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Sarkar S, Syed F, Webb-Robertson BJ, Melchior JT, Chang G, Gritsenko M, Wang YT, Tsai CF, Liu J, Yi X, Cui Y, Eizirik DL, Metz TO, Rewers M, Evans-Molina C, Mirmira RG, Nakayasu ES. Protection of β cells against pro-inflammatory cytokine stress by the GDF15-ERBB2 signaling. medRxiv 2023:2023.11.27.23298904. [PMID: 38076918 PMCID: PMC10705646 DOI: 10.1101/2023.11.27.23298904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Aim/hypothesis Growth/differentiation factor 15 (GDF15) is a therapeutic target for a variety of metabolic diseases, including type 1 diabetes (T1D). However, the nausea caused by GDF15 is a challenging point for therapeutic development. In addition, it is unknown why the endogenous GDF15 fails to protect from T1D development. Here, we investigate the GDF15 signaling in pancreatic islets towards opening possibilities for therapeutic targeting in β cells and to understand why this protection fails to occur naturally. Methods GDF15 signaling in islets was determined by proximity-ligation assay, untargeted proteomics, pathway analysis, and treatment of cells with specific inhibitors. To determine if GDF15 levels would increase prior to disease onset, plasma levels of GDF15 were measured in a longitudinal prospective study of children during T1D development (n=132 cases vs. n=40 controls) and in children with islet autoimmunity but normoglycemia (n=47 cases vs. n=40 controls) using targeted mass spectrometry. We also investigated the regulation of GDF15 production in islets by fluorescence microscopy and western blot analysis. Results The proximity-ligation assay identified ERBB2 as the GDF15 receptor in islets, which was confirmed using its specific antagonist, tucatinib. The untargeted proteomics analysis and caspase assay showed that ERBB2 activation by GDF15 reduces β cell apoptosis by downregulating caspase 8. In plasma, GDF15 levels were higher (p=0.0024) during T1D development compared to controls, but not in islet autoimmunity with normoglycemia. However, in the pancreatic islets GDF15 was depleted via sequestration of its mRNA into stress granules, resulting in translation halting. Conclusions/interpretation GDF15 protects against T1D via ERBB2-mediated decrease of caspase 8 expression in pancreatic islets. Circulating levels of GDF15 increases pre-T1D onset, which is insufficient to promote protection due to its localized depletion in the islets. These findings open opportunities for targeting GDF15 downstream signaling for pancreatic β cell protection in T1D and help to explain the lack of natural protection by the endogenous protein.
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2
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Sims EK, Kulkarni A, Hull A, Woerner SE, Cabrera S, Mastrandrea LD, Hammoud B, Sarkar S, Nakayasu ES, Mastracci TL, Perkins SM, Ouyang F, Webb-Robertson BJ, Enriquez JR, Tersey SA, Evans-Molina C, Long SA, Blanchfield L, Gerner EW, Mirmira RG, DiMeglio LA. Inhibition of polyamine biosynthesis preserves β cell function in type 1 diabetes. Cell Rep Med 2023; 4:101261. [PMID: 37918404 PMCID: PMC10694631 DOI: 10.1016/j.xcrm.2023.101261] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 03/23/2023] [Revised: 07/18/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023]
Abstract
In preclinical models, α-difluoromethylornithine (DFMO), an ornithine decarboxylase (ODC) inhibitor, delays the onset of type 1 diabetes (T1D) by reducing β cell stress. However, the mechanism of DFMO action and its human tolerability remain unclear. In this study, we show that mice with β cell ODC deletion are protected against toxin-induced diabetes, suggesting a cell-autonomous role of ODC during β cell stress. In a randomized controlled trial (ClinicalTrials.gov: NCT02384889) involving 41 recent-onset T1D subjects (3:1 drug:placebo) over a 3-month treatment period with a 3-month follow-up, DFMO (125-1,000 mg/m2) is shown to meet its primary outcome of safety and tolerability. DFMO dose-dependently reduces urinary putrescine levels and, at higher doses, preserves C-peptide area under the curve without apparent immunomodulation. Transcriptomics and proteomics of DFMO-treated human islets exposed to cytokine stress reveal alterations in mRNA translation, nascent protein transport, and protein secretion. These findings suggest that DFMO may preserve β cell function in T1D through islet cell-autonomous effects.
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Affiliation(s)
- Emily K Sims
- Division of Pediatric Endocrinology and Diabetology, Herman B. Wells Center for Pediatric Research, Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Abhishek Kulkarni
- Kovler Diabetes Center and Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Audrey Hull
- Division of Pediatric Endocrinology and Diabetology, Herman B. Wells Center for Pediatric Research, Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Nationwide Children's Hospital Pediatric Residency Program, Columbus, OH 43205, USA
| | - Stephanie E Woerner
- Division of Pediatric Endocrinology and Diabetology, Herman B. Wells Center for Pediatric Research, Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Susanne Cabrera
- Department of Pediatrics, Section of Endocrinology and Diabetes, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Lucy D Mastrandrea
- Division of Pediatric Endocrinology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Batoul Hammoud
- Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA
| | - Soumyadeep Sarkar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Teresa L Mastracci
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Susan M Perkins
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Fangqian Ouyang
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Jacob R Enriquez
- Kovler Diabetes Center and Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Sarah A Tersey
- Kovler Diabetes Center and Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Carmella Evans-Molina
- Division of Pediatric Endocrinology and Diabetology, Herman B. Wells Center for Pediatric Research, Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Medicine and the Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Roudebush VA Medical Center, Indianapolis, IN 46202, USA
| | - S Alice Long
- Benaroya Research Institute, Center for Translational Immunology, Seattle, WA 98101, USA
| | - Lori Blanchfield
- Benaroya Research Institute, Center for Translational Immunology, Seattle, WA 98101, USA
| | | | - Raghavendra G Mirmira
- Kovler Diabetes Center and Department of Medicine, The University of Chicago, Chicago, IL 60637, USA; Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA.
| | - Linda A DiMeglio
- Division of Pediatric Endocrinology and Diabetology, Herman B. Wells Center for Pediatric Research, Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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3
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Deng S, Kim J, Pomraning KR, Gao Y, Evans JE, Hofstad BA, Dai Z, Webb-Robertson BJ, Powell SM, Novikova IV, Munoz N, Kim YM, Swita M, Robles AL, Lemmon T, Duong RD, Nicora C, Burnum-Johnson KE, Magnuson J. Identification of a specific exporter that enables high production of aconitic acid in Aspergillus pseudoterreus. Metab Eng 2023; 80:163-172. [PMID: 37778408 DOI: 10.1016/j.ymben.2023.09.011] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/25/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023]
Abstract
Aconitic acid is an unsaturated tricarboxylic acid that is attractive for its potential use in manufacturing biodegradable and biocompatible polymers, plasticizers, and surfactants. Previously Aspergillus pseudoterreus was engineered as a platform to produce aconitic acid by deleting the cadA (cis-aconitic acid decarboxylase) gene in the itaconic acid biosynthetic pathway. In this study, the aconitic acid transporter gene (aexA) was identified using comparative global discovery proteomics analysis between the wild-type and cadA deletion strains. The protein AexA belongs to the Major Facilitator Superfamily (MFS). Deletion of aexA almost abolished aconitic acid secretion, while its overexpression led to a significant increase in aconitic acid production. Transportation of aconitic acid across the plasma membrane is a key limiting step in its production. In vitro, proteoliposome transport assay further validated AexA's function and substrate specificity. This research provides new approaches to efficiently pinpoint and characterize exporters of fungal organic acids and accelerate metabolic engineering to improve secretion capability and lower the cost of bioproduction.
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Affiliation(s)
- Shuang Deng
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Joonhoon Kim
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Kyle R Pomraning
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Yuqian Gao
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - James E Evans
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Beth A Hofstad
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Ziyu Dai
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Bobbie-Jo Webb-Robertson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Samantha M Powell
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Irina V Novikova
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Nathalie Munoz
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Young-Mo Kim
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Marie Swita
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Ana L Robles
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Teresa Lemmon
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Rylan D Duong
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Carrie Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Kristin E Burnum-Johnson
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Jon Magnuson
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
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4
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Sarkar S, Elliott EC, Henry HR, Ludovico ID, Melchior JT, Frazer-Abel A, Webb-Robertson BJ, Davidson WS, Holers VM, Rewers MJ, Metz TO, Nakayasu ES. Systematic review of type 1 diabetes biomarkers reveals regulation in circulating proteins related to complement, lipid metabolism, and immune response. Clin Proteomics 2023; 20:38. [PMID: 37735622 PMCID: PMC10512508 DOI: 10.1186/s12014-023-09429-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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] [Received: 03/13/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Type 1 diabetes (T1D) results from an autoimmune attack of the pancreatic β cells that progresses to dysglycemia and symptomatic hyperglycemia. Current biomarkers to track this evolution are limited, with development of islet autoantibodies marking the onset of autoimmunity and metabolic tests used to detect dysglycemia. Therefore, additional biomarkers are needed to better track disease initiation and progression. Multiple clinical studies have used proteomics to identify biomarker candidates. However, most of the studies were limited to the initial candidate identification, which needs to be further validated and have assays developed for clinical use. Here we curate these studies to help prioritize biomarker candidates for validation studies and to obtain a broader view of processes regulated during disease development. METHODS This systematic review was registered with Open Science Framework ( https://doi.org/10.17605/OSF.IO/N8TSA ). Using PRISMA guidelines, we conducted a systematic search of proteomics studies of T1D in the PubMed to identify putative protein biomarkers of the disease. Studies that performed mass spectrometry-based untargeted/targeted proteomic analysis of human serum/plasma of control, pre-seroconversion, post-seroconversion, and/or T1D-diagnosed subjects were included. For unbiased screening, 3 reviewers screened all the articles independently using the pre-determined criteria. RESULTS A total of 13 studies met our inclusion criteria, resulting in the identification of 266 unique proteins, with 31 (11.6%) being identified across 3 or more studies. The circulating protein biomarkers were found to be enriched in complement, lipid metabolism, and immune response pathways, all of which are found to be dysregulated in different phases of T1D development. We found 2 subsets: 17 proteins (C3, C1R, C8G, C4B, IBP2, IBP3, ITIH1, ITIH2, BTD, APOE, TETN, C1S, C6A3, SAA4, ALS, SEPP1 and PI16) and 3 proteins (C3, CLUS and C4A) have consistent regulation in at least 2 independent studies at post-seroconversion and post-diagnosis compared to controls, respectively, making them strong candidates for clinical assay development. CONCLUSIONS Biomarkers analyzed in this systematic review highlight alterations in specific biological processes in T1D, including complement, lipid metabolism, and immune response pathways, and may have potential for further use in the clinic as prognostic or diagnostic assays.
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Affiliation(s)
- Soumyadeep Sarkar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Emily C Elliott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hayden R Henry
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ivo Díaz Ludovico
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - John T Melchior
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ashley Frazer-Abel
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - W Sean Davidson
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - V Michael Holers
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Marian J Rewers
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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5
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Carfagno A, Lin SC, Chafran L, Akhrymuk I, Callahan V, Po M, Zhu Y, Altalhi A, Durkin DP, Russo P, Vliet KA, Webb-Robertson BJ, Kehn-Hall K, Bishop B. Bioprospecting the American Alligator Peptidome for antiviral peptides against Venezuelan equine encephalitis virus. Proteomics 2023; 23:e2200237. [PMID: 36480152 DOI: 10.1002/pmic.202200237] [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: 06/01/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
The innate immune protection provided by cationic antimicrobial peptides (CAMPs) has been shown to extend to antiviral activity, with putative mechanisms of action including direct interaction with host cells or pathogen membranes. The lack of therapeutics available for the treatment of viruses such as Venezuelan equine encephalitis virus (VEEV) underscores the urgency of novel strategies for antiviral discovery. American alligator plasma has been shown to exhibit strong in vitro antibacterial activity, and functionalized hydrogel particles have been successfully employed for the identification of specific CAMPs from alligator plasma. Here, a novel bait strategy in which particles were encapsulated in membranes from either healthy or VEEV-infected cells was implemented to identify peptides preferentially targeting infected cells for subsequent evaluation of antiviral activity. Statistical analysis of peptide identification results was used to select five candidate peptides for testing, of which one exhibited a dose-dependent inhibition of VEEV and also significantly inhibited infectious titers. Results suggest our bioprospecting strategy provides a versatile platform that may be adapted for antiviral peptide identification from complex biological samples.
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Affiliation(s)
- Amy Carfagno
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, USA
| | - Shih-Chao Lin
- School of Systems Biology, George Mason University, Manassas, Virginia, USA.,National Taiwan Ocean University, Keelung City, Taiwan
| | - Liana Chafran
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, USA
| | - Ivan Akhrymuk
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Victoria Callahan
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Marynet Po
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, USA
| | - Yaling Zhu
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, USA
| | - Amaal Altalhi
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, USA
| | - David P Durkin
- Chemistry Department, U.S. Naval Academy, Annapolis, Maryland, USA
| | - Paul Russo
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Kent A Vliet
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | | | - Kylene Kehn-Hall
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA.,Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Barney Bishop
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, USA
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6
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Sarkar S, Elliott EC, Henry HR, Ludovico ID, Melchior JT, Frazer-Abel A, Webb-Robertson BJ, Davidson WS, Holers VM, Rewers MJ, Metz TO, Nakayasu ES. Systematic review of type 1 diabetes biomarkers reveals regulation in circulating proteins related to complement, lipid metabolism, and immune response. medRxiv 2023:2023.02.21.23286132. [PMID: 36865103 PMCID: PMC9980237 DOI: 10.1101/2023.02.21.23286132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Aims Type 1 diabetes (T1D) results from an autoimmune attack of the pancreatic β cells that progresses to dysglycemia and symptomatic hyperglycemia. Current biomarkers to track this evolution are limited, with development of islet autoantibodies marking the onset of autoimmunity and metabolic tests used to detect dysglycemia. Therefore, additional biomarkers are needed to better track disease initiation and progression. Multiple clinical studies have used proteomics to identify biomarker candidates. However, most of the studies were limited to the initial candidate identification, which needs to be further validated and have assays developed for clinical use. Here we curate these studies to help prioritize biomarker candidates for validation studies and to obtain a broader view of processes regulated during disease development. Methods This systematic review was registered with Open Science Framework (DOI 10.17605/OSF.IO/N8TSA). Using PRISMA guidelines, we conducted a systematic search of proteomics studies of T1D in the PubMed to identify putative protein biomarkers of the disease. Studies that performed mass spectrometry-based untargeted/targeted proteomic analysis of human serum/plasma of control, pre-seroconversion, post-seroconversion, and/or T1D-diagnosed subjects were included. For unbiased screening, 3 reviewers screened all the articles independently using the pre-determined criteria. Results A total of 13 studies met our inclusion criteria, resulting in the identification of 251 unique proteins, with 27 (11%) being identified across 3 or more studies. The circulating protein biomarkers were found to be enriched in complement, lipid metabolism, and immune response pathways, all of which are found to be dysregulated in different phases of T1D development. We found a subset of 3 proteins (C3, KNG1 & CFAH), 6 proteins (C3, C4A, APOA4, C4B, A2AP & BTD) and 7 proteins (C3, CLUS, APOA4, C6, A2AP, C1R & CFAI) have consistent regulation between multiple studies in samples from individuals at pre-seroconversion, post-seroconversion and post-diagnosis compared to controls, respectively, making them strong candidates for clinical assay development. Conclusions Biomarkers analyzed in this systematic review highlight alterations in specific biological processes in T1D, including complement, lipid metabolism, and immune response pathways, and may have potential for further use in the clinic as prognostic or diagnostic assays.
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Rodland KD, Webb-Robertson BJ, Srivastava S. Introduction to the special issue on Applications of Artificial Intelligence in Biomarker Research. Cancer Biomark 2022; 33:171-172. [PMID: 35213364 DOI: 10.3233/cbm-229001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.,Cell, Developmental, and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Bobbie-Jo Webb-Robertson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.,Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
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8
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Anderson-Baucum E, Piñeros AR, Kulkarni A, Webb-Robertson BJ, Maier B, Anderson RM, Wu W, Tersey SA, Mastracci TL, Casimiro I, Scheuner D, Metz TO, Nakayasu ES, Evans-Molina C, Mirmira RG. Deoxyhypusine synthase promotes a pro-inflammatory macrophage phenotype. Cell Metab 2021; 33:1883-1893.e7. [PMID: 34496231 PMCID: PMC8432737 DOI: 10.1016/j.cmet.2021.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/01/2021] [Accepted: 08/05/2021] [Indexed: 12/24/2022]
Abstract
The metabolic inflammation (meta-inflammation) of obesity is characterized by proinflammatory macrophage infiltration into adipose tissue. Catalysis by deoxyhypusine synthase (DHPS) modifies the translation factor eIF5A to generate a hypusine (Hyp) residue. Hypusinated eIF5A (eIF5AHyp) controls the translation of mRNAs involved in inflammation, but its role in meta-inflammation has not been elucidated. Levels of eIF5AHyp were found to be increased in adipose tissue macrophages from obese mice and in murine macrophages activated to a proinflammatory M1-like state. Global proteomics and transcriptomics revealed that DHPS deficiency in macrophages altered the abundance of proteins involved in NF-κB signaling, likely through translational control of their respective mRNAs. DHPS deficiency in myeloid cells of obese mice suppressed M1 macrophage accumulation in adipose tissue and improved glucose tolerance. These findings indicate that DHPS promotes the post-transcriptional regulation of a subset of mRNAs governing inflammation and chemotaxis in macrophages and contributes to a proinflammatory M1-like phenotype.
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Affiliation(s)
- Emily Anderson-Baucum
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Annie R Piñeros
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Abhishek Kulkarni
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | | | - Bernhard Maier
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ryan M Anderson
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Wenting Wu
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sarah A Tersey
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Teresa L Mastracci
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - Isabel Casimiro
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Donalyn Scheuner
- Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Carmella Evans-Molina
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Roudebush VA Medical Center, Indianapolis, IN 46202, USA.
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9
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Myatt L, Wang E, Bramer L, Stratton K, Jarman S, Webb-Robertson BJ, Gao Y, Nicora C, Moore R, Kyle J, Burnum-Johnson K. Placental Proteomics Reveals Sexually Dimorphic Adaptive Changes to Maternal Obesity and Gestational Diabetes. Placenta 2021. [DOI: 10.1016/j.placenta.2021.07.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Moran A, Hampton S, Dowson S, Dagdelen J, Trewartha A, Ceder G, Persson K, Saxon E, Barker A, Charles L, Webb-Robertson BJ. Online Interactive Platform for COVID-19 Literature Visual Analytics: Platform Development Study. J Med Internet Res 2021; 23:e26995. [PMID: 34138726 PMCID: PMC8288648 DOI: 10.2196/26995] [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] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/29/2021] [Accepted: 06/12/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Papers on COVID-19 are being published at a high rate and concern many different topics. Innovative tools are needed to aid researchers to find patterns in this vast amount of literature to identify subsets of interest in an automated fashion. OBJECTIVE We present a new online software resource with a friendly user interface that allows users to query and interact with visual representations of relationships between publications. METHODS We publicly released an application called PLATIPUS (Publication Literature Analysis and Text Interaction Platform for User Studies) that allows researchers to interact with literature supplied by COVIDScholar via a visual analytics platform. This tool contains standard filtering capabilities based on authors, journals, high-level categories, and various research-specific details via natural language processing and dozens of customizable visualizations that dynamically update from a researcher's query. RESULTS PLATIPUS is available online and currently links to over 100,000 publications and is still growing. This application has the potential to transform how COVID-19 researchers use public literature to enable their research. CONCLUSIONS The PLATIPUS application provides the end user with a variety of ways to search, filter, and visualize over 100,00 COVID-19 publications.
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Affiliation(s)
- Addy Moran
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Shawn Hampton
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Scott Dowson
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - John Dagdelen
- Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, United States
| | - Amalie Trewartha
- Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Gerbrand Ceder
- Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, United States
| | - Kristin Persson
- Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, United States
| | - Elise Saxon
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Andrew Barker
- Pacific Northwest National Laboratory, Richland, WA, United States
| | - Lauren Charles
- Pacific Northwest National Laboratory, Richland, WA, United States
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11
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Frohnert BI, Webb-Robertson BJ, Bramer LM, Reehl SM, Waugh K, Steck AK, Norris JM, Rewers M. Predictive Modeling of Type 1 Diabetes Stages Using Disparate Data Sources. Diabetes 2020; 69:238-248. [PMID: 31740441 PMCID: PMC6971485 DOI: 10.2337/db18-1263] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 11/11/2019] [Indexed: 12/18/2022]
Abstract
This study aims to model genetic, immunologic, metabolomics, and proteomic biomarkers for development of islet autoimmunity (IA) and progression to type 1 diabetes in a prospective high-risk cohort. We studied 67 children: 42 who developed IA (20 of 42 progressed to diabetes) and 25 control subjects matched for sex and age. Biomarkers were assessed at four time points: earliest available sample, just prior to IA, just after IA, and just prior to diabetes onset. Predictors of IA and progression to diabetes were identified across disparate sources using an integrative machine learning algorithm and optimization-based feature selection. Our integrative approach was predictive of IA (area under the receiver operating characteristic curve [AUC] 0.91) and progression to diabetes (AUC 0.92) based on standard cross-validation (CV). Among the strongest predictors of IA were change in serum ascorbate, 3-methyl-oxobutyrate, and the PTPN22 (rs2476601) polymorphism. Serum glucose, ADP fibrinogen, and mannose were among the strongest predictors of progression to diabetes. This proof-of-principle analysis is the first study to integrate large, diverse biomarker data sets into a limited number of features, highlighting differences in pathways leading to IA from those predicting progression to diabetes. Integrated models, if validated in independent populations, could provide novel clues concerning the pathways leading to IA and type 1 diabetes.
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Affiliation(s)
- Brigitte I Frohnert
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO
| | - Bobbie-Jo Webb-Robertson
- Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, WA
| | - Lisa M Bramer
- Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, WA
| | - Sara M Reehl
- Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, WA
| | - Kathy Waugh
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO
| | - Andrea K Steck
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado, Aurora, CO
| | - Marian Rewers
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO
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12
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Myatt L, Wang E, Stratton K, Bramer L, Webb-Robertson BJ, Kyle J, Burnum-Johnson K. Changes in Placental Lipidomics with Obesity and Gestational Diabetes: Sexual Dimorphism. Placenta 2019. [DOI: 10.1016/j.placenta.2019.06.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Stanfill B, Reehl S, Bramer L, Nakayasu ES, Rich SS, Metz TO, Rewers M, Webb-Robertson BJ. Extending Classification Algorithms to Case-Control Studies. Biomed Eng Comput Biol 2019; 10:1179597219858954. [PMID: 31320812 PMCID: PMC6630079 DOI: 10.1177/1179597219858954] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/26/2019] [Indexed: 12/16/2022] Open
Abstract
Classification is a common technique applied to 'omics data to build predictive models and identify potential markers of biomedical outcomes. Despite the prevalence of case-control studies, the number of classification methods available to analyze data generated by such studies is extremely limited. Conditional logistic regression is the most commonly used technique, but the associated modeling assumptions limit its ability to identify a large class of sufficiently complicated 'omic signatures. We propose a data preprocessing step which generalizes and makes any linear or nonlinear classification algorithm, even those typically not appropriate for matched design data, available to be used to model case-control data and identify relevant biomarkers in these study designs. We demonstrate on simulated case-control data that both the classification and variable selection accuracy of each method is improved after applying this processing step and that the proposed methods are comparable to or outperform existing variable selection methods. Finally, we demonstrate the impact of conditional classification algorithms on a large cohort study of children with islet autoimmunity.
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Affiliation(s)
- Bryan Stanfill
- Computing and Analytics Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarah Reehl
- Computing and Analytics Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lisa Bramer
- Computing and Analytics Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Thomas O Metz
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Bobbie-Jo Webb-Robertson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
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14
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Ortega C, Frando A, Webb-Robertson BJ, Anderson LN, Fleck N, Flannery EL, Fishbaugher M, Murphree TA, Hansen JR, Smith RD, Kappe SHI, Wright AT, Grundner C. A Global Survey of ATPase Activity in Plasmodium falciparum Asexual Blood Stages and Gametocytes. Mol Cell Proteomics 2017; 17:111-120. [PMID: 29079720 DOI: 10.1074/mcp.ra117.000088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/03/2017] [Indexed: 01/12/2023] Open
Abstract
Effective malaria control and elimination in hyperendemic areas of the world will require treatment of the Plasmodium falciparum (Pf) blood stage that causes disease as well as the gametocyte stage that is required for transmission from humans to the mosquito vector. Most currently used therapies do not kill gametocytes, a highly specialized, non-replicating sexual parasite stage. Further confounding next generation drug development against Pf is the unknown metabolic state of the gametocyte and the lack of known biochemical activity for most parasite gene products in general. Here, we take a systematic activity-based proteomics approach to survey the activity of the large and druggable ATPase family in replicating blood stage asexual parasites and transmissible, non-replicating sexual gametocytes. ATPase activity broadly changes during the transition from asexual schizonts to sexual gametocytes, indicating altered metabolism and regulatory roles of ATPases specific for each lifecycle stage. We further experimentally confirm existing annotation and predict ATPase function for 38 uncharacterized proteins. By mapping the activity of ATPases associated with gametocytogenesis, we assign biochemical activity to a large number of uncharacterized proteins and identify new candidate transmission blocking targets.
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Affiliation(s)
- Corrie Ortega
- From the ‡Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109
| | - Andrew Frando
- From the ‡Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109.,§Department of Global Health, University of Washington, Seattle, Washington 98195
| | - Bobbie-Jo Webb-Robertson
- ¶Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Lindsey N Anderson
- ¶Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Neil Fleck
- From the ‡Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109
| | - Erika L Flannery
- From the ‡Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109
| | - Matthew Fishbaugher
- From the ‡Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109
| | - Taylor A Murphree
- ¶Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Joshua R Hansen
- ¶Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Richard D Smith
- ¶Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Stefan H I Kappe
- From the ‡Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109.,§Department of Global Health, University of Washington, Seattle, Washington 98195
| | - Aaron T Wright
- ¶Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Christoph Grundner
- From the ‡Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109; .,§Department of Global Health, University of Washington, Seattle, Washington 98195
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15
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Liu CW, Bramer L, Webb-Robertson BJ, Waugh K, Rewers MJ, Zhang Q. Temporal expression profiling of plasma proteins reveals oxidative stress in early stages of Type 1 Diabetes progression. J Proteomics 2017; 172:100-110. [PMID: 28993202 DOI: 10.1016/j.jprot.2017.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 04/11/2017] [Revised: 10/02/2017] [Accepted: 10/05/2017] [Indexed: 02/07/2023]
Abstract
Blood markers other than islet autoantibodies are greatly needed to indicate the pancreatic beta cell destruction process as early as possible, and more accurately reflect the progression of Type 1 Diabetes Mellitus (T1D). To this end, a longitudinal proteomic profiling of human plasma using TMT-10plex-based LC-MS/MS analysis was performed to track temporal proteomic changes of T1D patients (n=11) across 9 serial time points, spanning the period of T1D natural progression, in comparison with those of the matching healthy controls (n=10). To our knowledge, the current study represents the largest (>2000 proteins measured) longitudinal expression profiles of human plasma proteome in T1D research. By applying statistical trend analysis on the temporal expression patterns between T1D and controls, and Benjamini-Hochberg procedure for multiple-testing correction, 13 protein groups were regarded as having statistically significant differences during the entire follow-up period. Moreover, 16 protein groups, which play pivotal roles in response to oxidative stress, have consistently abnormal expression trend before seroconversion to islet autoimmunity. Importantly, the expression trends of two key reactive oxygen species-decomposing enzymes, Catalase and Superoxide dismutase were verified independently by ELISA. BIOLOGICAL SIGNIFICANCE The temporal changes of >2000 plasma proteins (at least quantified in two subjects), spanning the entire period of T1D natural progression were provided to the research community. Oxidative stress related proteins have consistently different dysregulated patterns in T1D group than in age-sex matched healthy controls, even prior to appearance of islet autoantibodies - the earliest sign of islet autoimmunity and pancreatic beta cell stress.
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Affiliation(s)
- Chih-Wei Liu
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, United States
| | - Lisa Bramer
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Bobbie-Jo Webb-Robertson
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kathleen Waugh
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Marian J Rewers
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Qibin Zhang
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, United States; Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, United States.
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16
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Bryant AE, Aldape MJ, Bayer CR, Katahira EJ, Bond L, Nicora CD, Fillmore TL, Clauss TRW, Metz TO, Webb-Robertson BJ, Stevens DL. Effects of delayed NSAID administration after experimental eccentric contraction injury - A cellular and proteomics study. PLoS One 2017; 12:e0172486. [PMID: 28245256 PMCID: PMC5330483 DOI: 10.1371/journal.pone.0172486] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 07/08/2016] [Accepted: 02/06/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Acute muscle injuries are exceedingly common and non-steroidal anti-inflammatory drugs (NSAIDs) are widely consumed to reduce the associated inflammation, swelling and pain that peak 1-2 days post-injury. While prophylactic use or early administration of NSAIDs has been shown to delay muscle regeneration and contribute to loss of muscle strength after healing, little is known about the effects of delayed NSAID use. Further, NSAID use following non-penetrating injury has been associated with increased risk and severity of infection, including that due to group A streptococcus, though the mechanisms remain to be elucidated. The present study investigated the effects of delayed NSAID administration on muscle repair and sought mechanisms supporting an injury/NSAID/infection axis. METHODS A murine model of eccentric contraction (EC)-induced injury of the tibialis anterior muscle was used to profile the cellular and molecular changes induced by ketorolac tromethamine administered 47 hr post injury. RESULTS NSAID administration inhibited several important muscle regeneration processes and down-regulated multiple cytoprotective proteins known to inhibit the intrinsic pathway of programmed cell death. These activities were associated with increased caspase activity in injured muscles but were independent of any NSAID effect on macrophage influx or phenotype switching. CONCLUSIONS These findings provide new molecular evidence supporting the notion that NSAIDs have a direct negative influence on muscle repair after acute strain injury in mice and thus add to renewed concern about the safety and benefits of NSAIDS in both children and adults, in those with progressive loss of muscle mass such as the elderly or patients with cancer or AIDS, and those at risk of secondary infection after trauma or surgery.
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Affiliation(s)
- Amy E. Bryant
- U.S. Department of Veterans Affairs, Office of Research and Development, Boise, ID, United States of America
- University of Washington School of Medicine, Seattle, WA, United States of America
- * E-mail: ,
| | - Michael J. Aldape
- U.S. Department of Veterans Affairs, Office of Research and Development, Boise, ID, United States of America
- Northwest Nazarene University, Nampa, ID, United States of America
| | - Clifford R. Bayer
- U.S. Department of Veterans Affairs, Office of Research and Development, Boise, ID, United States of America
| | - Eva J. Katahira
- U.S. Department of Veterans Affairs, Office of Research and Development, Boise, ID, United States of America
| | - Laura Bond
- Boise State University, Boise, ID, United States of America
| | - Carrie D. Nicora
- Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Thomas L. Fillmore
- Pacific Northwest National Laboratory, Richland, WA, United States of America
| | | | - Thomas O. Metz
- Pacific Northwest National Laboratory, Richland, WA, United States of America
| | | | - Dennis L. Stevens
- U.S. Department of Veterans Affairs, Office of Research and Development, Boise, ID, United States of America
- University of Washington School of Medicine, Seattle, WA, United States of America
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17
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Liu CW, Bramer L, Webb-Robertson BJ, Waugh K, Rewers MJ, Zhang Q. Temporal profiles of plasma proteome during childhood development. J Proteomics 2016; 152:321-328. [PMID: 27890796 DOI: 10.1016/j.jprot.2016.11.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 02/07/2023]
Abstract
Human blood plasma proteome reflects physiological changes associated with a child's development as well as development of disease states. While age-specific normative values are available for proteins routinely measured in clinical practice, there is paucity of comprehensive longitudinal data regarding changes in human plasma proteome during childhood. We applied TMT-10plex isobaric labeling-based quantitative proteomics to longitudinally profile the plasma proteome in 10 healthy children during their development, each with 9 serial time points from 9months to 15years of age. In total, 1828 protein groups were identified at peptide and protein level false discovery rate of 1% and with at least two razor and unique peptides. The longitudinal expression profiles of 1747 protein groups were statistically modeled and their temporal changes were categorized into 7 different patterns. The patterns and relative abundance of proteins obtained by LC-MS were also verified with ELISA. To our knowledge, this study represents the most comprehensive longitudinal profiling of human plasma proteome to date. The temporal profiles of plasma proteome obtained in this study provide a comprehensive resource and reference for biomarker studies in childhood diseases. Biological significance: A pediatric plasma proteome database with longitudinal expression patterns of 1747 proteins from neonate to adolescence was provided to the research community. 970 plasma proteins had age-dependent expression trends, which demonstrated the importance of longitudinal profiling study to identify the potential biomarkers specific to childhood diseases, and the requirement of strictly age-matched clinical samples in a cross-sectional study in pediatric population.
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Affiliation(s)
- Chih-Wei Liu
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, United States
| | - Lisa Bramer
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Bobbie-Jo Webb-Robertson
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kathleen Waugh
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Marian J Rewers
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, United States.
| | - Qibin Zhang
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, United States; Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, United States.
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18
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Nakayasu ES, Nicora CD, Sims AC, Burnum-Johnson KE, Kim YM, Kyle JE, Matzke MM, Shukla AK, Chu RK, Schepmoes AA, Jacobs JM, Baric RS, Webb-Robertson BJ, Smith RD, Metz TO. MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses. mSystems 2016. [PMID: 27822525 DOI: 10.1128/msystems.00043-16.editor] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. The metabolite, protein, and lipid extraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of this protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental, in vitro, and clinical). IMPORTANCE In systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample. Author Video: An author video summary of this article is available.
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Affiliation(s)
- Ernesto S Nakayasu
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie D Nicora
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Amy C Sims
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kristin E Burnum-Johnson
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Young-Mo Kim
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jennifer E Kyle
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Melissa M Matzke
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Anil K Shukla
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Rosalie K Chu
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Athena A Schepmoes
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jon M Jacobs
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Richard D Smith
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Thomas O Metz
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
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Sadler NC, Nandhikonda P, Webb-Robertson BJ, Ansong C, Anderson LN, Smith JN, Corley RA, Wright AT. Hepatic Cytochrome P450 Activity, Abundance, and Expression Throughout Human Development. ACTA ACUST UNITED AC 2016; 44:984-91. [PMID: 27084891 DOI: 10.1124/dmd.115.068593] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/13/2016] [Indexed: 01/20/2023]
Abstract
Cytochrome P450s are oxidative metabolic enzymes that play critical roles in the biotransformation of endogenous compounds and xenobiotics. The expression and activity of P450 enzymes varies considerably throughout human development; the deficit in our understanding of these dynamics limits our ability to predict environmental and pharmaceutical exposure effects. In an effort to develop a more comprehensive understanding of the ontogeny of P450 enzymes, we employed a multi-omic characterization of P450 transcript expression, protein abundance, and functional activity. Modified mechanism-based inhibitors of P450s were used as chemical probes for isolating active P450 proteoforms in human hepatic microsomes with developmental stages ranging from early gestation to late adult. High-resolution liquid chromatography-mass spectrometry was used to identify and quantify probe-labeled P450s, allowing for a functional profile of P450 ontogeny. Total protein abundance profiles and P450 rRNA was also measured, and our results reveal life-stage-dependent variability in P450 expression, abundance, and activity throughout human development and frequent discordant relationships between expression and activity. We have significantly expanded the knowledge of P450 ontogeny, particularly at the level of individual P450 activity. We anticipate that these results will be useful for enabling predictive therapeutic dosing, and for avoiding potentially adverse and harmful reactions during maturation from both therapeutic drugs and environmental xenobiotics.
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Affiliation(s)
- Natalie C Sadler
- Biological Sciences Division (N.C.S., P.N., C.A., L.N.A., J.N.S., R.A.C., A.T.W.) and Computational and Statistical Analytics Division (B.J.W.R.), Pacific Northwest National Laboratory, Richland, Washington
| | - Premchendar Nandhikonda
- Biological Sciences Division (N.C.S., P.N., C.A., L.N.A., J.N.S., R.A.C., A.T.W.) and Computational and Statistical Analytics Division (B.J.W.R.), Pacific Northwest National Laboratory, Richland, Washington
| | - Bobbie-Jo Webb-Robertson
- Biological Sciences Division (N.C.S., P.N., C.A., L.N.A., J.N.S., R.A.C., A.T.W.) and Computational and Statistical Analytics Division (B.J.W.R.), Pacific Northwest National Laboratory, Richland, Washington
| | - Charles Ansong
- Biological Sciences Division (N.C.S., P.N., C.A., L.N.A., J.N.S., R.A.C., A.T.W.) and Computational and Statistical Analytics Division (B.J.W.R.), Pacific Northwest National Laboratory, Richland, Washington
| | - Lindsey N Anderson
- Biological Sciences Division (N.C.S., P.N., C.A., L.N.A., J.N.S., R.A.C., A.T.W.) and Computational and Statistical Analytics Division (B.J.W.R.), Pacific Northwest National Laboratory, Richland, Washington
| | - Jordan N Smith
- Biological Sciences Division (N.C.S., P.N., C.A., L.N.A., J.N.S., R.A.C., A.T.W.) and Computational and Statistical Analytics Division (B.J.W.R.), Pacific Northwest National Laboratory, Richland, Washington
| | - Richard A Corley
- Biological Sciences Division (N.C.S., P.N., C.A., L.N.A., J.N.S., R.A.C., A.T.W.) and Computational and Statistical Analytics Division (B.J.W.R.), Pacific Northwest National Laboratory, Richland, Washington
| | - Aaron T Wright
- Biological Sciences Division (N.C.S., P.N., C.A., L.N.A., J.N.S., R.A.C., A.T.W.) and Computational and Statistical Analytics Division (B.J.W.R.), Pacific Northwest National Laboratory, Richland, Washington
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20
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Lovelace ES, Wagoner J, MacDonald J, Bammler T, Bruckner J, Brownell J, Beyer R, Zink EM, Kim YM, Kyle JE, Webb-Robertson BJ, Waters KM, Metz TO, Farin F, Oberlies NH, Polyak SJ. Silymarin Suppresses Cellular Inflammation By Inducing Reparative Stress Signaling. J Nat Prod 2015; 78:1990-2000. [PMID: 26186142 PMCID: PMC4703094 DOI: 10.1021/acs.jnatprod.5b00288] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Silymarin, a characterized extract of the seeds of milk thistle (Silybum marianum), suppresses cellular inflammation. To define how this occurs, transcriptional profiling, metabolomics, and signaling studies were performed in human liver and T cell lines. Cellular stress and metabolic pathways were modulated within 4 h of silymarin treatment: activation of Activating Transcription Factor 4 (ATF-4) and adenosine monophosphate protein kinase (AMPK) and inhibition of mammalian target of rapamycin (mTOR) signaling, the latter being associated with induction of DNA-damage-inducible transcript 4 (DDIT4). Metabolomics analyses revealed silymarin suppression of glycolytic, tricarboxylic acid (TCA) cycle, and amino acid metabolism. Anti-inflammatory effects arose with prolonged (i.e., 24 h) silymarin exposure, with suppression of multiple pro-inflammatory mRNAs and signaling pathways including nuclear factor kappa B (NF-κB) and forkhead box O (FOXO). Studies with murine knock out cells revealed that silymarin inhibition of both mTOR and NF-κB was partially AMPK dependent, whereas silymarin inhibition of mTOR required DDIT4. Other natural products induced similar stress responses, which correlated with their ability to suppress inflammation. Thus, natural products activate stress and repair responses that culminate in an anti-inflammatory cellular phenotype. Natural products like silymarin may be useful as tools to define how metabolic, stress, and repair pathways regulate cellular inflammation.
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Affiliation(s)
- Erica S. Lovelace
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States, 98104
| | - Jessica Wagoner
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States, 98104
| | - James MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, United States, 98105
| | - Theo Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, United States, 98105
| | - Jacob Bruckner
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States, 98104
| | | | - Richard Beyer
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, United States, 98105
| | - Erika M. Zink
- Biological Sciences Division Pacific Northwest National Laboratory, Richland, WA, United States
| | - Young-Mo Kim
- Biological Sciences Division Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jennifer E. Kyle
- Biological Sciences Division Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Katrina M. Waters
- Biological Sciences Division Pacific Northwest National Laboratory, Richland, WA, United States
| | - Thomas O. Metz
- Biological Sciences Division Pacific Northwest National Laboratory, Richland, WA, United States
| | - Federico Farin
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, United States, 98105
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, NC, United States
| | - Stephen J. Polyak
- Department of Laboratory Medicine, University of Washington, Seattle, WA, United States, 98104
- Department of Global Health, University of Washington, Seattle, WA, United States, 98104
- Department of Microbiology, University of Washington, Seattle, WA, United States, 98104Center for Ecogenetics and Environmental Health, University of Washington, Seattle, United States, 98105
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21
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Kebaabetswe LP, Haick AK, Gritsenko MA, Fillmore TL, Chu RK, Purvine SO, Webb-Robertson BJ, Matzke MM, Smith RD, Waters KM, Metz TO, Miura TA. Proteomic analysis reveals down-regulation of surfactant protein B in murine type II pneumocytes infected with influenza A virus. Virology 2015; 483:96-107. [PMID: 25965799 DOI: 10.1016/j.virol.2015.03.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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: 12/12/2014] [Revised: 01/13/2015] [Accepted: 03/18/2015] [Indexed: 11/29/2022]
Abstract
Infection of type II alveolar epithelial (ATII) cells by influenza A viruses (IAV) correlates with severe respiratory disease in humans and mice. To understand pathogenic mechanisms during IAV infection of ATII cells, murine ATII cells were cultured to maintain a differentiated phenotype, infected with IAV-PR8, which causes severe lung pathology in mice, and proteomics analyses were performed using liquid chromatography-mass spectrometry. PR8 infection increased levels of proteins involved in interferon signaling, antigen presentation, and cytoskeleton regulation. Proteins involved in mitochondrial membrane permeability, energy metabolism, and chromatin formation had reduced levels in PR8-infected cells. Phenotypic markers of ATII cells in vivo were identified, confirming the differentiation status of the cultures. Surfactant protein B had decreased levels in PR8-infected cells, which was confirmed by immunoblotting and immunofluorescence assays. Analysis of ATII cell protein profiles will elucidate cellular processes in IAV pathogenesis, which may provide insight into potential therapies to modulate disease severity.
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Affiliation(s)
- Lemme P Kebaabetswe
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Anoria K Haick
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Thomas L Fillmore
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Bobbie-Jo Webb-Robertson
- Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Melissa M Matzke
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Tanya A Miura
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
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22
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Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A, Bolles M, Carter V, Chang J, Clauss TRW, Dash P, Diercks AH, Eisfeld AJ, Ellis A, Fan S, Ferris MT, Gralinski LE, Green RR, Gritsenko MA, Hatta M, Heegel RA, Jacobs JM, Jeng S, Josset L, Kaiser SM, Kelly S, Law GL, Li C, Li J, Long C, Luna ML, Matzke M, McDermott J, Menachery V, Metz TO, Mitchell H, Monroe ME, Navarro G, Neumann G, Podyminogin RL, Purvine SO, Rosenberger CM, Sanders CJ, Schepmoes AA, Shukla AK, Sims A, Sova P, Tam VC, Tchitchek N, Thomas PG, Tilton SC, Totura A, Wang J, Webb-Robertson BJ, Wen J, Weiss JM, Yang F, Yount B, Zhang Q, McWeeney S, Smith RD, Waters KM, Kawaoka Y, Baric R, Aderem A, Katze MG, Scheuermann RH. A comprehensive collection of systems biology data characterizing the host response to viral infection. Sci Data 2014; 1:140033. [PMID: 25977790 PMCID: PMC4410982 DOI: 10.1038/sdata.2014.33] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 08/15/2014] [Indexed: 12/13/2022] Open
Abstract
The Systems Biology for Infectious Diseases Research program was established by
the U.S. National Institute of Allergy and Infectious Diseases to investigate
host-pathogen interactions at a systems level. This program generated 47
transcriptomic and proteomic datasets from 30 studies that investigate
in vivo and in vitro host responses to
viral infections. Human pathogens in the Orthomyxoviridae and
Coronaviridae families, especially pandemic H1N1 and avian
H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus
(SARS-CoV), were investigated. Study validation was demonstrated via
experimental quality control measures and meta-analysis of independent
experiments performed under similar conditions. Primary assay results are
archived at the GEO and PeptideAtlas public repositories, while processed
statistical results together with standardized metadata are publically available
at the Influenza Research Database (www.fludb.org) and the Virus Pathogen
Resource (www.viprbrc.org). By comparing data from mutant versus wild-type
virus and host strains, RNA versus protein differential expression, and
infection with genetically similar strains, these data can be used to further
investigate genetic and physiological determinants of host responses to viral
infection.
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Affiliation(s)
| | | | - Sanjeev Kumar
- Northrop Grumman Information Systems, Health IT , Rockville, MD 20850, USA
| | - Edward B Klem
- Northrop Grumman Information Systems, Health IT , Rockville, MD 20850, USA
| | - Sudhakar Agnihothram
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | | | - Armand Bankhead
- Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA ; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health Sciences University , Portland, Oregon 97239-3098, USA
| | - Meagen Bolles
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Victoria Carter
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Jean Chang
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Therese R W Clauss
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Pradyot Dash
- Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA
| | - Alan H Diercks
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Amie J Eisfeld
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Amy Ellis
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Shufang Fan
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7264, USA
| | - Lisa E Gralinski
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Richard R Green
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Masato Hatta
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Robert A Heegel
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Jon M Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Sophia Jeng
- Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA
| | - Laurence Josset
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Shari M Kaiser
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Sara Kelly
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - G Lynn Law
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Chengjun Li
- Division of Animal influenza, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Harbin, Heilongjiang Province 150001, China
| | - Jiangning Li
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Casey Long
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Maria L Luna
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Melissa Matzke
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Jason McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Vineet Menachery
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Hugh Mitchell
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Garnet Navarro
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Gabriele Neumann
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | | | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, WA 99354, USA
| | | | - Catherine J Sanders
- Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Anil K Shukla
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Amy Sims
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Pavel Sova
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Vincent C Tam
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Nicolas Tchitchek
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA
| | - Susan C Tilton
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Allison Totura
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Jing Wang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | | | - Ji Wen
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Jeffrey M Weiss
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Feng Yang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Qibin Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Shannon McWeeney
- Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA ; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health Sciences University , Portland, Oregon 97239-3098, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Yoshihiro Kawaoka
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA ; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Alan Aderem
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Michael G Katze
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA ; Washington National Primate Research Center, University of Washington , Seattle, WA 98195, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute , La Jolla, CA 92037, USA ; Department of Pathology, University of California , San Diego, CA 92093, USA
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23
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Webb-Robertson BJ, Kim YM, Zink EM, Hallaian KA, Zhang Q, Madupu R, Waters KM, Metz TO. A Statistical Analysis of the Effects of Urease Pre-treatment on the Measurement of the Urinary Metabolome by Gas Chromatography-Mass Spectrometry. Metabolomics 2014; 10:897-908. [PMID: 25254001 PMCID: PMC4169993 DOI: 10.1007/s11306-014-0642-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Urease pre-treatment of urine has been utilized since the early 1960s to remove high levels of urea from samples prior to further processing and analysis by gas chromatography-mass spectrometry (GC-MS). Aside from the obvious depletion or elimination of urea, the effect, if any, of urease pre-treatment on the urinary metabolome has not been studied in detail. Here, we report the results of three separate but related experiments that were designed to assess possible indirect effects of urease pre-treatment on the urinary metabolome as measured by GC-MS. In total, 235 GC-MS analyses were performed and over 106 identified and 200 unidentified metabolites were quantified across the three experiments. The results showed that data from urease pre-treated samples 1) had the same or lower coefficients of variance among reproducibly detected metabolites, 2) more accurately reflected quantitative differences and the expected ratios among different urine volumes, and 3) increased the number of metabolite identifications. Overall, we observed no negative consequences of urease pre-treatment. In contrast, urease pretreatment enhanced the ability to distinguish between volume-based and biological sample types compared to no treatment. Taken together, these results show that urease pretreatment of urine offers multiple beneficial effects that outweigh any artifacts that may be introduced to the data in urinary metabolomics analyses.
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Affiliation(s)
- Bobbie-Jo Webb-Robertson
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Young-Mo Kim
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Erika M. Zink
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Katherine A. Hallaian
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Qibin Zhang
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | | | - Katrina M. Waters
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Thomas O. Metz
- Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
- To whom correspondence should be addressed: Pacific Northwest National Laboratory, P.O. Box 999, MSIN K8-98, Richland, WA, USA, Tel.: (509) 371-6581, Fax: (509) 371-6555,
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24
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Zhang Q, Matzke M, Schepmoes AA, Moore RJ, Webb-Robertson BJ, Hu Z, Monroe ME, Qian WJ, Smith RD, Morgan WF. High and low doses of ionizing radiation induce different secretome profiles in a human skin model. PLoS One 2014; 9:e92332. [PMID: 24642900 PMCID: PMC3958549 DOI: 10.1371/journal.pone.0092332] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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: 12/05/2013] [Accepted: 02/21/2014] [Indexed: 12/28/2022] Open
Abstract
It is postulated that secreted soluble factors are important contributors of bystander effect and adaptive responses observed in low dose ionizing radiation. Using multidimensional liquid chromatography-mass spectrometry based proteomics, we quantified the changes of skin tissue secretome – the proteins secreted from a full thickness, reconstituted 3-dimensional skin tissue model 48 hr after exposure to 3, 10 and 200 cGy of X-rays. Overall, 135 proteins showed statistical significant difference between the sham (0 cGy) and any of the irradiated groups (3, 10 or 200 cGy) on the basis of Dunnett adjusted t-test; among these, 97 proteins showed a trend of downregulation and 9 proteins showed a trend of upregulation with increasing radiation dose. In addition, there were 21 and 8 proteins observed to have irregular trends with the 10 cGy irradiated group either having the highest or the lowest level among all three radiated doses. Moreover, two proteins, carboxypeptidase E and ubiquitin carboxyl-terminal hydrolase isozyme L1 were sensitive to ionizing radiation, but relatively independent of radiation dose. Conversely, proteasome activator complex subunit 2 protein appeared to be sensitive to the dose of radiation, as rapid upregulation of this protein was observed when radiation doses were increased from 3, to 10 or 200 cGy. These results suggest that different mechanisms of action exist at the secretome level for low and high doses of ionizing radiation.
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Affiliation(s)
- Qibin Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail:
| | - Melissa Matzke
- Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Athena A. Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Ronald J. Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Bobbie-Jo Webb-Robertson
- Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Zeping Hu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Matthew E. Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - William F. Morgan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
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25
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Tchitchek N, Eisfeld AJ, Tisoncik-Go J, Josset L, Gralinski LE, Bécavin C, Tilton SC, Webb-Robertson BJ, Ferris MT, Totura AL, Li C, Neumann G, Metz TO, Smith RD, Waters KM, Baric R, Kawaoka Y, Katze MG. Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice. BMC Syst Biol 2013; 7:69. [PMID: 23895213 PMCID: PMC3750405 DOI: 10.1186/1752-0509-7-69] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [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] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 06/27/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Influenza infection causes respiratory disease that can lead to death. The complex interplay between virus-encoded and host-specific pathogenicity regulators - and the relative contributions of each toward viral pathogenicity - is not well-understood. RESULTS By analyzing a collection of lung samples from mice infected by A/Vietnam/1203/2004 (H5N1; VN1203), we characterized a signature of transcripts and proteins associated with the kinetics of the host response. Using a new geometrical representation method and two criteria, we show that inoculation concentrations and four specific mutations in VN1203 mainly impact the magnitude and velocity of the host response kinetics, rather than specific sets of up- and down- regulated genes. We observed analogous kinetic effects using lung samples from mice infected with A/California/04/2009 (H1N1), and we show that these effects correlate with morbidity and viral titer. CONCLUSIONS We have demonstrated the importance of the kinetics of the host response to H5N1 pathogenesis and its relationship with clinical disease severity and virus replication. These kinetic properties imply that time-matched comparisons of 'omics profiles to viral infections give limited views to differentiate host-responses. Moreover, these results demonstrate that a fast activation of the host-response at the earliest time points post-infection is critical for protective mechanisms against fast replicating viruses.
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Affiliation(s)
- Nicolas Tchitchek
- Department of Microbiology, University of Washington, Seattle, WA 98195 USA
| | - Amie J Eisfeld
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Laurence Josset
- Department of Microbiology, University of Washington, Seattle, WA 98195 USA
| | - Lisa E Gralinski
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christophe Bécavin
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, 75015 Paris, France
| | - Susan C Tilton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Martin T Ferris
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Allison L Totura
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chengjun Li
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Gabriele Neumann
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ralph Baric
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yoshihiro Kawaoka
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael G Katze
- Department of Microbiology, University of Washington, Seattle, WA 98195 USA
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
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26
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Wiedner SD, Ansong C, Webb-Robertson BJ, Pederson LM, Fortuin S, Hofstad BA, Shukla AK, Panisko EA, Smith RD, Wright AT. Disparate proteome responses of pathogenic and nonpathogenic aspergilli to human serum measured by activity-based protein profiling (ABPP). Mol Cell Proteomics 2013; 12:1791-805. [PMID: 23599423 DOI: 10.1074/mcp.m112.026534] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aspergillus fumigatus is the primary pathogen causing the devastating pulmonary disease Invasive Aspergillosis in immunocompromised individuals. There is high genomic synteny between A. fumigatus and closely related rarely pathogenic Neosartorya fischeri and Aspergillus clavatus genomes. We applied activity-based protein profiling to compare unique or overexpressed activity-based probe-reactive proteins of all three fungi over time in minimal media growth and in response to human serum. We found 360 probe-reactive proteins exclusive to A. fumigatus, including known virulence associated proteins, and 13 proteins associated with stress response exclusive to A. fumigatus culture in serum. Though the fungi are highly orthologous, A. fumigatus has a significantly greater number of ABP-reactive proteins across varied biological process. Only 50% of expected orthologs of measured A. fumigatus reactive proteins were observed in N. fischeri and A. clavatus. Activity-based protein profiling identified a number of processes that were induced by human serum in A. fumigatus relative to N. fischeri and A. clavatus. These included actin organization and assembly, transport, and fatty acid, cell membrane, and cell wall synthesis. Additionally, signaling proteins regulating vegetative growth, conidiation, and cell wall integrity, required for appropriate cellular response to external stimuli, had higher activity-based probe-protein reaction over time in A. fumigatus and N. fisheri, but not in A. clavatus. Together, we show that measured proteins and physiological processes identified solely or significantly over-represented in A. fumigatus reveal a unique adaptive response to human protein not found in closely related, but rarely pathogenic aspergilli. These unique activity-based probe-protein responses to culture condition may reveal how A. fumigatus initiates pulmonary invasion leading to Invasive Aspergillosis.
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Affiliation(s)
- Susan D Wiedner
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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Webb-Robertson BJ, Corley C, McCue LA, Wahl K, Kreuzer H. Fusion of laboratory and textual data for investigative bioforensics. Forensic Sci Int 2013; 226:118-24. [PMID: 23313599 DOI: 10.1016/j.forsciint.2012.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 12/04/2012] [Accepted: 12/16/2012] [Indexed: 10/27/2022]
Abstract
Chemical and biological forensic programs focus on the identification of a threat and acquisition of laboratory measurements to determine how a threat agent may have been produced. However, to generate investigative leads, it might also be useful to identify institutions where the same agent has been produced by the same or a very similar process, since the producer of the agent may have learned methods at a university or similar institution. We have developed a Bayesian network framework that fuses hard and soft data sources to assign probability to production practices. It combines the results of laboratory measurements with an automatic text reader to scan scientific literature and rank institutions that had published papers on the agent of interest in order of the probability that the institution has the capability to generate the sample of interest based on laboratory data. We demonstrate the Bayesian network on an example case from microbial forensics, predicting the methods used to produce Bacillus anthracis spores based on mass spectrometric measurements and identifying institutions that have a history of growing Bacillus spores using the same or highly similar methods. We illustrate that the network model can assign a higher posterior probability than expected by random chance to appropriate institutions when trained using only a small set of manually analyzed documents. This is the first example of an automated methodology to integrate experimental and textual data for the purpose of investigative forensics.
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Affiliation(s)
- Bobbie-Jo Webb-Robertson
- Computational Biology & Bioinformatics, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352, USA.
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Matzke MM, Brown JN, Gritsenko MA, Metz TO, Pounds JG, Rodland KD, Shukla AK, Smith RD, Waters KM, McDermott JE, Webb-Robertson BJ. A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments. Proteomics 2012; 13:493-503. [PMID: 23019139 DOI: 10.1002/pmic.201200269] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 08/14/2012] [Accepted: 08/22/2012] [Indexed: 12/24/2022]
Abstract
Liquid chromatography coupled with mass spectrometry (LC-MS) is widely used to identify and quantify peptides in complex biological samples. In particular, label-free shotgun proteomics is highly effective for the identification of peptides and subsequently obtaining a global protein profile of a sample. As a result, this approach is widely used for discovery studies. Typically, the objective of these discovery studies is to identify proteins that are affected by some condition of interest (e.g. disease, exposure). However, for complex biological samples, label-free LC-MS proteomics experiments measure peptides and do not directly yield protein quantities. Thus, protein quantification must be inferred from one or more measured peptides. In recent years, many computational approaches to relative protein quantification of label-free LC-MS data have been published. In this review, we examine the most commonly employed quantification approaches to relative protein abundance from peak intensity values, evaluate their individual merits, and discuss challenges in the use of the various computational approaches.
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Yang F, Waters KM, Webb-Robertson BJ, Sowa MB, von Neubeck C, Aldrich JT, Markillie LM, Wirgau RM, Gritsenko MA, Zhao R, Camp DG, Smith RD, Stenoien DL. Quantitative phosphoproteomics identifies filaggrin and other targets of ionizing radiation in a human skin model. Exp Dermatol 2012; 21:352-7. [PMID: 22509832 DOI: 10.1111/j.1600-0625.2012.01470.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Our objective here was to perform a quantitative phosphoproteomic study on a reconstituted human skin tissue to identify low- and high-dose ionizing radiation-dependent signalling in a complex three-dimensional setting. Application of an isobaric labelling strategy using sham and three radiation doses (3, 10, 200 cGy) resulted in the identification of 1052 unique phosphopeptides. Statistical analyses identified 176 phosphopeptides showing significant changes in response to radiation and radiation dose. Proteins responsible for maintaining skin structural integrity including keratins and desmosomal proteins (desmoglein, desmoplakin, plakophilin 1, 2 and 3) had altered phosphorylation levels following exposure to both low and high doses of radiation. Altered phosphorylation of multiple sites in profilaggrin linker domains coincided with altered profilaggrin processing suggesting a role for linker phosphorylation in human profilaggrin regulation. These studies demonstrate that the reconstituted human skin system undergoes a coordinated response to both low and high doses of ionizing radiation involving multiple layers of the stratified epithelium that serve to maintain tissue integrity and mitigate effects of radiation exposure.
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Affiliation(s)
- Feng Yang
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
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McDermott JE, Wang J, Mitchell H, Webb-Robertson BJ, Hafen R, Ramey J, Rodland KD. Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data. ACTA ACUST UNITED AC 2012; 7:37-51. [PMID: 23335946 DOI: 10.1517/17530059.2012.718329] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION: The advent of high throughput technologies capable of comprehensive analysis of genes, transcripts, proteins and other significant biological molecules has provided an unprecedented opportunity for the identification of molecular markers of disease processes. However, it has simultaneously complicated the problem of extracting meaningful molecular signatures of biological processes from these complex datasets. The process of biomarker discovery and characterization provides opportunities for more sophisticated approaches to integrating purely statistical and expert knowledge-based approaches. AREAS COVERED: In this review we will present examples of current practices for biomarker discovery from complex omic datasets and the challenges that have been encountered in deriving valid and useful signatures of disease. We will then present a high-level review of data-driven (statistical) and knowledge-based methods applied to biomarker discovery, highlighting some current efforts to combine the two distinct approaches. EXPERT OPINION: Effective, reproducible and objective tools for combining data-driven and knowledge-based approaches to identify predictive signatures of disease are key to future success in the biomarker field. We will describe our recommendations for possible approaches to this problem including metrics for the evaluation of biomarkers.
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Webb-Robertson BJ, Kreuzer H, Hart G, Ehleringer J, West J, Gill G, Duckworth D. Bayesian integration of isotope ratio for geographic sourcing of castor beans. J Biomed Biotechnol 2012; 2012:450967. [PMID: 22919270 PMCID: PMC3418698 DOI: 10.1155/2012/450967] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 05/13/2012] [Indexed: 12/03/2022] Open
Abstract
Recent years have seen an increase in the forensic interest associated with the poison ricin, which is extracted from the seeds of the Ricinus communis plant. Both light element (C, N, O, and H) and strontium (Sr) isotope ratios have previously been used to associate organic material with geographic regions of origin. We present a Bayesian integration methodology that can more accurately predict the region of origin for a castor bean than individual models developed independently for light element stable isotopes or Sr isotope ratios. Our results demonstrate a clear improvement in the ability to correctly classify regions based on the integrated model with a class accuracy of 60.9 ± 2.1% versus 55.9 ± 2.1% and 40.2 ± 1.8% for the light element and strontium (Sr) isotope ratios, respectively. In addition, we show graphically the strengths and weaknesses of each dataset in respect to class prediction and how the integration of these datasets strengthens the overall model.
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Affiliation(s)
- Bobbie-Jo Webb-Robertson
- Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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32
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Diamond DL, Krasnoselsky AL, Burnum KE, Monroe ME, Webb-Robertson BJ, McDermott JE, Yeh MM, Dzib JFG, Susnow N, Strom S, Proll SC, Belisle SE, Purdy DE, Rasmussen AL, Walters KA, Jacobs JM, Gritsenko MA, Camp DG, Bhattacharya R, Perkins JD, Carithers RL, Liou IW, Larson AM, Benecke A, Waters KM, Smith RD, Katze MG. Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation. Hepatology 2012; 56:28-38. [PMID: 22331615 PMCID: PMC3387320 DOI: 10.1002/hep.25649] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 01/25/2012] [Indexed: 12/23/2022]
Abstract
UNLABELLED Liver transplant tissues offer the unique opportunity to model the longitudinal protein abundance changes occurring during hepatitis C virus (HCV)-associated liver disease progression in vivo. In this study, our goal was to identify molecular signatures, and potential key regulatory proteins, representative of the processes influencing early progression to fibrosis. We performed global protein profiling analyses on 24 liver biopsy specimens obtained from 15 HCV(+) liver transplant recipients at 6 and/or 12 months posttransplantation. Differentially regulated proteins associated with early progression to fibrosis were identified by analysis of the area under the receiver operating characteristic curve. Analysis of serum metabolites was performed on samples obtained from an independent cohort of 60 HCV(+) liver transplant patients. Computational modeling approaches were applied to identify potential key regulatory proteins of liver fibrogenesis. Among 4,324 proteins identified, 250 exhibited significant differential regulation in patients with rapidly progressive fibrosis. Patients with rapid fibrosis progression exhibited enrichment in differentially regulated proteins associated with various immune, hepatoprotective, and fibrogenic processes. The observed increase in proinflammatory activity and impairment in antioxidant defenses suggests that patients who develop significant liver injury experience elevated oxidative stresses. This was supported by an independent study demonstrating the altered abundance of oxidative stress-associated serum metabolites in patients who develop severe liver injury. Computational modeling approaches further highlight a potentially important link between HCV-associated oxidative stress and epigenetic regulatory mechanisms impacting on liver fibrogenesis. CONCLUSION Our proteome and metabolome analyses provide new insights into the role for increased oxidative stress in the rapid fibrosis progression observed in HCV(+) liver transplant recipients. These findings may prove useful in prognostic applications for predicting early progression to fibrosis.
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Affiliation(s)
- Deborah L. Diamond
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | | | - Kristin E. Burnum
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Matthew E. Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | | | - Jason E. McDermott
- Computational Biology & Bioinformatics, Pacific Northwest National Laboratory, Richland, WA
| | - Matthew M. Yeh
- Dept. of Pathology, University of Washington School of Medicine, Seattle, WA
| | | | - Nathan Susnow
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Susan Strom
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Sean C. Proll
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Sarah E. Belisle
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - David E. Purdy
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Angela L. Rasmussen
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Kathie-Anne Walters
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Jon M. Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Marina A. Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - David G. Camp
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Renuka Bhattacharya
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - James D. Perkins
- Dept. of Surgery, University of Washington School of Medicine, Seattle, WA
| | - Robert L. Carithers
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Iris W. Liou
- Institut des Hautes Etudes Scientifiques, CNRS, Bures-sur-Yvette, France
| | - Anne M. Larson
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Arndt Benecke
- Institut des Hautes Etudes Scientifiques, CNRS, Bures-sur-Yvette, France
| | - Katrina M. Waters
- Computational Biology & Bioinformatics, Pacific Northwest National Laboratory, Richland, WA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Michael G. Katze
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA,Washington National Primate Research Center, University of Washington, Seattle, WA
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Jin H, Webb-Robertson BJ, Peterson ES, Tan R, Bigelow DJ, Scholand MB, Hoidal JR, Pounds JG, Zangar RC. Smoking, COPD, and 3-nitrotyrosine levels of plasma proteins. Environ Health Perspect 2011; 119:1314-1320. [PMID: 21652289 PMCID: PMC3230408 DOI: 10.1289/ehp.1103745] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [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: 03/28/2011] [Accepted: 06/06/2011] [Indexed: 05/30/2023]
Abstract
BACKGROUND Nitric oxide is a physiological regulator of endothelial function and hemodynamics. Oxidized products of nitric oxide can form nitrotyrosine, which is a marker of nitrative stress. Cigarette smoking decreases exhaled nitric oxide, and the underlying mechanism may be important in the cardiovascular toxicity of smoking. Even so, it is unclear if this effect results from decreased nitric oxide production or increased oxidative degradation of nitric oxide to reactive nitrating species. These two processes would be expected to have opposite effects on nitrotyrosine levels, a marker of nitrative stress. OBJECTIVE In this study, we evaluated associations of cigarette smoking and chronic obstructive pulmonary disease (COPD) with nitrotyrosine modifications of specific plasma proteins to gain insight into the processes regulating nitrotyrosine formation. METHODS A custom antibody microarray platform was developed to analyze the levels of 3-nitrotyrosine modifications on 24 proteins in plasma. In a cross-sectional study, plasma samples from 458 individuals were analyzed. RESULTS Average nitrotyrosine levels in plasma proteins were consistently lower in smokers and former smokers than in never smokers but increased in smokers with COPD compared with smokers who had normal lung-function tests. CONCLUSIONS Smoking is associated with a broad decrease in 3-nitrotyrosine levels of plasma proteins, consistent with an inhibitory effect of cigarette smoke on endothelial nitric oxide production. In contrast, we observed higher nitrotyrosine levels in smokers with COPD than in smokers without COPD. This finding is consistent with increased nitration associated with inflammatory processes. This study provides insight into a mechanism through which smoking could induce endothelial dysfunction and increase the risk of cardiovascular disease.
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Affiliation(s)
- Hongjun Jin
- Cell Biology and Biochemistry, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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Webb-Robertson BJ, Bunn AL, Bailey VL. Phospholipid fatty acid biomarkers in a freshwater periphyton community exposed to uranium: discovery by non-linear statistical learning. J Environ Radioact 2011; 102:64-71. [PMID: 20952106 DOI: 10.1016/j.jenvrad.2010.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 09/15/2010] [Accepted: 09/16/2010] [Indexed: 05/30/2023]
Abstract
Phospholipid fatty acids (PLFA) have been widely used to characterize environmental microbial communities, generating community profiles that can distinguish phylogenetic or functional groups within the community. The poor specificity of organism groups with fatty acid biomarkers in the classic PLFA-microorganism associations is a confounding factor in many of the statistical classification/clustering approaches traditionally used to interpret PLFA profiles. In this paper we demonstrate that non-linear statistical learning methods, such as a support vector machine (SVM), can more accurately find patterns related to uranyl nitrate exposure in a freshwater periphyton community than linear methods, such as partial least squares discriminant analysis. In addition, probabilistic models of exposure can be derived from the identified lipid biomarkers to demonstrate the potential model-based approach that could be used in remediation. The SVM probability model separates dose groups at accuracies of ∼87.0%, ∼71.4%, ∼87.5%, and 100% for the four groups; Control (non-amended system), low dose (amended at 10 μg UL⁻¹), medium dose (amended at 100 μg UL⁻¹), and high dose (500 μg UL⁻¹). The SVM model achieved an overall cross-validated classification accuracy of ∼87% in contrast to ∼59% for the best linear classifier.
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Affiliation(s)
- Bobbie-Jo Webb-Robertson
- Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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Teeguarden JG, Webb-Robertson BJ, Waters KM, Murray AR, Kisin ER, Varnum SM, Jacobs JM, Pounds JG, Zanger RC, Shvedova AA. Comparative proteomics and pulmonary toxicity of instilled single-walled carbon nanotubes, crocidolite asbestos, and ultrafine carbon black in mice. Toxicol Sci 2010; 120:123-35. [PMID: 21135415 DOI: 10.1093/toxsci/kfq363] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [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: 01/30/2023] Open
Abstract
Reflecting their exceptional potential to advance a range of biomedical, aeronautic, and other industrial products, carbon nanotube (CNT) production and the potential for human exposure to aerosolized CNTs are increasing. CNTs have toxicologically significant structural and chemical similarities to asbestos (AB) and have repeatedly been shown to cause pulmonary inflammation, granuloma formation, and fibrosis after inhalation/instillation/aspiration exposure in rodents, a pattern of effects similar to those observed following exposure to AB. To determine the degree to which responses to single-walled CNTs (SWCNT) and AB are similar or different, the pulmonary response of C57BL/6 mice to repeated exposures to SWCNTs, crocidolite AB, and ultrafine carbon black (UFCB) were compared using high-throughput global high performance liquid chromatography fourier transform ion cyclotron resonance mass spectrometry (HPLC-FTICR-MS) proteomics, histopathology, and bronchoalveolar lavage cytokine analyses. Mice were exposed to material suspensions (40 micrograms per mouse) twice a week for 3 weeks by pharyngeal aspiration. Histologically, the incidence and severity of inflammatory and fibrotic responses were greatest in mice treated with SWCNTs. SWCNT treatment affected the greatest changes in abundance of identified lung tissue proteins. The trend in number of proteins affected (SWCNT [376] > AB [231] > UFCB [184]) followed the potency of these materials in three biochemical assays of inflammation (cytokines). SWCNT treatment uniquely affected the abundance of 109 proteins, but these proteins largely represent cellular processes affected by AB treatment as well, further evidence of broad similarity in the tissue-level response to AB and SWCNTs. Two high-sensitivity markers of inflammation, one (S100a9) observed in humans exposed to AB, were found and may be promising biomarkers of human response to SWCNT exposure.
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McClay JL, Adkins DE, Isern NG, O’Connell TM, Wooten JB, Zedler BK, Dasika MS, Webb BT, Webb-Robertson BJ, Pounds JG, Murrelle EL, Leppert MF, van den Oord EJCG. 1H Nuclear Magnetic Resonance Metabolomics Analysis Identifies Novel Urinary Biomarkers for Lung Function. J Proteome Res 2010; 9:3083-90. [DOI: 10.1021/pr1000048] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joseph L. McClay
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, Pacific Northwest National Laboratory, Richland, Washington 99352, Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27709, Venebio Group, Virginia Biotechnology Research Park, Richmond, Virginia 23219, ClearPoint Resources, Virginia Biotech Research Park, Richmond, Virginia 23219,
| | - Daniel E. Adkins
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, Pacific Northwest National Laboratory, Richland, Washington 99352, Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27709, Venebio Group, Virginia Biotechnology Research Park, Richmond, Virginia 23219, ClearPoint Resources, Virginia Biotech Research Park, Richmond, Virginia 23219,
| | - Nancy G. Isern
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, Pacific Northwest National Laboratory, Richland, Washington 99352, Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27709, Venebio Group, Virginia Biotechnology Research Park, Richmond, Virginia 23219, ClearPoint Resources, Virginia Biotech Research Park, Richmond, Virginia 23219,
| | - Thomas M. O’Connell
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, Pacific Northwest National Laboratory, Richland, Washington 99352, Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27709, Venebio Group, Virginia Biotechnology Research Park, Richmond, Virginia 23219, ClearPoint Resources, Virginia Biotech Research Park, Richmond, Virginia 23219,
| | - Jan B. Wooten
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, Pacific Northwest National Laboratory, Richland, Washington 99352, Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27709, Venebio Group, Virginia Biotechnology Research Park, Richmond, Virginia 23219, ClearPoint Resources, Virginia Biotech Research Park, Richmond, Virginia 23219,
| | - Barbara K. Zedler
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, Pacific Northwest National Laboratory, Richland, Washington 99352, Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27709, Venebio Group, Virginia Biotechnology Research Park, Richmond, Virginia 23219, ClearPoint Resources, Virginia Biotech Research Park, Richmond, Virginia 23219,
| | - Madhukar S. Dasika
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, Pacific Northwest National Laboratory, Richland, Washington 99352, Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27709, Venebio Group, Virginia Biotechnology Research Park, Richmond, Virginia 23219, ClearPoint Resources, Virginia Biotech Research Park, Richmond, Virginia 23219,
| | - Bradley Todd Webb
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, Pacific Northwest National Laboratory, Richland, Washington 99352, Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27709, Venebio Group, Virginia Biotechnology Research Park, Richmond, Virginia 23219, ClearPoint Resources, Virginia Biotech Research Park, Richmond, Virginia 23219,
| | - Bobbie-Jo Webb-Robertson
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, Pacific Northwest National Laboratory, Richland, Washington 99352, Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27709, Venebio Group, Virginia Biotechnology Research Park, Richmond, Virginia 23219, ClearPoint Resources, Virginia Biotech Research Park, Richmond, Virginia 23219,
| | - Joel G. Pounds
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, Pacific Northwest National Laboratory, Richland, Washington 99352, Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27709, Venebio Group, Virginia Biotechnology Research Park, Richmond, Virginia 23219, ClearPoint Resources, Virginia Biotech Research Park, Richmond, Virginia 23219,
| | - Edward L. Murrelle
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, Pacific Northwest National Laboratory, Richland, Washington 99352, Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27709, Venebio Group, Virginia Biotechnology Research Park, Richmond, Virginia 23219, ClearPoint Resources, Virginia Biotech Research Park, Richmond, Virginia 23219,
| | - Mark F. Leppert
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, Pacific Northwest National Laboratory, Richland, Washington 99352, Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27709, Venebio Group, Virginia Biotechnology Research Park, Richmond, Virginia 23219, ClearPoint Resources, Virginia Biotech Research Park, Richmond, Virginia 23219,
| | - Edwin J. C. G. van den Oord
- Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, Pacific Northwest National Laboratory, Richland, Washington 99352, Division of Pharmacotherapy and Experimental Therapeutics, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27709, Venebio Group, Virginia Biotechnology Research Park, Richmond, Virginia 23219, ClearPoint Resources, Virginia Biotech Research Park, Richmond, Virginia 23219,
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Wunschel D, Webb-Robertson BJ, Frevert CW, Skerrett S, Beagley N, Willse A, Colburn H, Antolick K. Differentiation of gram-negative bacterial aerosol exposure using detected markers in bronchial-alveolar lavage fluid. PLoS One 2009; 4:e7047. [PMID: 19756149 PMCID: PMC2737641 DOI: 10.1371/journal.pone.0007047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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: 02/18/2009] [Accepted: 08/11/2009] [Indexed: 12/28/2022] Open
Abstract
The identification of biosignatures of aerosol exposure to pathogens has the potential to provide useful diagnostic information. In particular, markers of exposure to different types of respiratory pathogens may yield diverse sets of markers that can be used to differentiate exposure. We examine a mouse model of aerosol exposure to known Gram negative bacterial pathogens, Francisella tularensis novicida and Pseudomonas aeruginosa. Mice were subjected to either a pathogen or control exposure and bronchial alveolar lavage fluid (BALF) was collected at four and twenty four hours post exposure. Small protein and peptide markers within the BALF were detected by matrix assisted laser desorption/ionization (MALDI) mass spectrometry (MS) and analyzed using both exploratory and predictive data analysis methods; principle component analysis and degree of association. The markers detected were successfully used to accurately identify the four hour exposed samples from the control samples. This report demonstrates the potential for small protein and peptide marker profiles to identify aerosol exposure in a short post-exposure time frame.
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Affiliation(s)
- David Wunschel
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, Washington, United States of America.
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Bystroff C, Webb-Robertson BJ. Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure. BMC Bioinformatics 2008; 9:429. [PMID: 18847485 PMCID: PMC2579440 DOI: 10.1186/1471-2105-9-429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Accepted: 10/10/2008] [Indexed: 11/25/2022] Open
Abstract
Background Amino acid sequence probability distributions, or profiles, have been used successfully to predict secondary structure and local structure in proteins. Profile models assume the statistical independence of each position in the sequence, but the energetics of protein folding is better captured in a scoring function that is based on pairwise interactions, like a force field. Results I-sites motifs are short sequence/structure motifs that populate the protein structure database due to energy-driven convergent evolution. Here we show that a pairwise covariant sequence model does not predict alpha helix or beta strand significantly better overall than a profile-based model, but it does improve the prediction of certain loop motifs. The finding is best explained by considering secondary structure profiles as multivariant, all-or-none models, which subsume covariant models. Pairwise covariance is nonetheless present and energetically rational. Examples of negative design are present, where the covariances disfavor non-native structures. Conclusion Measured pairwise covariances are shown to be statistically robust in cross-validation tests, as long as the amino acid alphabet is reduced to nine classes. An updated I-sites local structure motif library that provides sequence covariance information for all types of local structure in globular proteins and a web server for local structure prediction are available at .
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Affiliation(s)
- Christopher Bystroff
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy NY, USA.
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Havre SL, Webb-Robertson BJ, Shah A, Posse C, Gopalan B, Brockman FJ. Bioinformatic insights from metagenomics through visualization. Proc IEEE Comput Syst Bioinform Conf 2007:341-50. [PMID: 16447991 DOI: 10.1109/csb.2005.19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cutting-edge biological and bioinformatics research seeks a systems perspective through the analysis of multiple types of high-throughput and other experimental data for the same sample. Systems-level analysis requires the integration and fusion of such data, typically through advanced statistics and mathematics. Visualization is a complementary computational approach that supports integration and analysis of complex data or its derivatives. We present a bioinformatics visualization prototype, Juxter, which depicts categorical information derived from or assigned to these diverse data for the purpose of comparing patterns across categorizations. The visualization allows users to easily discern correlated and anomalous patterns in the data. These patterns, which might not be detected automatically by algorithms, may reveal valuable information leading to insight and discovery. We describe the visualization and interaction capabilities and demonstrate its utility in a new field, metagenomics, which combines molecular biology and genetics to identify and characterize genetic material from multi-species microbial samples.
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Webb-Robertson BJ, Oehmen C, Matzke M. SVM-BALSA: remote homology detection based on Bayesian sequence alignment. Comput Biol Chem 2005; 29:440-3. [PMID: 16290168 DOI: 10.1016/j.compbiolchem.2005.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Revised: 07/07/2005] [Accepted: 09/27/2005] [Indexed: 10/25/2022]
Abstract
Biopolymer sequence comparison to identify evolutionarily related proteins, or homologs, is one of the most common tasks in bioinformatics. Support vector machines (SVMs) represent a new approach to the problem in which statistical learning theory is employed to classify proteins into families, thus identifying homologous relationships. Current SVM approaches have been shown to outperform iterative profile methods, such as PSI-BLAST, for protein homology classification. In this study, we demonstrate that the utilization of a Bayesian alignment score, which accounts for the uncertainty of all possible alignments, in the SVM construction improves sensitivity compared to the traditional dynamic programming implementation over a benchmark dataset consisting of 54 unique protein families. The SVM-BALSA algorithms returns a higher area under the receiver operating characteristic (ROC) curves for 37 of the 54 families and achieves an improved overall performance curve at a significance level of 0.07.
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Affiliation(s)
- Bobbie-Jo Webb-Robertson
- Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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