces, which are expected to be covered by a thin water film. The findings suggest that under ambient conditions, glycoprotein adhesion to metal oxides is primarily controlled by the water capillary forces, and they depend on the surface tension of the liquid water. We discuss further strategies warranted to decipher the intricate nanoscale forces for improved quantification of the adhesion.
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Affiliation(s)
- Brian O’Callahan
- Earth
and Biological Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington 99352, United States
| | - Odeta Qafoku
- Earth
and Biological Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington 99352, United States
| | - Viktor Balema
- Ames
Laboratory, U.S. Department of Energy, Iowa
State University, Ames, Iowa 50011, United States
| | - Oscar A. Negrete
- Biotechnology
and Bioengineering Department, Sandia National
Laboratories, Livermore, California 94550, United States
| | - Ali Passian
- Quantum
Information Science Group, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Mark H. Engelhard
- Earth
and Biological Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington 99352, United States
| | - Katrina M. Waters
- Earth
and Biological Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington 99352, United States
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17
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Mansouri K, Karmaus AL, Fitzpatrick J, Patlewicz G, Pradeep P, Alberga D, Alepee N, Allen TEH, Allen D, Alves VM, Andrade CH, Auernhammer TR, Ballabio D, Bell S, Benfenati E, Bhattacharya S, Bastos JV, Boyd S, Brown JB, Capuzzi SJ, Chushak Y, Ciallella H, Clark AM, Consonni V, Daga PR, Ekins S, Farag S, Fedorov M, Fourches D, Gadaleta D, Gao F, Gearhart JM, Goh G, Goodman JM, Grisoni F, Grulke CM, Hartung T, Hirn M, Karpov P, Korotcov A, Lavado GJ, Lawless M, Li X, Luechtefeld T, Lunghini F, Mangiatordi GF, Marcou G, Marsh D, Martin T, Mauri A, Muratov EN, Myatt GJ, Nguyen DT, Nicolotti O, Note R, Pande P, Parks AK, Peryea T, Polash AH, Rallo R, Roncaglioni A, Rowlands C, Ruiz P, Russo DP, Sayed A, Sayre R, Sheils T, Siegel C, Silva AC, Simeonov A, Sosnin S, Southall N, Strickland J, Tang Y, Teppen B, Tetko IV, Thomas D, Tkachenko V, Todeschini R, Toma C, Tripodi I, Trisciuzzi D, Tropsha A, Varnek A, Vukovic K, Wang Z, Wang L, Waters KM, Wedlake AJ, Wijeyesakere SJ, Wilson D, Xiao Z, Yang H, Zahoranszky-Kohalmi G, Zakharov AV, Zhang FF, Zhang Z, Zhao T, Zhu H, Zorn KM, Casey W, Kleinstreuer NC. Erratum: CATMoS: Collaborative Acute Toxicity Modeling Suite. Environ Health Perspect 2021; 129:109001. [PMID: 34647794 PMCID: PMC8516060 DOI: 10.1289/ehp10369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 05/21/2023]
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18
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Shankar P, McClure RS, Waters KM, Tanguay RL. Gene co-expression network analysis in zebrafish reveals chemical class specific modules. BMC Genomics 2021; 22:658. [PMID: 34517816 PMCID: PMC8438978 DOI: 10.1186/s12864-021-07940-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/15/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Zebrafish is a popular animal model used for high-throughput screening of chemical hazards, however, investigations of transcriptomic mechanisms of toxicity are still needed. Here, our goal was to identify genes and biological pathways that Aryl Hydrocarbon Receptor 2 (AHR2) Activators and flame retardant chemicals (FRCs) alter in developing zebrafish. Taking advantage of a compendium of phenotypically-anchored RNA sequencing data collected from 48-h post fertilization (hpf) zebrafish, we inferred a co-expression network that grouped genes based on their transcriptional response. RESULTS Genes responding to the FRCs and AHR2 Activators localized to distinct regions of the network, with FRCs inducing a broader response related to neurobehavior. AHR2 Activators centered in one region related to chemical stress responses. We also discovered several highly co-expressed genes in this module, including cyp1a, and we subsequently show that these genes are definitively within the AHR2 signaling pathway. Systematic removal of the two chemical types from the data, and analysis of network changes identified neurogenesis associated with FRCs, and regulation of vascular development associated with both chemical classes. We also identified highly connected genes responding specifically to each class that are potential biomarkers of exposure. CONCLUSIONS Overall, we created the first zebrafish chemical-specific gene co-expression network illuminating how chemicals alter the transcriptome relative to each other. In addition to our conclusions regarding FRCs and AHR2 Activators, our network can be leveraged by other studies investigating chemical mechanisms of toxicity.
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Affiliation(s)
- Prarthana Shankar
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, 28645 East Highway 34, Oregon State University, Corvallis, OR, 97331, USA
| | - Ryan S McClure
- Biological Sciences Division, Pacific National Northwest Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, WA, 99352, USA
| | - Katrina M Waters
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, 28645 East Highway 34, Oregon State University, Corvallis, OR, 97331, USA.,Biological Sciences Division, Pacific National Northwest Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, WA, 99352, USA
| | - Robyn L Tanguay
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, 28645 East Highway 34, Oregon State University, Corvallis, OR, 97331, USA.
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19
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Mansouri K, Karmaus A, Fitzpatrick J, Patlewicz G, Pradeep P, Alberga D, Alepee N, Allen TEH, Allen D, Alves VM, Andrade CH, Auernhammer TR, Ballabio D, Bell S, Benfenati E, Bhattacharya S, Bastos JV, Boyd S, Brown JB, Capuzzi SJ, Chushak Y, Ciallella H, Clark AM, Consonni V, Daga PR, Ekins S, Farag S, Fedorov M, Fourches D, Gadaleta D, Gao F, Gearhart JM, Goh G, Goodman JM, Grisoni F, Grulke CM, Hartung T, Hirn M, Karpov P, Korotcov A, Lavado GJ, Lawless M, Li X, Luechtefeld T, Lunghini F, Mangiatordi GF, Marcou G, Marsh D, Martin T, Mauri A, Muratov EN, Myatt GJ, Nguyen DT, Nicolotti O, Note R, Pande P, Parks AK, Peryea T, Polash A, Rallo R, Roncaglioni A, Rowlands C, Ruiz P, Russo D, Sayed A, Sayre R, Sheils T, Siegel C, Silva AC, Simeonov A, Sosnin S, Southall N, Strickland J, Tang Y, Teppen B, Tetko IV, Thomas D, Tkachenko V, Todeschini R, Toma C, Tripodi I, Trisciuzzi D, Tropsha A, Varnek A, Vukovic K, Wang Z, Wang L, Waters KM, Wedlake AJ, Wijeyesakere SJ, Wilson D, Xiao Z, Yang H, Zahoranszky-Kohalmi G, Zakharov AV, Zhang FF, Zhang Z, Zhao T, Zhu H, Zorn KM, Casey W, Kleinstreuer NC. Erratum: CATMoS: Collaborative Acute Toxicity Modeling Suite. Environ Health Perspect 2021; 129:79001. [PMID: 34242083 PMCID: PMC8270350 DOI: 10.1289/ehp9883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 05/28/2023]
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20
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Feng S, Heath E, Jefferson B, Joslyn C, Kvinge H, Mitchell HD, Praggastis B, Eisfeld AJ, Sims AC, Thackray LB, Fan S, Walters KB, Halfmann PJ, Westhoff-Smith D, Tan Q, Menachery VD, Sheahan TP, Cockrell AS, Kocher JF, Stratton KG, Heller NC, Bramer LM, Diamond MS, Baric RS, Waters KM, Kawaoka Y, McDermott JE, Purvine E. Hypergraph models of biological networks to identify genes critical to pathogenic viral response. BMC Bioinformatics 2021; 22:287. [PMID: 34051754 PMCID: PMC8164482 DOI: 10.1186/s12859-021-04197-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 05/13/2021] [Indexed: 12/25/2022] Open
Abstract
Background Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems. Hypergraphs are generalizations of graphs that naturally model multi-way relationships and have shown promise in modeling systems such as protein complexes and metabolic reactions. In this paper we seek to understand how hypergraphs can more faithfully identify, and potentially predict, important genes based on complex relationships inferred from genomic expression data sets. Results We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges represent significantly perturbed genes, and vertices represent individual biological samples with specific experimental conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Conclusions Our results demonstrate the utility of using hypergraphs to represent complex biological systems and highlight central important responses in common to a variety of highly pathogenic viruses. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04197-2.
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Affiliation(s)
- Song Feng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Emily Heath
- Department of Mathematics, University of Illinois, Urbana-Champaign, IL, USA
| | - Brett Jefferson
- Computing and Analytics Division, Pacific Northwest National Laboratory, Seattle, WA, USA
| | - Cliff Joslyn
- Computing and Analytics Division, Pacific Northwest National Laboratory, Seattle, WA, USA.,Systems Science Program, Portland State University, Portland, OR, USA
| | - Henry Kvinge
- Computing and Analytics Division, Pacific Northwest National Laboratory, Seattle, WA, USA
| | - Hugh D Mitchell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Brenda Praggastis
- Computing and Analytics Division, Pacific Northwest National Laboratory, Seattle, WA, USA
| | - Amie J Eisfeld
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, 575 Science Drive, 53711, Madison, WI, USA
| | - Amy C Sims
- Signature Science and Technology Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, 63110, Saint Louis, MO, USA
| | - Shufang Fan
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, 575 Science Drive, 53711, Madison, WI, USA
| | - Kevin B Walters
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, 575 Science Drive, 53711, Madison, WI, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, 575 Science Drive, 53711, Madison, WI, USA
| | - Danielle Westhoff-Smith
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, 575 Science Drive, 53711, Madison, WI, USA
| | - Qing Tan
- Department of Medicine, Washington University School of Medicine, 63110, Saint Louis, MO, USA
| | - Vineet D Menachery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Jacob F Kocher
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kelly G Stratton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Natalie C Heller
- Computing and Analytics Division, Pacific Northwest National Laboratory, Seattle, WA, USA
| | - Lisa M Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, 63110, Saint Louis, MO, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.,Department of Comparative Medicine, University of Washington, Seattle, WA, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, 575 Science Drive, 53711, Madison, WI, USA.,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.,ERATO Infection-Induced Host Responses Project, Saitama, 332-0012, Japan.,Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.,Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
| | - Emilie Purvine
- Computing and Analytics Division, Pacific Northwest National Laboratory, Seattle, WA, USA.
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21
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Kyle JE, Stratton KG, Zink EM, Kim YM, Bloodsworth KJ, Monroe ME, Waters KM, Webb-Robertson BJM, Koeller DM, Metz TO. A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases. Sci Data 2021; 8:114. [PMID: 33883556 PMCID: PMC8060404 DOI: 10.1038/s41597-021-00894-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/09/2021] [Indexed: 12/27/2022] Open
Abstract
Every year individuals experience symptoms that remain undiagnosed by healthcare providers. In the United States, these rare diseases are defined as a condition that affects fewer than 200,000 individuals. However, there are an estimated 7000 rare diseases, and there are an estimated 25-30 million Americans in total (7.6-9.2% of the population as of 2018) affected by such disorders. The NIH Common Fund Undiagnosed Diseases Network (UDN) seeks to provide diagnoses for individuals with undiagnosed disease. Mass spectrometry-based metabolomics and lipidomics analyses could advance the collective understanding of individual symptoms and advance diagnoses for individuals with heretofore undiagnosed disease. Here, we report the mass spectrometry-based metabolomics and lipidomics analyses of blood plasma, urine, and cerebrospinal fluid from 148 patients within the UDN and their families, as well as from a reference population of over 100 individuals with no known metabolic diseases. The raw and processed data are available to the research community so that they might be useful in the diagnoses of current or future patients suffering from undiagnosed disorders.
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Affiliation(s)
- Jennifer E Kyle
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kelly G Stratton
- Computing and Analytics Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Erika M Zink
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Young-Mo Kim
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kent J Bloodsworth
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Matthew E Monroe
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Katrina M Waters
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Bobbie-Jo M Webb-Robertson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - David M Koeller
- Molecular and Medical Genetics, School of Medicine, Oregon Health and Science University, Portland, OR, 97239, USA.
| | - Thomas O Metz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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22
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Mansouri K, Karmaus AL, Fitzpatrick J, Patlewicz G, Pradeep P, Alberga D, Alepee N, Allen TE, Allen D, Alves VM, Andrade CH, Auernhammer TR, Ballabio D, Bell S, Benfenati E, Bhattacharya S, Bastos JV, Boyd S, Brown J, Capuzzi SJ, Chushak Y, Ciallella H, Clark AM, Consonni V, Daga PR, Ekins S, Farag S, Fedorov M, Fourches D, Gadaleta D, Gao F, Gearhart JM, Goh G, Goodman JM, Grisoni F, Grulke CM, Hartung T, Hirn M, Karpov P, Korotcov A, Lavado GJ, Lawless M, Li X, Luechtefeld T, Lunghini F, Mangiatordi GF, Marcou G, Marsh D, Martin T, Mauri A, Muratov EN, Myatt GJ, Nguyen DT, Nicolotti O, Note R, Pande P, Parks AK, Peryea T, Polash AH, Rallo R, Roncaglioni A, Rowlands C, Ruiz P, Russo DP, Sayed A, Sayre R, Sheils T, Siegel C, Silva AC, Simeonov A, Sosnin S, Southall N, Strickland J, Tang Y, Teppen B, Tetko IV, Thomas D, Tkachenko V, Todeschini R, Toma C, Tripodi I, Trisciuzzi D, Tropsha A, Varnek A, Vukovic K, Wang Z, Wang L, Waters KM, Wedlake AJ, Wijeyesakere SJ, Wilson D, Xiao Z, Yang H, Zahoranszky-Kohalmi G, Zakharov AV, Zhang FF, Zhang Z, Zhao T, Zhu H, Zorn KM, Casey W, Kleinstreuer NC. CATMoS: Collaborative Acute Toxicity Modeling Suite. Environ Health Perspect 2021; 129:47013. [PMID: 33929906 PMCID: PMC8086800 DOI: 10.1289/ehp8495] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
BACKGROUND Humans are exposed to tens of thousands of chemical substances that need to be assessed for their potential toxicity. Acute systemic toxicity testing serves as the basis for regulatory hazard classification, labeling, and risk management. However, it is cost- and time-prohibitive to evaluate all new and existing chemicals using traditional rodent acute toxicity tests. In silico models built using existing data facilitate rapid acute toxicity predictions without using animals. OBJECTIVES The U.S. Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) Acute Toxicity Workgroup organized an international collaboration to develop in silico models for predicting acute oral toxicity based on five different end points: Lethal Dose 50 (LD50 value, U.S. Environmental Protection Agency hazard (four) categories, Globally Harmonized System for Classification and Labeling hazard (five) categories, very toxic chemicals [LD50 (LD50≤50mg/kg)], and nontoxic chemicals (LD50>2,000mg/kg). METHODS An acute oral toxicity data inventory for 11,992 chemicals was compiled, split into training and evaluation sets, and made available to 35 participating international research groups that submitted a total of 139 predictive models. Predictions that fell within the applicability domains of the submitted models were evaluated using external validation sets. These were then combined into consensus models to leverage strengths of individual approaches. RESULTS The resulting consensus predictions, which leverage the collective strengths of each individual model, form the Collaborative Acute Toxicity Modeling Suite (CATMoS). CATMoS demonstrated high performance in terms of accuracy and robustness when compared with in vivo results. DISCUSSION CATMoS is being evaluated by regulatory agencies for its utility and applicability as a potential replacement for in vivo rat acute oral toxicity studies. CATMoS predictions for more than 800,000 chemicals have been made available via the National Toxicology Program's Integrated Chemical Environment tools and data sets (ice.ntp.niehs.nih.gov). The models are also implemented in a free, standalone, open-source tool, OPERA, which allows predictions of new and untested chemicals to be made. https://doi.org/10.1289/EHP8495.
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Affiliation(s)
- Kamel Mansouri
- Integrated Laboratory Systems, LLC, Morrisville, North Carolina, USA
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, Research Triangle Park, North Carolina, USA
| | - Agnes L. Karmaus
- Integrated Laboratory Systems, LLC, Morrisville, North Carolina, USA
| | | | - Grace Patlewicz
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Prachi Pradeep
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
- Oak Ridge Institute for Science and Education (ORISE) Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Domenico Alberga
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | | | - Timothy E.H. Allen
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Dave Allen
- Integrated Laboratory Systems, LLC, Morrisville, North Carolina, USA
| | - Vinicius M. Alves
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
- Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Federal University of Goiás, Goiania, Brazil
| | - Carolina H. Andrade
- Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Federal University of Goiás, Goiania, Brazil
| | | | - Davide Ballabio
- Milano Chemometrics & QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Shannon Bell
- Integrated Laboratory Systems, LLC, Morrisville, North Carolina, USA
| | - Emilio Benfenati
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Sudin Bhattacharya
- Institute for Quantitative Health Science and Engineering, Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan, USA
| | - Joyce V. Bastos
- Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Federal University of Goiás, Goiania, Brazil
| | - Stephen Boyd
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - J.B. Brown
- Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Stephen J. Capuzzi
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Yaroslav Chushak
- Aeromedical Research Department, Force Health Protection, USAFSAM, Dayton, Ohio, USA
- Henry M Jackson Foundation for the Advancement of Military Medicine, Dayton, Ohio, USA
| | - Heather Ciallella
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
| | - Alex M. Clark
- Collaborations Pharmaceuticals, Inc., Raleigh, North Carolina, USA
| | - Viviana Consonni
- Milano Chemometrics & QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | | | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., Raleigh, North Carolina, USA
| | - Sherif Farag
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Maxim Fedorov
- Skoltech, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Denis Fourches
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Domenico Gadaleta
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Feng Gao
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Jeffery M. Gearhart
- Aeromedical Research Department, Force Health Protection, USAFSAM, Dayton, Ohio, USA
- Henry M Jackson Foundation for the Advancement of Military Medicine, Dayton, Ohio, USA
| | - Garett Goh
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jonathan M. Goodman
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Francesca Grisoni
- Milano Chemometrics & QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Christopher M. Grulke
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | | | - Matthew Hirn
- Department of Computational Mathematics, Science & Engineering, Department of Mathematics, Michigan State University, East Lansing, Michigan, USA
| | - Pavel Karpov
- Institute of Structural Biology, Helmholtz Zentrum München (GmbH), Neuherberg, Germany
| | | | - Giovanna J. Lavado
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | | | - Xinhao Li
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
| | | | - Filippo Lunghini
- Laboratoire de Chemoinformatique, URM7140, Université de Strasbourg, Strasbourg, France
| | - Giuseppe F. Mangiatordi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Gilles Marcou
- Laboratoire de Chemoinformatique, URM7140, Université de Strasbourg, Strasbourg, France
| | - Dan Marsh
- Underwriters Laboratories, Northbrook, Illinois, USA
| | - Todd Martin
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
| | | | - Eugene N. Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
- Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Federal University of Goiás, Goiania, Brazil
| | | | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Orazio Nicolotti
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Reine Note
- L’Oréal Research & Innovation, Aulnay-sous-Bois, France
| | - Paritosh Pande
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Tyler Peryea
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | | | - Robert Rallo
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Alessandra Roncaglioni
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | | | - Patricia Ruiz
- Office of Innovation and Analytics, Agency for Toxic Substances and Disease Registry, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Daniel P. Russo
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
| | - Ahmed Sayed
- Rosettastein Consulting UG, Freising, Germany
| | - Risa Sayre
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
- Oak Ridge Institute for Science and Education (ORISE) Research Participation Program, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Timothy Sheils
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Charles Siegel
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Arthur C. Silva
- Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Federal University of Goiás, Goiania, Brazil
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Sergey Sosnin
- Skoltech, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Judy Strickland
- Integrated Laboratory Systems, LLC, Morrisville, North Carolina, USA
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Brian Teppen
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Igor V. Tetko
- Institute of Structural Biology, Helmholtz Zentrum München (GmbH), Neuherberg, Germany
- BIGCHEM GmbH, Unterschleissheim, Germany
| | - Dennis Thomas
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Roberto Todeschini
- Milano Chemometrics & QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Cosimo Toma
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Ignacio Tripodi
- Computer Science/Interdisciplinary Quantitative Biology, University of Colorado, Boulder, Colorado, USA
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alexandre Varnek
- Laboratoire de Chemoinformatique, URM7140, Université de Strasbourg, Strasbourg, France
| | - Kristijan Vukovic
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Zhongyu Wang
- School of Environmental Sciences and Technology, Dalian University of Technology; Dalian, Liaoning, China
| | - Liguo Wang
- School of Environmental Sciences and Technology, Dalian University of Technology; Dalian, Liaoning, China
| | | | - Andrew J. Wedlake
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Dan Wilson
- The Dow Chemical Company, Midland, Michigan, USA
| | - Zijun Xiao
- School of Environmental Sciences and Technology, Dalian University of Technology; Dalian, Liaoning, China
| | - Hongbin Yang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Gergely Zahoranszky-Kohalmi
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Alexey V. Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | | | - Zhen Zhang
- Dow Agrosciences, Indianapolis, Indiana, USA
| | - Tongan Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Hao Zhu
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
| | | | - Warren Casey
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, Research Triangle Park, North Carolina, USA
| | - Nicole C. Kleinstreuer
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, Research Triangle Park, North Carolina, USA
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23
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Truong L, Marvel S, Reif DM, Thomas DG, Pande P, Dasgupta S, Simonich MT, Waters KM, Tanguay RL. The multi-dimensional embryonic zebrafish platform predicts flame retardant bioactivity. Reprod Toxicol 2020; 96:359-369. [PMID: 32827657 PMCID: PMC7892636 DOI: 10.1016/j.reprotox.2020.08.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 07/30/2020] [Accepted: 08/11/2020] [Indexed: 11/15/2022]
Abstract
Flame retardant chemicals (FRCs) commonly added to many consumer products present a human exposure burden associated with adverse health effects. Under pressure from consumers, FRC manufacturers have adopted some purportedly safer replacements for first-generation brominated diphenyl ethers (BDEs). In contrast, second and third-generation organophosphates and other alternative chemistries have limited bioactivity data available to estimate their hazard potential. In order to evaluate the toxicity of existing and potential replacement FRCs, we need efficient screening methods. We built a 61-FRC library in which we systemically assessed developmental toxicity and potential neurotoxicity effects in the embryonic zebrafish model. Data were compared to publicly available data generated in a battery of cell-based in vitro assays from ToxCast, Tox21, and other alternative models. Of the 61 FRCs, 19 of 45 that were tested in the ToxCast assays were bioactive in our zebrafish model. The zebrafish assays detected bioactivity for 10 of the 12 previously classified developmental neurotoxic FRCs. Developmental zebrafish were sufficiently sensitive at detecting FRC structure-bioactivity impacts that we were able to build a classification model using 13 physicochemical properties and 3 embryonic zebrafish assays that achieved a balanced accuracy of 91.7%. This work illustrates the power of a multi-dimensional in vivo platform to expand our ability to predict the hazard potential of new compounds based on structural relatedness, ultimately leading to reliable toxicity predictions based on chemical structure.
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Affiliation(s)
- Lisa Truong
- Department of Environmental and Molecular Toxicology, the Sinnhuber Aquatic Research Laboratory and the Environmental Health Sciences Center at Oregon State University, Corvallis, OR, USA
| | - Skylar Marvel
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - David M Reif
- Bioinformatics Research Center, Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Dennis G Thomas
- Biological Sciences Division, Pacific Northwest Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, WA 99352 USA
| | - Paritosh Pande
- Biological Sciences Division, Pacific Northwest Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, WA 99352 USA
| | - Subham Dasgupta
- Department of Environmental and Molecular Toxicology, the Sinnhuber Aquatic Research Laboratory and the Environmental Health Sciences Center at Oregon State University, Corvallis, OR, USA
| | - Michael T Simonich
- Department of Environmental and Molecular Toxicology, the Sinnhuber Aquatic Research Laboratory and the Environmental Health Sciences Center at Oregon State University, Corvallis, OR, USA
| | - Katrina M Waters
- Department of Environmental and Molecular Toxicology, the Sinnhuber Aquatic Research Laboratory and the Environmental Health Sciences Center at Oregon State University, Corvallis, OR, USA; Biological Sciences Division, Pacific Northwest Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, WA 99352 USA
| | - Robyn L Tanguay
- Department of Environmental and Molecular Toxicology, the Sinnhuber Aquatic Research Laboratory and the Environmental Health Sciences Center at Oregon State University, Corvallis, OR, USA.
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24
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Webb-Robertson BJM, Stratton KG, Kyle JE, Kim YM, Bramer LM, Waters KM, Koeller DM, Metz TO. Statistically Driven Metabolite and Lipid Profiling of Patients from the Undiagnosed Diseases Network. Anal Chem 2020; 92:1796-1803. [PMID: 31742994 PMCID: PMC7183858 DOI: 10.1021/acs.analchem.9b03522] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Advancements in molecular separations coupled with mass spectrometry have enabled metabolome analyses for clinical cohorts. A population of interest for metabolome profiling is patients with rare disease for which abnormal metabolic signatures may yield clues into the genetic basis, as well as mechanistic drivers of the disease and possible treatment options. We undertook the metabolome profiling of a large cohort of patients with mysterious conditions characterized through the Undiagnosed Diseases Network (UDN). Due to the size and enrollment procedures, collection of the metabolomes for UDN patients took place over 2 years. We describe the study designed to adjust for measurements collected over a long time scale and how this enabled statistical analyses to summarize the metabolome of individual patients. We demonstrate the removal of time-based batch effects, overall statistical characteristics of the UDN population, and two case studies of interest that demonstrate the utility of metabolome profiling for rare diseases.
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Affiliation(s)
- Bobbie-Jo M. Webb-Robertson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kelly G. Stratton
- Computing Analytics Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jennifer E. Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Lisa M. Bramer
- Computing Analytics Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Katrina M. Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - David M. Koeller
- Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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25
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Mitchell HD, Eisfeld AJ, Stratton KG, Heller NC, Bramer LM, Wen J, McDermott JE, Gralinski LE, Sims AC, Le MQ, Baric RS, Kawaoka Y, Waters KM. The Role of EGFR in Influenza Pathogenicity: Multiple Network-Based Approaches to Identify a Key Regulator of Non-lethal Infections. Front Cell Dev Biol 2019; 7:200. [PMID: 31616667 PMCID: PMC6763731 DOI: 10.3389/fcell.2019.00200] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/05/2019] [Indexed: 12/14/2022] Open
Abstract
Despite high sequence similarity between pandemic and seasonal influenza viruses, there is extreme variation in host pathogenicity from one viral strain to the next. Identifying the underlying mechanisms of variability in pathogenicity is a critical task for understanding influenza virus infection and effective management of highly pathogenic influenza virus disease. We applied a network-based modeling approach to identify critical functions related to influenza virus pathogenicity using large transcriptomic and proteomic datasets from mice infected with six influenza virus strains or mutants. Our analysis revealed two pathogenicity-related gene expression clusters; these results were corroborated by matching proteomics data. We also identified parallel downstream processes that were altered during influenza pathogenesis. We found that network bottlenecks (nodes that bridge different network regions) were highly enriched in pathogenicity-related genes, while network hubs (highly connected network nodes) were significantly depleted in these genes. We confirmed that this trend persisted in a distinct virus: Severe Acute Respiratory Syndrome Coronavirus (SARS). The role of epidermal growth factor receptor (EGFR) in influenza pathogenesis, one of the bottleneck regulators with corroborating signals across transcript and protein expression data, was tested and validated in additional mouse infection experiments. We demonstrate that EGFR is important during influenza infection, but the role it plays changes for lethal versus non-lethal infections. Our results show that by using association networks, bottleneck genes that lack hub characteristics can be used to predict a gene's involvement in influenza virus pathogenicity. We also demonstrate the utility of employing multiple network approaches for analyzing host response data from viral infections.
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Affiliation(s)
- Hugh D Mitchell
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Amie J Eisfeld
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Kelly G Stratton
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Natalie C Heller
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Lisa M Bramer
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ji Wen
- Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Lisa E Gralinski
- Department of Microbiology and Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Amy C Sims
- Department of Microbiology and Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Mai Q Le
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Ralph S Baric
- Department of Microbiology and Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States.,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Sciences, The University of Tokyo, Tokyo, Japan.,International Research Center for Infectious Diseases, Institute of Medical Sciences, The University of Tokyo, Tokyo, Japan
| | - Katrina M Waters
- Pacific Northwest National Laboratory, Richland, WA, United States
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26
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Thomas DG, Shankaran H, Truong L, Tanguay RL, Waters KM. Time-dependent behavioral data from zebrafish reveals novel signatures of chemical toxicity using point of departure analysis. ACTA ACUST UNITED AC 2019; 9:50-60. [PMID: 31485548 DOI: 10.1016/j.comtox.2018.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
High-content imaging of larval zebrafish behavior can be used as a screening approach to rapidly evaluate the relative potential for chemicals to cause toxicity. However, most statistical methods applied to these data transform movement values to incidence-based "hits" and calculate lowest effect levels (LELs), which loses individual fish resolution of behavior and defies hazard ranking due to reliance on applied dose levels. We developed a parallelizable workflow to calculate benchmark dose (BMD) values from dynamic, high-content zebrafish behavior data that scales for high-throughput chemical screening. To capture the zebrafish movement response from light to dark stimulus, we summarized time-dependent data using both area under the curve and the immediate change at the transition point into two novel metrics that characterized abnormal behavior as a function of chemical concentration. The BMD workflow was applied to calculate BMD10 values of 1,060 ToxCast chemicals for 24 zebrafish endpoints, including behavior, mortality and morphology. The BMD10 values provided better precision and separation than LELs for clustering chemicals since they were derived from models that best-fit their concentration-response curves. Analysis of BMD10 values revealed behavioral signatures as the most sensitive endpoints. High concordance in chemical activity was observed between ToxCast in vitro data and zebrafish in vivo behavioral data, however ToxPi analysis indicated that rankings based on in vitro data were not a reliable predictor of in vivo rankings for lower potency chemicals. This analysis method will enable the use of high-content zebrafish behavioral screening data for BMD analysis in toxicological hazard assessment.
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Affiliation(s)
- Dennis G Thomas
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Harish Shankaran
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Lisa Truong
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Robert L Tanguay
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352
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27
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McClure RS, Wendler JP, Adkins JN, Swanstrom J, Baric R, Kaiser BLD, Oxford KL, Waters KM, McDermott JE. Unified feature association networks through integration of transcriptomic and proteomic data. PLoS Comput Biol 2019; 15:e1007241. [PMID: 31527878 PMCID: PMC6748406 DOI: 10.1371/journal.pcbi.1007241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 07/02/2019] [Indexed: 11/18/2022] Open
Abstract
High-throughput multi-omics studies and corresponding network analyses of multi-omic data have rapidly expanded their impact over the last 10 years. As biological features of different types (e.g. transcripts, proteins, metabolites) interact within cellular systems, the greatest amount of knowledge can be gained from networks that incorporate multiple types of -omic data. However, biological and technical sources of variation diminish the ability to detect cross-type associations, yielding networks dominated by communities comprised of nodes of the same type. We describe here network building methods that can maximize edges between nodes of different data types leading to integrated networks, networks that have a large number of edges that link nodes of different-omic types (transcripts, proteins, lipids etc). We systematically rank several network inference methods and demonstrate that, in many cases, using a random forest method, GENIE3, produces the most integrated networks. This increase in integration does not come at the cost of accuracy as GENIE3 produces networks of approximately the same quality as the other network inference methods tested here. Using GENIE3, we also infer networks representing antibody-mediated Dengue virus cell invasion and receptor-mediated Dengue virus invasion. A number of functional pathways showed centrality differences between the two networks including genes responding to both GM-CSF and IL-4, which had a higher centrality value in an antibody-mediated vs. receptor-mediated Dengue network. Because a biological system involves the interplay of many different types of molecules, incorporating multiple data types into networks will improve their use as models of biological systems. The methods explored here are some of the first to specifically highlight and address the challenges associated with how such multi-omic networks can be assembled and how the greatest number of interactions can be inferred from different data types. The resulting networks can lead to the discovery of new host response patterns and interactions during viral infection, generate new hypotheses of pathogenic mechanisms and confirm mechanisms of disease.
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Affiliation(s)
- Ryan S. McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA, United States of America
| | - Jason P. Wendler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA, United States of America
| | - Joshua N. Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA, United States of America
| | - Jesica Swanstrom
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC, United States of America
| | - Ralph Baric
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC, United States of America
| | - Brooke L. Deatherage Kaiser
- Signatures Science and Technology Division, Pacific Northwest National Laboratory, Richland WA, United States of America
| | - Kristie L. Oxford
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA, United States of America
| | - Katrina M. Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA, United States of America
| | - Jason E. McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA, United States of America
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, OR, United States of America
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28
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Rohlman D, Dixon HM, Kincl L, Larkin A, Evoy R, Barton M, Phillips A, Peterson E, Scaffidi C, Herbstman JB, Waters KM, Anderson KA. Development of an environmental health tool linking chemical exposures, physical location and lung function. BMC Public Health 2019; 19:854. [PMID: 31262274 PMCID: PMC6604385 DOI: 10.1186/s12889-019-7217-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 06/20/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND A challenge in environmental health research is collecting robust data sets to facilitate comparisons between personal chemical exposures, the environment and health outcomes. To address this challenge, the Exposure, Location and lung Function (ELF) tool was designed in collaboration with communities that share environmental health concerns. These concerns centered on respiratory health and ambient air quality. The ELF collects exposure to polycyclic aromatic hydrocarbons (PAHs), given their association with diminished lung function. Here, we describe the ELF as a novel environmental health assessment tool. METHODS The ELF tool collects chemical exposure for 62 PAHs using passive sampling silicone wristbands, geospatial location data and respiratory lung function measures using a paired hand-held spirometer. The ELF was tested by 10 individuals with mild to moderate asthma for 7 days. Participants wore a wristband each day to collect PAH exposure, carried a cell phone, and performed spirometry daily to collect respiratory health measures. Location data was gathered using the geospatial positioning system technology in an Android cell-phone. RESULTS We detected and quantified 31 PAHs across the study population. PAH exposure data showed spatial and temporal sensitivity within and between participants. Location data was used with existing datasets such as the Toxics Release Inventory and the National Oceanic and Atmospheric Administration (NOAA) Hazard Mapping System. Respiratory health outcomes were validated using criteria from the American Thoracic Society with 94% of participant data meeting standards. Finally, the ELF was used with a high degree of compliance (> 90%) by community members. CONCLUSIONS The ELF is a novel environmental health assessment tool that allows for personal data collection spanning chemical exposures, location and lung function measures as well as self-reported information.
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Affiliation(s)
- Diana Rohlman
- College of Public Health and Human Sciences; Superfund Research Program, Oregon State University, 101 Milam Hall, Corvallis, Oregon USA
| | - Holly M. Dixon
- Environmental and Molecular Toxicology, Food Safety and Environmental Stewardship Program, Oregon State University, Corvallis, Oregon USA
| | - Laurel Kincl
- College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon USA
| | - Andrew Larkin
- College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon USA
| | - Richard Evoy
- College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon USA
| | - Michael Barton
- Superfund Research Program, Food Safety and Environmental Stewardship Program, Oregon State University, Corvallis, Oregon USA
| | - Aaron Phillips
- Computing & Analytics Division, Pacific Northwest National Laboratory, Richland, Washington USA
| | - Elena Peterson
- Computing & Analytics Division, Pacific Northwest National Laboratory, Richland, Washington USA
| | | | - Julie B. Herbstman
- Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York City, USA
| | - Katrina M. Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Pacific Northwest National Laboratory, Richland, WA USA
| | - Kim A. Anderson
- Environmental and Molecular Toxicology, Food Safety and Environmental Stewardship Program, Oregon State University, Corvallis, Oregon USA
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29
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Brown J, Phillips AR, Lewis DA, Mans MA, Chang Y, Tanguay RL, Peterson ES, Waters KM, Tilton SC. Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration. BMC Bioinformatics 2019; 20:255. [PMID: 31101000 PMCID: PMC6525352 DOI: 10.1186/s12859-019-2805-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/10/2019] [Indexed: 12/27/2022] Open
Abstract
Background The Bioinformatics Resource Manager (BRM) is a web-based tool developed to facilitate identifier conversion and data integration for Homo sapiens (human), Mus musculus (mouse), Rattus norvegicus (rat), Danio rerio (zebrafish), and Macaca mulatta (macaque), as well as perform orthologous conversions among the supported species. In addition to providing a robust means of identifier conversion, BRM also incorporates a suite of microRNA (miRNA)-target databases upon which to query target genes or to perform reverse target lookups using gene identifiers. Results BRM has the capability to perform cross-species identifier lookups across common identifier types, directly integrate datasets across platform or species by performing identifier retrievals in the background, and retrieve miRNA targets from multiple databases simultaneously and integrate the resulting gene targets with experimental mRNA data. Here we use workflows provided in BRM to integrate RNA sequencing data across species to identify common biomarkers of exposure after treatment of human lung cells and zebrafish to benzo[a]pyrene (BAP). We further use the miRNA Target workflow to experimentally determine the role of miRNAs as regulators of BAP toxicity and identify the predicted functional consequences of miRNA-target regulation in our system. The output from BRM can easily and directly be uploaded to freely available visualization tools for further analysis. From these examples, we were able to identify an important role for several miRNAs as potential regulators of BAP toxicity in human lung cells associated with cell migration, cell communication, cell junction assembly and regulation of cell death. Conclusions Overall, BRM provides bioinformatics tools to assist biologists having minimal programming skills with analysis and integration of high-content omics’ data from various transcriptomic and proteomic platforms. BRM workflows were developed in Java and other open-source technologies and are served publicly using Apache Tomcat at https://cbb.pnnl.gov/brm/. Electronic supplementary material The online version of this article (10.1186/s12859-019-2805-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joseph Brown
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.,Present address: Department of Human Genetics, University of Utah, Salt Lake City, UT, 84105, USA
| | - Aaron R Phillips
- Computing & Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - David A Lewis
- Computing & Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Michael-Andres Mans
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA
| | - Yvonne Chang
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA
| | - Robert L Tanguay
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA.,Superfund Research Center, Oregon State University, Corvallis, OR, USA
| | - Elena S Peterson
- Computing & Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. .,Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA. .,Superfund Research Center, Oregon State University, Corvallis, OR, USA.
| | - Susan C Tilton
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, USA. .,Superfund Research Center, Oregon State University, Corvallis, OR, USA.
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30
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Burnum-Johnson KE, Zheng X, Dodds JN, Ash J, Fourches D, Nicora CD, Wendler JP, Metz TO, Waters KM, Jansson JK, Smith RD, Baker ES. Ion Mobility Spectrometry and the Omics: Distinguishing Isomers, Molecular Classes and Contaminant Ions in Complex Samples. Trends Analyt Chem 2019; 116:292-299. [PMID: 31798197 DOI: 10.1016/j.trac.2019.04.022] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ion mobility spectrometry (IMS) is a widely used analytical technique providing rapid gas phase separations. IMS alone is useful, but its coupling with mass spectrometry (IMS-MS) and various front-end separation techniques has greatly increased the molecular information achievable from different omic analyses. IMS-MS analyses are specifically gaining attention for improving metabolomic, lipidomic, glycomic, proteomic and exposomic analyses by increasing measurement sensitivity (e.g. S/N ratio), reducing the detection limit, and amplifying peak capacity. Numerous studies including national security-related analyses, disease screenings and environmental evaluations are illustrating that IMS-MS is able to extract information not possible with MS alone. Furthermore, IMS-MS has shown great utility in salvaging molecular information for low abundance molecules of interest when high concentration contaminant ions are present in the sample by reducing detector suppression. This review highlights how IMS-MS is currently being used in omic analyses to distinguish structurally similar molecules, isomers, molecular classes and contaminant ions.
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Affiliation(s)
| | - Xueyun Zheng
- Department of Chemistry, Texas A &M University, College Station, TX
| | - James N Dodds
- Department of Chemistry, NC State University, Raleigh, NC
| | - Jeremy Ash
- Department of Chemistry, NC State University, Raleigh, NC
| | - Denis Fourches
- Department of Chemistry, NC State University, Raleigh, NC
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Jason P Wendler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Erin S Baker
- Department of Chemistry, NC State University, Raleigh, NC
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31
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Bramer LM, Stratton KG, White AM, Bleeker AH, Kobold MA, Waters KM, Metz TO, Rodland KD, Webb-Robertson BJM. P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data. J Proteome Res 2019; 18:1426-1432. [PMID: 30667224 DOI: 10.1021/acs.jproteome.8b00840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The use of mass-spectrometry-based techniques for global protein profiling of biomedical or environmental experiments has become a major focus in research centered on biomarker discovery; however, one of the most important issues recently highlighted in the new era of omics data generation is the ability to perform analyses in a robust and reproducible manner. This has been hypothesized to be one of the issues hindering the ability of clinical proteomics to successfully identify clinical diagnostic and prognostic biomarkers of disease. P-Mart ( https://pmart.labworks.org ) is a new interactive web-based software environment that enables domain scientists to perform quality-control processing, statistics, and exploration of large-complex proteomics data sets without requiring statistical programming. P-Mart is developed in a manner that allows researchers to perform analyses via a series of modules, explore the results using interactive visualization, and finalize the analyses with a collection of output files documenting all stages of the analysis and a report to allow reproduction of the analysis.
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Affiliation(s)
- Lisa M Bramer
- Computing & Analytics Division , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99352 , United States
| | - Kelly G Stratton
- Computing & Analytics Division , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99352 , United States
| | - Amanda M White
- Computing & Analytics Division , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99352 , United States
| | - Ameila H Bleeker
- Computing & Analytics Division , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99352 , United States
| | - Markus A Kobold
- Computing & Analytics Division , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99352 , United States
| | - Katrina M Waters
- Biological Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99352 , United States
| | - Thomas O Metz
- Biological Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99352 , United States
| | - Karin D Rodland
- Biological Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99352 , United States.,Department of Cell, Developmental, and Cancer Biology , Oregon Health & Science University , Portland , Oregon 97221 , United States
| | - Bobbie-Jo M Webb-Robertson
- Computing & Analytics Division , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99352 , United States
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Dixon HM, Armstrong G, Barton M, Bergmann AJ, Bondy M, Halbleib ML, Hamilton W, Haynes E, Herbstman J, Hoffman P, Jepson P, Kile ML, Kincl L, Laurienti PJ, North P, Paulik LB, Petrosino J, Points GL, Poutasse CM, Rohlman D, Scott RP, Smith B, Tidwell LG, Walker C, Waters KM, Anderson KA. Discovery of common chemical exposures across three continents using silicone wristbands. R Soc Open Sci 2019; 6:181836. [PMID: 30891293 PMCID: PMC6408398 DOI: 10.1098/rsos.181836] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 01/14/2019] [Indexed: 05/21/2023]
Abstract
To assess differences and trends in personal chemical exposure, volunteers from 14 communities in Africa (Senegal, South Africa), North America (United States (U.S.)) and South America (Peru) wore 262 silicone wristbands. We analysed wristband extracts for 1530 unique chemicals, resulting in 400 860 chemical data points. The number of chemical detections ranged from 4 to 43 per wristband, with 191 different chemicals detected, and 1339 chemicals were not detected in any wristband. No two wristbands had identical chemical detections. We detected 13 potential endocrine disrupting chemicals in over 50% of all wristbands and found 36 chemicals in common between chemicals detected in three geographical wristband groups (Africa, North America and South America). U.S. children (less than or equal to 11 years) had the highest percentage of flame retardant detections compared with all other participants. Wristbands worn in Texas post-Hurricane Harvey had the highest mean number of chemical detections (28) compared with other study locations (10-25). Consumer product-related chemicals and phthalates were a high percentage of chemical detections across all study locations (36-53% and 18-42%, respectively). Chemical exposures varied among individuals; however, many individuals were exposed to similar chemical mixtures. Our exploratory investigation uncovered personal chemical exposure trends that can help prioritize certain mixtures and chemical classes for future studies.
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Affiliation(s)
- Holly M. Dixon
- Food Safety and Environmental Stewardship Program, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Georgina Armstrong
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Michael Barton
- Food Safety and Environmental Stewardship Program, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Alan J. Bergmann
- Food Safety and Environmental Stewardship Program, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Melissa Bondy
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Mary L. Halbleib
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
| | - Winifred Hamilton
- Department of Medicine, Environmental Health Section, Baylor College of Medicine, Houston, TX, USA
| | - Erin Haynes
- College of Medicine, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Julie Herbstman
- Columbia Center for Children's Environmental Health, Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Peter Hoffman
- Food Safety and Environmental Stewardship Program, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Paul Jepson
- Integrated Plant Protection Center, Oregon State University, Corvallis, OR, USA
| | - Molly L. Kile
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| | - Laurel Kincl
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| | - Paul J. Laurienti
- Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Paula North
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - L. Blair Paulik
- Food Safety and Environmental Stewardship Program, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Joe Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Gary L. Points
- Food Safety and Environmental Stewardship Program, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Carolyn M. Poutasse
- Food Safety and Environmental Stewardship Program, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Diana Rohlman
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| | - Richard P. Scott
- Food Safety and Environmental Stewardship Program, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Brian Smith
- Food Safety and Environmental Stewardship Program, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Lane G. Tidwell
- Food Safety and Environmental Stewardship Program, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Cheryl Walker
- Department of Medicine, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - Katrina M. Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kim A. Anderson
- Food Safety and Environmental Stewardship Program, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
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Stratton KG, Webb-Robertson BJM, McCue LA, Stanfill B, Claborne D, Godinez I, Johansen T, Thompson AM, Burnum-Johnson KE, Waters KM, Bramer LM. pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data. J Proteome Res 2019; 18:1418-1425. [PMID: 30638385 PMCID: PMC6750869 DOI: 10.1021/acs.jproteome.8b00760] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Prior
to statistical analysis of mass spectrometry (MS) data, quality
control (QC) of the identified biomolecule peak intensities is imperative
for reducing process-based sources of variation and extreme biological
outliers. Without this step, statistical results can be biased. Additionally,
liquid chromatography–MS proteomics data present inherent challenges
due to large amounts of missing data that require special consideration
during statistical analysis. While a number of R packages exist to
address these challenges individually, there is no single R package
that addresses all of them. We present pmartR, an
open-source R package, for QC (filtering and normalization), exploratory
data analysis (EDA), visualization, and statistical analysis robust
to missing data. Example analysis using proteomics data from a mouse
study comparing smoke exposure to control demonstrates the core functionality
of the package and highlights the capabilities for handling missing
data. In particular, using a combined quantitative and qualitative
statistical test, 19 proteins whose statistical significance would
have been missed by a quantitative test alone were identified. The pmartR package provides a single software tool for QC, EDA,
and statistical comparisons of MS data that is robust to missing data
and includes numerous visualization capabilities.
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Affiliation(s)
- Kelly G Stratton
- National Security Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Bobbie-Jo M Webb-Robertson
- National Security Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Lee Ann McCue
- Earth & Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulavard , Richland , Washington 99354 , United States
| | - Bryan Stanfill
- National Security Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Daniel Claborne
- National Security Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Iobani Godinez
- National Security Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Thomas Johansen
- Department of Statistics , Florida State University , 117 North Woodward Avenue , Tallahassee , Florida 32306 , United States
| | - Allison M Thompson
- Earth & Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulavard , Richland , Washington 99354 , United States
| | - Kristin E Burnum-Johnson
- Earth & Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulavard , Richland , Washington 99354 , United States
| | - Katrina M Waters
- Earth & Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulavard , Richland , Washington 99354 , United States
| | - Lisa M Bramer
- National Security Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
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Machol K, Rousseau J, Ehresmann S, Garcia T, Nguyen TTM, Spillmann RC, Sullivan JA, Shashi V, Jiang YH, Stong N, Fiala E, Willing M, Pfundt R, Kleefstra T, Cho MT, McLaughlin H, Rosello Piera M, Orellana C, Martínez F, Caro-Llopis A, Monfort S, Roscioli T, Nixon CY, Buckley MF, Turner A, Jones WD, van Hasselt PM, Hofstede FC, van Gassen KL, Brooks AS, van Slegtenhorst MA, Lachlan K, Sebastian J, Madan-Khetarpal S, Sonal D, Sakkubai N, Thevenon J, Faivre L, Maurel A, Petrovski S, Krantz ID, Tarpinian JM, Rosenfeld JA, Lee BH, Campeau PM, Adams DR, Alejandro ME, Allard P, Azamian MS, Bacino CA, Balasubramanyam A, Barseghyan H, Batzli GF, Beggs AH, Behnam B, Bican A, Bick DP, Birch CL, Bonner D, Boone BE, Bostwick BL, Briere LC, Brown DM, Brush M, Burke EA, Burrage LC, Chen S, Clark GD, Coakley TR, Cogan JD, Cooper CM, Cope H, Craigen WJ, D’Souza P, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dillon A, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Douine ED, Draper DD, Eckstein DJ, Emrick LT, Eng CM, Eskin A, Esteves C, Estwick T, Ferreira C, Fogel BL, Friedman ND, Gahl WA, Glanton E, Godfrey RA, Goldstein DB, Gould SE, Gourdine JPF, Groden CA, Gropman AL, Haendel M, Hamid R, Hanchard NA, Handley LH, Herzog MR, Holm IA, Hom J, Howerton EM, Huang Y, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Kohane IS, Krasnewich DM, Krieg EL, Krier JB, Lalani SR, Lau CC, Lazar J, Lee BH, Lee H, Levy SE, Lewis RA, Lincoln SA, Lipson A, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Marom R, Martínez-Agosto JA, Marwaha S, May T, McConkie-Rosell A, McCormack CE, McCray AT, Might M, Moretti PM, Morimoto M, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Parker NH, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Reuter CM, Robertson AK, Rodan LH, Rosenfeld JA, Sampson JB, Samson SL, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Signer R, Silverman EK, Sinsheimer JS, Smith KS, Spillmann RC, Splinter K, Stoler JM, Stong N, Sullivan JA, Sweetser DA, Tifft CJ, Toro C, Tran AA, Urv TK, Valivullah ZM, Vilain E, Vogel TP, Wahl CE, Walley NM, Walsh CA, Ward PA, Waters KM, Westerfield M, Wise AL, Wolfe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zastrow DB, Zheng A. Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay. Am J Hum Genet 2019; 104:164-178. [PMID: 30580808 DOI: 10.1016/j.ajhg.2018.11.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022] Open
Abstract
SMARCC2 (BAF170) is one of the invariable core subunits of the ATP-dependent chromatin remodeling BAF (BRG1-associated factor) complex and plays a crucial role in embryogenesis and corticogenesis. Pathogenic variants in genes encoding other components of the BAF complex have been associated with intellectual disability syndromes. Despite its significant biological role, variants in SMARCC2 have not been directly associated with human disease previously. Using whole-exome sequencing and a web-based gene-matching program, we identified 15 individuals with variable degrees of neurodevelopmental delay and growth retardation harboring one of 13 heterozygous variants in SMARCC2, most of them novel and proven de novo. The clinical presentation overlaps with intellectual disability syndromes associated with other BAF subunits, such as Coffin-Siris and Nicolaides-Baraitser syndromes and includes prominent speech impairment, hypotonia, feeding difficulties, behavioral abnormalities, and dysmorphic features such as hypertrichosis, thick eyebrows, thin upper lip vermilion, and upturned nose. Nine out of the fifteen individuals harbor variants in the highly conserved SMARCC2 DNA-interacting domains (SANT and SWIRM) and present with a more severe phenotype. Two of these individuals present cardiac abnormalities. Transcriptomic analysis of fibroblasts from affected individuals highlights a group of differentially expressed genes with possible roles in regulation of neuronal development and function, namely H19, SCRG1, RELN, and CACNB4. Our findings suggest a novel SMARCC2-related syndrome that overlaps with neurodevelopmental disorders associated with variants in BAF-complex subunits.
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Madeen E, Siddens LK, Uesugi S, McQuistan T, Corley RA, Smith J, Waters KM, Tilton SC, Anderson KA, Ognibene T, Turteltaub K, Williams DE. Toxicokinetics of benzo[a]pyrene in humans: Extensive metabolism as determined by UPLC-accelerator mass spectrometry following oral micro-dosing. Toxicol Appl Pharmacol 2018; 364:97-105. [PMID: 30582946 DOI: 10.1016/j.taap.2018.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/13/2018] [Accepted: 12/17/2018] [Indexed: 10/27/2022]
Abstract
Benzo[a]pyrene (BaP), is a known human carcinogen (International Agency for Research on Cancer (IARC) class 1). The remarkable sensitivity (zepto-attomole 14C in biological samples) of accelerator mass spectrometry (AMS) makes possible, with de minimus risk, pharmacokinetic (PK) analysis following [14C]-BaP micro-dosing of humans. A 46 ng (5 nCi) dose was given thrice to 5 volunteers with minimum 2 weeks between dosing and plasma collected over 72 h. [14C]-BaPeq PK analysis gave plasma Tmax and Cmax values of 1.25 h and 29-82 fg/mL, respectively. PK parameters were assessed by non- compartment and compartment models. Intervals between dosing ranged from 20 to 420 days and had little impact on intra-individual variation. DNA, extracted from peripheral blood mononuclear cells (PBMCs) of 4 volunteers, showed measurable levels (LOD ~ 0.5 adducts/1011 nucleotides) in two individuals 2-3 h post-dose, approximately three orders of magnitude lower than smokers or occupationally-exposed individuals. Little or no DNA binding was detectable at 48-72 h. In volunteers the allelic variants CYP1B1*1/*⁎1, *1/*3 or *3/*3 and GSTM1*0/0 or *1 had no impact on [14C]-BaPeq PK or DNA adduction with this very limited sample. Plasma metabolites over 72 h from two individuals (one CYP1B1*1/*1 and one CYP1B1*3/*3) were analyzed by UPLC-AMS. In both individuals, parent [14C]-BaP was a minor constituent even at the earliest time points and metabolite profiles markedly distinct. AMS, coupled with UPLC, could be used in humans to enhance the accuracy of pharmacokinetics, toxicokinetics and risk assessment of environmental carcinogens.
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Affiliation(s)
- Erin Madeen
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA; NIEHS Superfund Research Program, Oregon State University, Corvallis, OR, USA
| | - Lisbeth K Siddens
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA; NIEHS Superfund Research Program, Oregon State University, Corvallis, OR, USA; Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - Sandra Uesugi
- Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | | | - Richard A Corley
- NIEHS Superfund Research Program, Oregon State University, Corvallis, OR, USA; Chemical Biology and Exposure Science, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jordan Smith
- NIEHS Superfund Research Program, Oregon State University, Corvallis, OR, USA; Chemical Biology and Exposure Science, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Katrina M Waters
- NIEHS Superfund Research Program, Oregon State University, Corvallis, OR, USA; Chemical Biology and Exposure Science, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Susan C Tilton
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA; NIEHS Superfund Research Program, Oregon State University, Corvallis, OR, USA
| | - Kim A Anderson
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA; NIEHS Superfund Research Program, Oregon State University, Corvallis, OR, USA
| | - Ted Ognibene
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kenneth Turteltaub
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA, USA; Biology and Biotechnology Research Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - David E Williams
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA; NIEHS Superfund Research Program, Oregon State University, Corvallis, OR, USA; Linus Pauling Institute, Oregon State University, Corvallis, OR, USA.
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36
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Dorman DC, Chiu W, Hales BF, Hauser R, Johnson KJ, Mantus E, Martel S, Robinson KA, Rooney AA, Rudel R, Sathyanarayana S, Schantz SL, Waters KM. Polybrominated diphenyl ether (PBDE) neurotoxicity: a systematic review and meta-analysis of animal evidence. J Toxicol Environ Health B Crit Rev 2018; 21:269-289. [PMID: 30352012 PMCID: PMC6786272 DOI: 10.1080/10937404.2018.1514829] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
A recent systematic review (SR) and meta-analysis of human studies found an association between prenatal serum polybrominated diphenyl ethers (PBDE) concentrations and a decrease in the IQ of children. A SR of experimental developmental animal PBDE-mediated neurotoxicity studies was performed in the present study. Outcomes assessed included measures related to learning, memory, and attention, which parallel the intelligence-related outcomes evaluated in the human studies SR. PubMed, Embase, and Toxline were searched for relevant experimental non-human mammalian studies. Evaluation of risk of bias (RoB) and overall body of evidence followed guidance developed by the National Toxicology Program. Animal studies using varying designs and outcomes were available for BDEs 47, 99, 153, 203, 206, and 209 and the technical mixture DE-71. Study reporting of methods and results was often incomplete leading to concerns regarding RoB. A meta-analysis of 6 Morris water maze studies showed evidence of a significant increase in last trial latency (effect size of 25.8 [CI, 20.3 to 31.2]) in PBDE-exposed animals with low heterogeneity. For most endpoints, there were unexplained inconsistencies across studies and no consistent evidence of a dose-response relationship. There is a "moderate" level of evidence that exposure to BDEs 47, 99, and 209 affects learning. For other PBDEs and other endpoints, the level of evidence was "low" or "very low". The meta-analysis led to stronger conclusions than that based upon a qualitative review of the evidence. The SR also identified RoB concerns that might be remedied by better study reporting.
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Affiliation(s)
- David C. Dorman
- Department of Molecular and Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Weihsueh Chiu
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
| | - Barbara F. Hales
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Russ Hauser
- Department of Environmental Health and Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kamin J. Johnson
- Predictive Safety Center, Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA
| | - Ellen Mantus
- Board on Environmental Studies and Toxicology at the National Academies of Sciences, Engineering, and Medicine, Washington DC, USA
| | - Susan Martel
- Board on Environmental Studies and Toxicology at the National Academies of Sciences, Engineering, and Medicine, Washington DC, USA
| | - Karen A. Robinson
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew A. Rooney
- Office of Health Assessment and Translation, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | | | - Sheela Sathyanarayana
- Department of Pediatrics, University of Washington, Seattle Children’s Research Institute, Seattle WA, USA
| | - Susan L. Schantz
- Department of Comparative Biosciences, College of Veterinary Medicine and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Katrina M. Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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Marcogliese PC, Shashi V, Spillmann RC, Stong N, Rosenfeld JA, Koenig MK, Martínez-Agosto JA, Herzog M, Chen AH, Dickson PI, Lin HJ, Vera MU, Salamon N, Graham JM, Ortiz D, Infante E, Steyaert W, Dermaut B, Poppe B, Chung HL, Zuo Z, Lee PT, Kanca O, Xia F, Yang Y, Smith EC, Jasien J, Kansagra S, Spiridigliozzi G, El-Dairi M, Lark R, Riley K, Koeberl DD, Golden-Grant K, Yamamoto S, Wangler MF, Mirzaa G, Hemelsoet D, Lee B, Nelson SF, Goldstein DB, Bellen HJ, Pena LD, Callens S, Coucke P, Dermaut B, Hemelsoet D, Poppe B, Steyaert W, Terryn W, Van Coster R, Adams DR, Alejandro ME, Allard P, Azamian MS, Bacino CA, Balasubramanyam A, Barseghyan H, Batzli GF, Beggs AH, Behnam B, Bican A, Bick DP, Birch CL, Bonner D, Boone BE, Bostwick BL, Briere LC, Brown DM, Brush M, Burke EA, Burrage LC, Chen S, Clark GD, Coakley TR, Cogan JD, Cooper CM, Cope H, Craigen WJ, D’Souza P, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dillon A, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Douine ED, Draper DD, Eckstein DJ, Emrick LT, Eng CM, Eskin A, Esteves C, Estwick T, Ferreira C, Fogel BL, Friedman ND, Gahl WA, Glanton E, Godfrey RA, Goldstein DB, Gould SE, Gourdine JPF, Groden CA, Gropman AL, Haendel M, Hamid R, Hanchard NA, Handley LH, Herzog MR, Holm IA, Hom J, Howerton EM, Huang Y, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Kohane IS, Krasnewich DM, Krieg EL, Krier JB, Lalani SR, Lau CC, Lazar J, Lee BH, Lee H, Levy SE, Lewis RA, Lincoln SA, Lipson A, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Marom R, Martínez-Agosto JA, Marwaha S, May T, McConkie-Rosell A, McCormack CE, McCray AT, Might M, Moretti PM, Morimoto M, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Parker NH, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Reuter CM, Robertson AK, Rodan LH, Rosenfeld JA, Sampson JB, Samson SL, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Signer R, Silverman EK, Sinsheimer JS, Smith KS, Spillmann RC, Splinter K, Stoler JM, Stong N, Sullivan JA, Sweetser DA, Tifft CJ, Toro C, Tran AA, Urv TK, Valivullah ZM, Vilain E, Vogel TP, Wahl CE, Walley NM, Walsh CA, Ward PA, Waters KM, Westerfield M, Wise AL, Wolfe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zastrow DB, Zheng A. IRF2BPL Is Associated with Neurological Phenotypes. Am J Hum Genet 2018; 103:456. [PMID: 30193138 PMCID: PMC6128320 DOI: 10.1016/j.ajhg.2018.08.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Dixon HM, Scott RP, Holmes D, Calero L, Kincl LD, Waters KM, Camann DE, Calafat AM, Herbstman JB, Anderson KA. Silicone wristbands compared with traditional polycyclic aromatic hydrocarbon exposure assessment methods. Anal Bioanal Chem 2018; 410:3059-3071. [PMID: 29607448 PMCID: PMC5910488 DOI: 10.1007/s00216-018-0992-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/31/2018] [Accepted: 03/01/2018] [Indexed: 12/16/2022]
Abstract
Currently there is a lack of inexpensive, easy-to-use technology to evaluate human exposure to environmental chemicals, including polycyclic aromatic hydrocarbons (PAHs). This is the first study in which silicone wristbands were deployed alongside two traditional personal PAH exposure assessment methods: active air monitoring with samplers (i.e., polyurethane foam (PUF) and filter) housed in backpacks, and biological sampling with urine. We demonstrate that wristbands worn for 48 h in a non-occupational setting recover semivolatile PAHs, and we compare levels of PAHs in wristbands to PAHs in PUFs-filters and to hydroxy-PAH (OH-PAH) biomarkers in urine. We deployed all samplers simultaneously for 48 h on 22 pregnant women in an established urban birth cohort. Each woman provided one spot urine sample at the end of the 48-h period. Wristbands recovered PAHs with similar detection frequencies to PUFs-filters. Of the 62 PAHs tested for in the 22 wristbands, 51 PAHs were detected in at least one wristband. In this cohort of pregnant women, we found more significant correlations between OH-PAHs and PAHs in wristbands than between OH-PAHs and PAHs in PUFs-filters. Only two comparisons between PAHs in PUFs-filters and OH-PAHs correlated significantly (rs = 0.53 and p = 0.01; rs = 0.44 and p = 0.04), whereas six comparisons between PAHs in wristbands and OH-PAHs correlated significantly (rs = 0.44 to 0.76 and p = 0.04 to <0.0001). These results support the utility of wristbands as a biologically relevant exposure assessment tool which can be easily integrated into environmental health studies. PAHs detected in samples collected from urban pregnant women ![]()
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Affiliation(s)
- Holly M Dixon
- Food Safety and Environmental Stewardship Program, Environmental and Molecular Toxicology, Oregon State University, 1007 Agricultural and Life Sciences Building, Corvallis, OR, 97331, USA
| | - Richard P Scott
- Food Safety and Environmental Stewardship Program, Environmental and Molecular Toxicology, Oregon State University, 1007 Agricultural and Life Sciences Building, Corvallis, OR, 97331, USA
| | - Darrell Holmes
- Columbia Center for Children's Environmental Health, Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY, 10032, USA
| | - Lehyla Calero
- Columbia Center for Children's Environmental Health, Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY, 10032, USA
| | - Laurel D Kincl
- College of Public Health and Human Sciences, Department of Environmental and Occupational Health, Oregon State University, 160 SW 26th St, Corvallis, OR, 97331, USA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA, 99352, USA
| | - David E Camann
- Chemistry and Chemical Engineering Division, Southwest Research Institute, P.O. Drawer 28510, San Antonio, TX, 78228-0510, USA
| | - Antonia M Calafat
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30333, USA
| | - Julie B Herbstman
- Columbia Center for Children's Environmental Health, Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY, 10032, USA
| | - Kim A Anderson
- Food Safety and Environmental Stewardship Program, Environmental and Molecular Toxicology, Oregon State University, 1007 Agricultural and Life Sciences Building, Corvallis, OR, 97331, USA.
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39
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Haggard DE, Noyes PD, Waters KM, Tanguay RL. Transcriptomic and phenotypic profiling in developing zebrafish exposed to thyroid hormone receptor agonists. Reprod Toxicol 2018; 77:80-93. [PMID: 29458080 PMCID: PMC5878140 DOI: 10.1016/j.reprotox.2018.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 01/15/2018] [Accepted: 02/13/2018] [Indexed: 02/08/2023]
Abstract
There continues to be a need to develop in vivo high-throughput screening (HTS) and computational methods to screen chemicals for interaction with the estrogen, androgen, and thyroid pathways and as complements to in vitro HTS assays. This study explored the utility of an embryonic zebrafish HTS approach to identify and classify endocrine bioactivity using phenotypically-anchored transcriptome profiling. Transcriptome analysis was conducted on zebrafish embryos exposed to 25 estrogen-, androgen-, or thyroid-active chemicals at concentrations that elicited adverse malformations or mortality at 120 h post-fertilization in 80% of animals exposed. Analysis of the top 1000 significant differentially expressed transcripts and developmental toxicity profiles across all treatments identified a unique transcriptional and phenotypic signature for thyroid hormone receptor agonists. This unique signature has the potential to be used as a tiered in vivo HTS and may aid in identifying chemicals that interact with the thyroid hormone receptor.
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Affiliation(s)
- Derik E Haggard
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Pamela D Noyes
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States; Current: National Center for Environmental Assessment, Office of Research and Development, U.S. Environmental Protection Agency, Washington, DC, United States
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Robert L Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States.
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40
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Oláhová M, Yoon WH, Thompson K, Jangam S, Fernandez L, Davidson JM, Kyle JE, Grove ME, Fisk DG, Kohler JN, Holmes M, Dries AM, Huang Y, Zhao C, Contrepois K, Zappala Z, Frésard L, Waggott D, Zink EM, Kim YM, Heyman HM, Stratton KG, Webb-Robertson BJM, Snyder M, Merker JD, Montgomery SB, Fisher PG, Feichtinger RG, Mayr JA, Hall J, Barbosa IA, Simpson MA, Deshpande C, Waters KM, Koeller DM, Metz TO, Morris AA, Schelley S, Cowan T, Friederich MW, McFarland R, Van Hove JLK, Enns GM, Yamamoto S, Ashley EA, Wangler MF, Taylor RW, Bellen HJ, Bernstein JA, Wheeler MT. Biallelic Mutations in ATP5F1D, which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder. Am J Hum Genet 2018; 102:494-504. [PMID: 29478781 PMCID: PMC6117612 DOI: 10.1016/j.ajhg.2018.01.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/26/2018] [Indexed: 01/07/2023] Open
Abstract
ATP synthase, H+ transporting, mitochondrial F1 complex, δ subunit (ATP5F1D; formerly ATP5D) is a subunit of mitochondrial ATP synthase and plays an important role in coupling proton translocation and ATP production. Here, we describe two individuals, each with homozygous missense variants in ATP5F1D, who presented with episodic lethargy, metabolic acidosis, 3-methylglutaconic aciduria, and hyperammonemia. Subject 1, homozygous for c.245C>T (p.Pro82Leu), presented with recurrent metabolic decompensation starting in the neonatal period, and subject 2, homozygous for c.317T>G (p.Val106Gly), presented with acute encephalopathy in childhood. Cultured skin fibroblasts from these individuals exhibited impaired assembly of F1FO ATP synthase and subsequent reduced complex V activity. Cells from subject 1 also exhibited a significant decrease in mitochondrial cristae. Knockdown of Drosophila ATPsynδ, the ATP5F1D homolog, in developing eyes and brains caused a near complete loss of the fly head, a phenotype that was fully rescued by wild-type human ATP5F1D. In contrast, expression of the ATP5F1D c.245C>T and c.317T>G variants rescued the head-size phenotype but recapitulated the eye and antennae defects seen in other genetic models of mitochondrial oxidative phosphorylation deficiency. Our data establish c.245C>T (p.Pro82Leu) and c.317T>G (p.Val106Gly) in ATP5F1D as pathogenic variants leading to a Mendelian mitochondrial disease featuring episodic metabolic decompensation.
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Affiliation(s)
- Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Wan Hee Yoon
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Sharayu Jangam
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liliana Fernandez
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - Jean M Davidson
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Megan E Grove
- Clinical Genomics Program, Stanford Health Care, Stanford, CA 94305, USA
| | - Dianna G Fisk
- Clinical Genomics Program, Stanford Health Care, Stanford, CA 94305, USA
| | - Jennefer N Kohler
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - Matthew Holmes
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Annika M Dries
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - Yong Huang
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - Chunli Zhao
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zachary Zappala
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laure Frésard
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Daryl Waggott
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - Erika M Zink
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Young-Mo Kim
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Heino M Heyman
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Kelly G Stratton
- Computing & Analytics Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Bobbie-Jo M Webb-Robertson
- Computing & Analytics Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jason D Merker
- Clinical Genomics Program, Stanford Health Care, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Stephen B Montgomery
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Paul G Fisher
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
| | - René G Feichtinger
- Department of Pediatrics, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Johannes A Mayr
- Department of Pediatrics, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Julie Hall
- Department of Neuroradiology, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK
| | - Ines A Barbosa
- Department of Medical and Molecular Genetics, King's College London School of Basic and Medical Biosciences, London SE1 9RT, UK
| | - Michael A Simpson
- Department of Medical and Molecular Genetics, King's College London School of Basic and Medical Biosciences, London SE1 9RT, UK
| | - Charu Deshpande
- Clinical Genetics Unit, Guys and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Katrina M Waters
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - David M Koeller
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Thomas O Metz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Andrew A Morris
- Institute of Human Development, University of Manchester, Manchester M13 9PL, UK; Willink Metabolic Unit, Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK
| | - Susan Schelley
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tina Cowan
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Marisa W Friederich
- Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado at Denver, Aurora, CO 80045, USA
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Johan L K Van Hove
- Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado at Denver, Aurora, CO 80045, USA
| | - Gregory M Enns
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Euan A Ashley
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA; Clinical Genomics Program, Stanford Health Care, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Hugo J Bellen
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan A Bernstein
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew T Wheeler
- Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Dorman DC, Chiu W, Hales BF, Hauser R, Johnson KJ, Mantus E, Martel S, Robinson KA, Rooney AA, Rudel R, Sathyanarayana S, Schantz SL, Waters KM. Systematic reviews and meta-analyses of human and animal evidence of prenatal diethylhexyl phthalate exposure and changes in male anogenital distance. J Toxicol Environ Health B Crit Rev 2018; 21:207-226. [PMID: 30199328 DOI: 10.1080/10937404.2018.1505354.systematic] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Male reproductive alterations found in animals and humans following in utero phthalate exposure include decreased anogenital distance (AGD) and other reproductive-tract malformations. The aim of this investigation was to conduct systematic reviews of human and animal evidence of the effect of in utero exposure to diethylhexyl phthalate (DEHP) on anogenital distance (AGD) in males. PubMed, Embase, and Toxline were searched for relevant human and experimental animal studies on August 15, 2016. Search results were screened for relevance, and studies that met the inclusion criteria were evaluated for quality and data extracted for analysis. Confidence in the human and animal bodies of evidence was assessed and hazard conclusions reached by integrating evidence streams. The search yielded 6 relevant human studies and 19 animal studies. Meta-analysis of 5 human observational prospective cohort studies showed that increased maternal urinary concentrations of DEHP metabolites were associated with decreased AGD in boys (-4.07 [CI, -6.49 to -1.66] % decrease per log10 rise in DEHP metabolites). Meta-analysis and meta-regression of the 19 experimental animal studies found reduced AGD with DEHP treatment, with a dose-response gradient, and with heterogeneity explained by species and strain. There is a moderate level of evidence from human investigations and a high level of data from animal studies that in utero exposure to DEHP decreases AGD. Based upon the available human and animal evidence, and consideration of mechanistic data, DEHP is presumed to be a reproductive hazard to humans on the basis of effects on AGD.
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Affiliation(s)
- David C Dorman
- a Department of Molecular and Biomedical Sciences, College of Veterinary Medicine , North Carolina State University , Raleigh , NC , USA
| | - Weihsueh Chiu
- b Department of Veterinary Integrative Biosciences, College of Veterinary Medicine , Texas A&M University , College Station , TX , USA
| | - Barbara F Hales
- c Department of Pharmacology and Therapeutics , McGill University , Montreal , Quebec , Canada
| | - Russ Hauser
- d Department of Environmental Health and Department of Epidemiology , Harvard T.H. Chan School of Public Health , Boston , MA , USA
| | - Kamin J Johnson
- e Predictive Safety Center , The Dow Chemical Company , Midland , MI , USA
| | - Ellen Mantus
- f Board on Environmental Studies and Toxicology at the National Academies of Sciences , Engineering, and Medicine , Washington , DC , USA
| | - Susan Martel
- f Board on Environmental Studies and Toxicology at the National Academies of Sciences , Engineering, and Medicine , Washington , DC , USA
| | - Karen A Robinson
- g Department of Medicine , Johns Hopkins University , Baltimore , MD , USA
| | - Andrew A Rooney
- h Office of Health Assessment and Translation, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services , Research Triangle Park , NC , USA
| | | | - Sheela Sathyanarayana
- j Department of Pediatrics , University of Washington, Seattle Children's Research Institute , Seattle , WA , USA
| | - Susan L Schantz
- k Department of Comparative Biosciences, College of Veterinary Medicine and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , IL , USA
| | - Katrina M Waters
- l Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
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42
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Dorman DC, Chiu W, Hales BF, Hauser R, Johnson KJ, Mantus E, Martel S, Robinson KA, Rooney AA, Rudel R, Sathyanarayana S, Schantz SL, Waters KM. Systematic reviews and meta-analyses of human and animal evidence of prenatal diethylhexyl phthalate exposure and changes in male anogenital distance. J Toxicol Environ Health B Crit Rev 2018; 21:207-226. [PMID: 30199328 PMCID: PMC6786271 DOI: 10.1080/10937404.2018.1505354] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Male reproductive alterations found in animals and humans following in utero phthalate exposure include decreased anogenital distance (AGD) and other reproductive-tract malformations. The aim of this investigation was to conduct systematic reviews of human and animal evidence of the effect of in utero exposure to diethylhexyl phthalate (DEHP) on anogenital distance (AGD) in males. PubMed, Embase, and Toxline were searched for relevant human and experimental animal studies on August 15, 2016. Search results were screened for relevance, and studies that met the inclusion criteria were evaluated for quality and data extracted for analysis. Confidence in the human and animal bodies of evidence was assessed and hazard conclusions reached by integrating evidence streams. The search yielded 6 relevant human studies and 19 animal studies. Meta-analysis of 5 human observational prospective cohort studies showed that increased maternal urinary concentrations of DEHP metabolites were associated with decreased AGD in boys (-4.07 [CI, -6.49 to -1.66] % decrease per log10 rise in DEHP metabolites). Meta-analysis and meta-regression of the 19 experimental animal studies found reduced AGD with DEHP treatment, with a dose-response gradient, and with heterogeneity explained by species and strain. There is a moderate level of evidence from human investigations and a high level of data from animal studies that in utero exposure to DEHP decreases AGD. Based upon the available human and animal evidence, and consideration of mechanistic data, DEHP is presumed to be a reproductive hazard to humans on the basis of effects on AGD.
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Affiliation(s)
- David C. Dorman
- Department of Molecular and Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Weihsueh Chiu
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
| | - Barbara F. Hales
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Russ Hauser
- Department of Environmental Health and Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kamin J. Johnson
- Predictive Safety Center, The Dow Chemical Company, Midland, MI, USA
| | - Ellen Mantus
- Board on Environmental Studies and Toxicology at the National Academies of Sciences, Engineering, and Medicine, Washington, DC, USA
| | - Susan Martel
- Board on Environmental Studies and Toxicology at the National Academies of Sciences, Engineering, and Medicine, Washington, DC, USA
| | - Karen A. Robinson
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew A. Rooney
- Office of Health Assessment and Translation, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | | | - Sheela Sathyanarayana
- Department of Pediatrics, University of Washington, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Susan L. Schantz
- Department of Comparative Biosciences, College of Veterinary Medicine and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Katrina M. Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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43
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Eisfeld AJ, Halfmann PJ, Wendler JP, Kyle JE, Burnum-Johnson KE, Peralta Z, Maemura T, Walters KB, Watanabe T, Fukuyama S, Yamashita M, Jacobs JM, Kim YM, Casey CP, Stratton KG, Webb-Robertson BJM, Gritsenko MA, Monroe ME, Weitz KK, Shukla AK, Tian M, Neumann G, Reed JL, van Bakel H, Metz TO, Smith RD, Waters KM, N'jai A, Sahr F, Kawaoka Y. Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis. Cell Host Microbe 2017; 22:817-829.e8. [PMID: 29154144 DOI: 10.1016/j.chom.2017.10.011] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/13/2017] [Accepted: 09/20/2017] [Indexed: 12/11/2022]
Abstract
The pathogenesis of human Ebola virus disease (EVD) is complex. EVD is characterized by high levels of virus replication and dissemination, dysregulated immune responses, extensive virus- and host-mediated tissue damage, and disordered coagulation. To clarify how host responses contribute to EVD pathophysiology, we performed multi-platform 'omics analysis of peripheral blood mononuclear cells and plasma from EVD patients. Our results indicate that EVD molecular signatures overlap with those of sepsis, imply that pancreatic enzymes contribute to tissue damage in fatal EVD, and suggest that Ebola virus infection may induce aberrant neutrophils whose activity could explain hallmarks of fatal EVD. Moreover, integrated biomarker prediction identified putative biomarkers from different data platforms that differentiated survivors and fatalities early after infection. This work reveals insight into EVD pathogenesis, suggests an effective approach for biomarker identification, and provides an important community resource for further analysis of human EVD severity.
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Affiliation(s)
- Amie J Eisfeld
- Department of Pathobiological Sciences, University of Wisconsin - Madison (UW-Madison), Madison, WI 53706, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin - Madison (UW-Madison), Madison, WI 53706, USA
| | - Jason P Wendler
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA 99352, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA 99352, USA
| | - Kristin E Burnum-Johnson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA 99352, USA
| | - Zuleyma Peralta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai (ISMMS), New York City, NY 10029, USA
| | - Tadashi Maemura
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science (IMS), University of Tokyo, Tokyo 108-8639, Japan
| | - Kevin B Walters
- Department of Pathobiological Sciences, University of Wisconsin - Madison (UW-Madison), Madison, WI 53706, USA
| | - Tokiko Watanabe
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science (IMS), University of Tokyo, Tokyo 108-8639, Japan
| | - Satoshi Fukuyama
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science (IMS), University of Tokyo, Tokyo 108-8639, Japan
| | - Makoto Yamashita
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science (IMS), University of Tokyo, Tokyo 108-8639, Japan
| | - Jon M Jacobs
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA 99352, USA
| | - Young-Mo Kim
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA 99352, USA
| | - Cameron P Casey
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA 99352, USA
| | - Kelly G Stratton
- Computing and Analytics Division, National Security Directorate, PNNL, Richland, WA 99352, USA
| | | | - Marina A Gritsenko
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA 99352, USA
| | - Matthew E Monroe
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA 99352, USA
| | - Karl K Weitz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA 99352, USA
| | - Anil K Shukla
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA 99352, USA
| | - Mingyuan Tian
- Department of Chemical and Biological Engineering, UW-Madison, Madison, WI 53706, USA
| | - Gabriele Neumann
- Department of Pathobiological Sciences, University of Wisconsin - Madison (UW-Madison), Madison, WI 53706, USA
| | - Jennifer L Reed
- Department of Chemical and Biological Engineering, UW-Madison, Madison, WI 53706, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai (ISMMS), New York City, NY 10029, USA; Icahn Institute for Genomics and Multiscale Biology, ISMMS, New York City, NY 10029, USA.
| | - Thomas O Metz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA 99352, USA.
| | - Richard D Smith
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA 99352, USA.
| | - Katrina M Waters
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA 99352, USA.
| | - Alhaji N'jai
- Department of Pathobiological Sciences, University of Wisconsin - Madison (UW-Madison), Madison, WI 53706, USA; Department of Biological Sciences, Fourah Bay College, College of Medicine & Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Foday Sahr
- 34(th) Regimental Military Hospital at Wilberforce, Freetown, Sierra Leone.
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin - Madison (UW-Madison), Madison, WI 53706, USA; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science (IMS), University of Tokyo, Tokyo 108-8639, Japan; International Research Center for Infectious Diseases, IMS, University of Tokyo, Tokyo 108-8639, Japan.
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44
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Davie-Martin CL, Stratton KG, Teeguarden JG, Waters KM, Simonich SLM. Implications of Bioremediation of Polycyclic Aromatic Hydrocarbon-Contaminated Soils for Human Health and Cancer Risk. Environ Sci Technol 2017; 51:9458-9468. [PMID: 28836766 DOI: 10.1021/acs.est.7b02956] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Bioremediation uses soil microorganisms to degrade polycyclic aromatic hydrocarbons (PAHs) into less toxic compounds and can be performed in situ, without the need for expensive infrastructure or amendments. This review provides insights into the cancer risks associated with PAH-contaminated soils and places bioremediation outcomes in a context relevant to human health. We evaluated which bioremediation strategies were most effective for degrading PAHs and estimated the cancer risks associated with PAH-contaminated soils. Cancer risk was statistically reduced in 89% of treated soils following bioremediation, with a mean degradation of 44% across the B2 group PAHs. However, all 180 treated soils had postbioremediation cancer risk values that exceeded the U.S. Environmental Protection Agency (USEPA) health-based acceptable risk level (by at least a factor of 2), with 32% of treated soils exceeding recommended levels by greater than 2 orders of magnitude. Composting treatments were most effective at biodegrading PAHs in soils (70% average reduction compared with 28-53% for the other treatment types), which was likely due to the combined influence of the rich source of nutrients and microflora introduced with organic compost amendments. Ultimately, bioremediation strategies, in the studies reviewed, were unable to successfully remove carcinogenic PAHs from contaminated soils to concentrations below the target cancer risk levels recommended by the USEPA.
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Affiliation(s)
- Cleo L Davie-Martin
- Department of Environmental and Molecular Toxicology, Oregon State University , Corvallis, Oregon 97331, United States
- Department of Microbiology, Oregon State University , Corvallis, Oregon 97331, United States
| | - Kelly G Stratton
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Justin G Teeguarden
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Katrina M Waters
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Staci L Massey Simonich
- Department of Environmental and Molecular Toxicology, Oregon State University , Corvallis, Oregon 97331, United States
- Department of Chemistry, Oregon State University , Corvallis, Oregon 97331, United States
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45
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Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 2017; 34:828-837. [PMID: 27504778 DOI: 10.1038/nbt.3597] [Citation(s) in RCA: 2254] [Impact Index Per Article: 322.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 05/10/2016] [Indexed: 12/14/2022]
Abstract
The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
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Affiliation(s)
- Mingxun Wang
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jeremy J Carver
- Computer Science and Engineering, UC San Diego, La Jolla, United States.,Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Vanessa V Phelan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Laura M Sanchez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Yao Peng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Don Duy Nguyen
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Jeramie Watrous
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Clifford A Kapono
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Carla Porto
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Wei-Ting Liu
- Department of Microbiology and Immunology, Stanford University, Palo Alto, United States
| | - Max Crüsemann
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Paul D Boudreau
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | | | | | - Laura A Pace
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Robert A Quinn
- Biology Department, San Diego State University, San Diego, United States
| | - Katherine R Duncan
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Cheng-Chih Hsu
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Dimitrios J Floros
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | - Ronnie G Gavilan
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Karin Kleigrewe
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Trent Northen
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Rachel J Dutton
- FAS Center for Systems Biology, Harvard, Cambridge, United States
| | - Delphine Parrot
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Erin E Carlson
- Chemistry, University of Minnesota, Minneapolis, United States
| | - Bertrand Aigle
- Dynamique des Génomes et Adaptation Microbienne, University of Lorraine, Vandœuvre-lès-Nancy, France
| | | | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico
| | - Pavel Pevzner
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Computer Science and Engineering, UC San Diego, La Jolla, United States
| | - Anna Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jeffrey McLean
- Department of Periodontics, University of Washington, Seattle, United States.,School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Jörn Piel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Brian T Murphy
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Chih-Chuang Liaw
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, University of Münster, Münster, Germany
| | - Maria Maansson
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Robert A Keyzers
- School of Chemical & Physical Sciences, and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Amy C Sims
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Andrew R Johnson
- Department of Chemistry, Indiana University, Bloomington, United States
| | | | - Brian E Sedio
- Smithsonian Tropical Research Institute, Ancón, Panama.,Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Andreas Klitgaard
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Charles B Larson
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Cristopher A Boya P
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | | | - David J Gonzalez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Denise B Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil.,Centro de Ciencias Biologicas e da Saude, Universidade Fderal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Lucas M Marques
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Daniel P Demarque
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Egle Pociute
- Sirenas Marine Discovery, San Diego, United States
| | - Ellis C O'Neill
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Enora Briand
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes Cedex, France
| | | | - Eve A Granatosky
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Florian Ryffel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Hosein Mohimani
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States
| | - Jenan J Kharbush
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Yi Zeng
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, United States
| | | | - Kenji L Kurita
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Pep Charusanti
- Department of Bioengineering, UC San Diego, La Jolla, United States
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | | | - Lisa Vuong
- Sirenas Marine Discovery, San Diego, United States
| | - Maryam Elfeki
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois Chicago, Chicago, United States
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, United States
| | - Niclas Engene
- Department of Biological Sciences, Florida International University, Miami, United States
| | - Nobuhiro Koyama
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Oliver B Vining
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, United States
| | - Ralph Baric
- Gillings School of Global Public Health, Department of Epidemiology, UNC Chapel Hill, Chapel Hill, United States
| | - Ricardo R Silva
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Samantha J Mascuch
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Sophie Tomasi
- Produits naturels - Synthèses - Chimie Médicinale, University of Rennes 1, Rennes Cedex, France
| | - Stefan Jenkins
- Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, United States
| | | | - Thomas Hoffman
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Philip G Williams
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Jingqui Dai
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Ram Neupane
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Joshua Gurr
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, United States
| | - Andrés M C Rodríguez
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - Anne Lamsa
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Chen Zhang
- Department of Nanoengineering, UC San Diego, La Jolla, United States
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Brendan M Duggan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Jehad Almaliti
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Prasad Phapale
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Louis-Felix Nothias
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Theodore Alexandrov
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS-ICSN, UPR 2301, Labex CEBA, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jennifer E Kyle
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Thomas O Metz
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Tyler Peryea
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Danielle VanLeer
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institute of Health, Rockville, United States
| | - Rolf Müller
- Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Katrina M Waters
- Biological Sciences, Pacific Northwest National Laboratory, Richland, United States
| | - Wenyuan Shi
- School of Dentistry, UC Los Angeles, Los Angeles, United States
| | - Xueting Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lixin Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rob Knight
- Department of Pediatrics, UC San Diego, La Jolla, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | | | - Kit Pogliano
- Division of Biological Sciences, UC San Diego, La Jolla, United States
| | - Roger G Linington
- PBSci-Chemistry & Biochemistry Department, UC Santa Cruz, Santa Cruz, United States
| | - Marcelino Gutiérrez
- Center for Drug Discovery and Biodiversity, INDICASAT, City of Knowledge, Panama
| | - Norberto P Lopes
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, São Paulo, Brazil
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Bradley S Moore
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Center for Oceans and Human Health, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institute of Oceanography, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
| | - Nuno Bandeira
- Center for Computational Mass Spectrometry, UC San Diego, La Jolla, United States.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, United States
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Wittwehr C, Aladjov H, Ankley G, Byrne HJ, de Knecht J, Heinzle E, Klambauer G, Landesmann B, Luijten M, MacKay C, Maxwell G, Meek MEB, Paini A, Perkins E, Sobanski T, Villeneuve D, Waters KM, Whelan M. How Adverse Outcome Pathways Can Aid the Development and Use of Computational Prediction Models for Regulatory Toxicology. Toxicol Sci 2017; 155:326-336. [PMID: 27994170 PMCID: PMC5340205 DOI: 10.1093/toxsci/kfw207] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Efforts are underway to transform regulatory toxicology and chemical safety assessment from a largely empirical science based on direct observation of apical toxicity outcomes in whole organism toxicity tests to a predictive one in which outcomes and risk are inferred from accumulated mechanistic understanding. The adverse outcome pathway (AOP) framework provides a systematic approach for organizing knowledge that may support such inference. Likewise, computational models of biological systems at various scales provide another means and platform to integrate current biological understanding to facilitate inference and extrapolation. We argue that the systematic organization of knowledge into AOP frameworks can inform and help direct the design and development of computational prediction models that can further enhance the utility of mechanistic and in silico data for chemical safety assessment. This concept was explored as part of a workshop on AOP-Informed Predictive Modeling Approaches for Regulatory Toxicology held September 24-25, 2015. Examples of AOP-informed model development and its application to the assessment of chemicals for skin sensitization and multiple modes of endocrine disruption are provided. The role of problem formulation, not only as a critical phase of risk assessment, but also as guide for both AOP and complementary model development is described. Finally, a proposal for actively engaging the modeling community in AOP-informed computational model development is made. The contents serve as a vision for how AOPs can be leveraged to facilitate development of computational prediction models needed to support the next generation of chemical safety assessment.
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Affiliation(s)
| | | | - Gerald Ankley
- US Environmental Protection Agency, Duluth, Minnesota 55804
| | | | - Joop de Knecht
- National Institute for Public Health and the Environment (RIVM), Bilthoven, MA 3721, The Netherlands
| | - Elmar Heinzle
- Universität des Saarlandes, 66123 Saarbrücken, Germany
| | | | | | - Mirjam Luijten
- National Institute for Public Health and the Environment (RIVM), Bilthoven, MA 3721, The Netherlands
| | - Cameron MacKay
- Unilever Safety and Environmenta Assurance Centre, Sharnbrook, MK44 1LQ, UK
| | - Gavin Maxwell
- Unilever Safety and Environmenta Assurance Centre, Sharnbrook, MK44 1LQ, UK
| | | | - Alicia Paini
- European Commission, Joint Research Centre, Ispra 21027, Italy
| | - Edward Perkins
- US Army Engineer Research and Development Center, Vicksburg, Mississippi 39180
| | | | - Dan Villeneuve
- US Environmental Protection Agency, Duluth, Minnesota 55804
| | - Katrina M Waters
- Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Maurice Whelan
- European Commission, Joint Research Centre, Ispra 21027, Italy
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47
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Burnum-Johnson KE, Kyle JE, Eisfeld AJ, Casey CP, Stratton KG, Gonzalez JF, Habyarimana F, Negretti NM, Sims AC, Chauhan S, Thackray LB, Halfmann PJ, Walters KB, Kim YM, Zink EM, Nicora CD, Weitz KK, Webb-Robertson BJM, Nakayasu ES, Ahmer B, Konkel ME, Motin V, Baric RS, Diamond MS, Kawaoka Y, Waters KM, Smith RD, Metz TO. MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling. Analyst 2017; 142:442-448. [PMID: 28091625 PMCID: PMC5283721 DOI: 10.1039/c6an02486f] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can take place only subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements. This single-sample metabolite, protein and lipid extraction (MPLEx) method resulted in complete inactivation of clinically important bacterial and viral pathogens with exposed lipid membranes, including Yersinia pestis, Salmonella Typhimurium, and Campylobacter jejuni in pure culture, and Yersinia pestis, Campylobacter jejuni, and West Nile, MERS-CoV, Ebola, and influenza H7N9 viruses in infection studies. In addition, >99% inactivation, which increased with solvent exposure time, was also observed for pathogens without exposed lipid membranes including community-associated methicillin-resistant Staphylococcus aureus, Clostridium difficile spores and vegetative cells, and adenovirus type 5. The overall pipeline of inactivation and subsequent proteomic, metabolomic, and lipidomic analyses was evaluated using a human epithelial lung cell line infected with wild-type and mutant influenza H7N9 viruses, thereby demonstrating that MPLEx yields biomaterial of sufficient quality for subsequent multi-omics analyses. Based on these experimental results, we believe that MPLEx will facilitate systems biology studies of infectious samples by enabling simultaneous pathogen inactivation and multi-omics measurements from a single specimen with high success for pathogens with exposed lipid membranes.
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Affiliation(s)
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Amie J Eisfeld
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Cameron P Casey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Kelly G Stratton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Juan F Gonzalez
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA
| | - Fabien Habyarimana
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA
| | - Nicholas M Negretti
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Amy C Sims
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sadhana Chauhan
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Larissa B Thackray
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Kevin B Walters
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Erika M Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Bobbie-Jo M Webb-Robertson
- Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Brian Ahmer
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA
| | - Michael E Konkel
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Vladimir Motin
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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Chao HT, Davids M, Burke E, Pappas JG, Rosenfeld JA, McCarty AJ, Davis T, Wolfe L, Toro C, Tifft C, Xia F, Stong N, Johnson TK, Warr CG, Yamamoto S, Adams DR, Markello TC, Gahl WA, Bellen HJ, Wangler MF, Malicdan MCV, Adams DR, Adams CJ, Alejandro ME, Allard P, Ashley EA, Bacino CA, Balasubramanyam A, Barseghyan H, Beggs AH, Bellen HJ, Bernstein JA, Bick DP, Birch CL, Boone BE, Briere LC, Brown DM, Brush M, Burrage LC, Chao KR, Clark GD, Cogan JD, Cooper CM, Craigen WJ, Davids M, Dayal JG, Dell'Angelica EC, Dhar SU, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Draper DD, Dries AM, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fisher PG, Frisby TS, Frost K, Gahl WA, Gartner V, Godfrey RA, Goheen M, Golas GA, Goldstein DB, Gordon M“GG, Gould SE, Gourdine JPF, Graham BH, Groden CA, Gropman AL, Hackbarth ME, Haendel M, Hamid R, Hanchard NA, Handley LH, Hardee I, Herzog MR, Holm IA, Howerton EM, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Koehler AE, Koeller DM, Kohane IS, Kohler JN, Krasnewich DM, Krieg EL, Krier JB, Kyle JE, Lalani SR, Latham L, Latour YL, Lau CC, Lazar J, Lee BH, Lee H, Lee PR, Levy SE, Levy DJ, Lewis RA, Liebendorder AP, Lincoln SA, Loomis CR, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Mashid AS, Mazur P, McCarty AJ, McConkie-Rosell A, McCray AT, Metz TO, Might M, Moretti PM, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Ramoni RB, Rodan LH, Sadozai S, Schaffer KE, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Silverman EK, Sinsheimer JS, Soldatos AG, Spillmann RC, Splinter K, Stoler JM, Stong N, Strong KA, Sullivan JA, Sweetser DA, Thomas SP, Tift CJ, Tolman NJ, Toro C, Tran AA, Valivullah ZM, Vilain E, Waggott DM, Wahl CE, Walley NM, Walsh CA, Wangler MF, Warburton M, Ward PA, Waters KM, Webb-Robertson BJM, Weech AA, Westerfield M, Wheeler MT, Wise AL, Worthe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zornio PA. A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3. Am J Hum Genet 2017; 100:128-137. [PMID: 28017372 PMCID: PMC5223093 DOI: 10.1016/j.ajhg.2016.11.018] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
Early B cell factor 3 (EBF3) is a member of the highly evolutionarily conserved Collier/Olf/EBF (COE) family of transcription factors. Prior studies on invertebrate and vertebrate animals have shown that EBF3 homologs are essential for survival and that loss-of-function mutations are associated with a range of nervous system developmental defects, including perturbation of neuronal development and migration. Interestingly, aristaless-related homeobox (ARX), a homeobox-containing transcription factor critical for the regulation of nervous system development, transcriptionally represses EBF3 expression. However, human neurodevelopmental disorders related to EBF3 have not been reported. Here, we describe three individuals who are affected by global developmental delay, intellectual disability, and expressive speech disorder and carry de novo variants in EBF3. Associated features seen in these individuals include congenital hypotonia, structural CNS malformations, ataxia, and genitourinary abnormalities. The de novo variants affect a single conserved residue in a zinc finger motif crucial for DNA binding and are deleterious in a fly model. Our findings indicate that mutations in EBF3 cause a genetic neurodevelopmental syndrome and suggest that loss of EBF3 function might mediate a subset of neurologic phenotypes shared by ARX-related disorders, including intellectual disability, abnormal genitalia, and structural CNS malformations.
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McDermott JE, Mitchell HD, Gralinski LE, Eisfeld AJ, Josset L, Bankhead A, Neumann G, Tilton SC, Schäfer A, Li C, Fan S, McWeeney S, Baric RS, Katze MG, Waters KM. The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus. BMC Syst Biol 2016; 10:93. [PMID: 27663205 PMCID: PMC5035469 DOI: 10.1186/s12918-016-0336-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 09/08/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND The complex interplay between viral replication and host immune response during infection remains poorly understood. While many viruses are known to employ anti-immune strategies to facilitate their replication, highly pathogenic virus infections can also cause an excessive immune response that exacerbates, rather than reduces pathogenicity. To investigate this dichotomy in severe acute respiratory syndrome coronavirus (SARS-CoV), we developed a transcriptional network model of SARS-CoV infection in mice and used the model to prioritize candidate regulatory targets for further investigation. RESULTS We validated our predictions in 18 different knockout (KO) mouse strains, showing that network topology provides significant predictive power to identify genes that are important for viral infection. We identified a novel player in the immune response to virus infection, Kepi, an inhibitory subunit of the protein phosphatase 1 (PP1) complex, which protects against SARS-CoV pathogenesis. We also found that receptors for the proinflammatory cytokine tumor necrosis factor alpha (TNFα) promote pathogenesis, presumably through excessive inflammation. CONCLUSIONS The current study provides validation of network modeling approaches for identifying important players in virus infection pathogenesis, and a step forward in understanding the host response to an important infectious disease. The results presented here suggest the role of Kepi in the host response to SARS-CoV, as well as inflammatory activity driving pathogenesis through TNFα signaling in SARS-CoV infections. Though we have reported the utility of this approach in bacterial and cell culture studies previously, this is the first comprehensive study to confirm that network topology can be used to predict phenotypes in mice with experimental validation.
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Affiliation(s)
- Jason E. McDermott
- Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Hugh D. Mitchell
- Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Lisa E. Gralinski
- Department of Epidemiology, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| | - Amie J. Eisfeld
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI 53715 USA
| | - Laurence Josset
- Department of Microbiology, University of Washington, Seattle, WA 98195 USA
| | - Armand Bankhead
- Division of Biostatistics, Department of Public Health and Preventive Medicine, Oregon Health and Science University, Portland, OR 97239 USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239 USA
| | - Gabriele Neumann
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI 53715 USA
| | - Susan C. Tilton
- Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| | - Chengjun Li
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI 53715 USA
| | - Shufang Fan
- Department of Pathobiological Sciences, School of Veterinary Medicine, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI 53715 USA
| | - Shannon McWeeney
- Division of Biostatistics, Department of Public Health and Preventive Medicine, Oregon Health and Science University, Portland, OR 97239 USA
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Michael G. Katze
- Department of Microbiology, University of Washington, Seattle, WA 98195 USA
| | - Katrina M. Waters
- Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, Richland, WA 99354 USA
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Teeguarden JG, Tan YM, Edwards SW, Leonard JA, Anderson KA, Corley RA, Kile ML, L Massey Simonich S, Stone D, Tanguay RL, Waters KM, Harper SL, Williams DE. Expanding on Successful Concepts, Models, and Organization. Environ Sci Technol 2016; 50:8921-8922. [PMID: 27509267 DOI: 10.1021/acs.est.6b03027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Justin G Teeguarden
- Health Effects and Exposure Science, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
- Department of Environmental and Molecular Toxicology, Oregon State University , Corvallis, Oregon 93771, United States
| | - Yu-Mei Tan
- National Exposure Research Laboratory, U.S. Environmental Protection Agency , Durham, North Carolina 27709, United States
| | - Stephen W Edwards
- National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency , Durham, North Carolina 27709, United States
| | - Jeremy A Leonard
- Oak Ridge Institute for Science and Education , Oak Ridge, Tennessee 37831, United States
| | - Kim A Anderson
- Department of Environmental and Molecular Toxicology, Oregon State University , Corvallis, Oregon 93771, United States
| | - Richard A Corley
- Health Effects and Exposure Science, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
- Department of Environmental and Molecular Toxicology, Oregon State University , Corvallis, Oregon 93771, United States
| | - Molly L Kile
- School of Biological and Population Health Sciences, Oregon State University , Corvallis, Oregon 93771, United States
| | - Staci L Massey Simonich
- Department of Environmental and Molecular Toxicology, Oregon State University , Corvallis, Oregon 93771, United States
| | - David Stone
- Department of Environmental and Molecular Toxicology, Oregon State University , Corvallis, Oregon 93771, United States
| | - Robert L Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University , Corvallis, Oregon 93771, United States
| | - Katrina M Waters
- Health Effects and Exposure Science, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
- Department of Environmental and Molecular Toxicology, Oregon State University , Corvallis, Oregon 93771, United States
| | - Stacey L Harper
- Department of Environmental and Molecular Toxicology, Oregon State University , Corvallis, Oregon 93771, United States
- School of Chemical, Biological and Environmental Engineering, Oregon State University , Corvallis, Oregon 97331, United States
| | - David E Williams
- Department of Environmental and Molecular Toxicology, Oregon State University , Corvallis, Oregon 93771, United States
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