1
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Cala SE, Carruthers NJ, Stemmer PM, Chen Z, Chen X. Activation of Ca 2+ transport in cardiac microsomes enriches functional sets of ER and SR proteins. Mol Cell Biochem 2024; 479:85-98. [PMID: 37036634 PMCID: PMC10786961 DOI: 10.1007/s11010-023-04708-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/12/2023] [Indexed: 04/11/2023]
Abstract
The importance of sarcoplasmic reticulum (SR) Ca2+-handling in heart has led to detailed understanding of Ca2+-release and re-uptake protein complexes, while less is known about other endoplasmic reticulum (ER) functions in the heart. To more fully understand cardiac SR and ER functions, we analyzed cardiac microsomes based on their increased density through the actions of the SR Ca2+-ATPase (SERCA) and the ryanodine receptor that are highly active in cardiomyocytes. Crude cardiac microsomal vesicles loaded with Ca oxalate produced two higher density subfractions, MedSR and HighSR. Proteins from 20.0 μg of MV, MedSR, and HighSR protein were fractionated using SDS-PAGE, then trypsinized from 20 separate gel pieces, and analyzed by LC-MS/MS to determine protein content. From 62,000 individual peptide spectra obtained, we identified 1105 different proteins, of which 354 were enriched ≥ 2.0-fold in SR fractions compared to the crude membrane preparation. Previously studied SR proteins were all enriched, as were proteins associated with canonical ER functions. Contractile, mitochondrial, and sarcolemmal proteins were not enriched. Comparing the levels of SERCA-positive SR proteins in MedSR versus HighSR vesicles produced a range of SR subfraction enrichments signifying differing levels of Ca2+ leak co-localized in the same membrane patch. All known junctional SR proteins were more enriched in MedSR, while canonical ER proteins were more enriched in HighSR membrane. Proteins constituting other putative ER/SR subdomains also exhibited average Esub enrichment values (mean ± S.D.) that spanned the range of possible Esub values, suggesting that functional sets of proteins are localized to the same areas of the ER/SR membrane. We conclude that active Ca2+ loading of cardiac microsomes, reflecting the combined activities of Ca2+ uptake by SERCA, and Ca2+ leak by RyR, permits evaluation of multiple functional ER/SR subdomains. Sets of proteins from these subdomains exhibited similar enrichment patterns across membrane subfractions, reflecting the relative levels of SERCA and RyR present within individual patches of cardiac ER and SR.
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Affiliation(s)
- Steven E Cala
- Department of Physiology, Wayne State University, Detroit, MI, 48201, USA.
| | | | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, USA
| | - Zhenhui Chen
- Krannert Institute of Cardiology, Indiana University, Indianapolis, IN, USA
| | - Xuequn Chen
- Department of Physiology, Wayne State University, Detroit, MI, 48201, USA
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2
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Searle BC, Chien A, Koller A, Hawke D, Herren AW, Kim Kim J, Lee KA, Leib RD, Nelson AJ, Patel P, Ren JM, Stemmer PM, Zhu Y, Neely BA, Patel B. A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development. Mol Cell Proteomics 2023; 22:100639. [PMID: 37657519 PMCID: PMC10561125 DOI: 10.1016/j.mcpro.2023.100639] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
Recent advances in methodology have made phosphopeptide analysis a tractable problem for many proteomics researchers. There are now a wide variety of robust and accessible enrichment strategies to generate phosphoproteomes while free or inexpensive software tools for quantitation and site localization have simplified phosphoproteome analysis workflow tremendously. As a research group under the Association for Biomolecular Resource Facilities umbrella, the Proteomics Standards Research Group has worked to develop a multipathway phosphopeptide standard based on a mixture of heavy-labeled phosphopeptides designed to enable researchers to rapidly develop assays. This mixture contains 131 mass spectrometry vetted phosphopeptides specifically chosen to cover as many known biologically interesting phosphosites as possible from seven different signaling networks: AMPK signaling, death and apoptosis signaling, ErbB signaling, insulin/insulin-like growth factor-1 signaling, mTOR signaling, PI3K/AKT signaling, and stress (p38/SAPK/JNK) signaling. Here, we describe a characterization of this mixture spiked into a HeLa tryptic digest stimulated with both epidermal growth factor and insulin-like growth factor-1 to activate the MAPK and PI3K/AKT/mTOR pathways. We further demonstrate a comparison of phosphoproteomic profiling of HeLa performed independently in five labs using this phosphopeptide mixture with data-independent acquisition. Despite different experimental and instrumentation processes, we found that labs could produce reproducible, harmonized datasets by reporting measurements as ratios to the standard, while intensity measurements showed lower consistency between labs even after normalization. Our results suggest that widely available, biologically relevant phosphopeptide standards can act as a quantitative "yardstick" across laboratories and sample preparations enabling experimental designs larger than a single laboratory can perform. Raw data files are publicly available in the MassIVE dataset MSV000090564.
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Affiliation(s)
- Brian C Searle
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA.
| | - Allis Chien
- Mass Spectrometry Center, Stanford University, Stanford, California, USA
| | | | | | - Anthony W Herren
- UC Davis Genome Center, Proteomics Core, University of California Davis, Davis California, USA
| | - Jenny Kim Kim
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Kimberly A Lee
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Ryan D Leib
- Mass Spectrometry Center, Stanford University, Stanford, California, USA
| | | | - Purvi Patel
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Jian Min Ren
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Paul M Stemmer
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Yiying Zhu
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Benjamin A Neely
- National Institute of Standards and Technology, Charleston, South Carolina, USA
| | - Bhavin Patel
- Thermo Fisher Scientific, Rockford, Illinois, USA
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3
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Carruthers NJ, Guo C, Gill R, Stemmer PM, Rosenspire AJ. Mercury intoxication disrupts tonic signaling in B cells, and may promote autoimmunity due to abnormal phosphorylation of STIM-1 and other autoimmunity risk associated phosphoproteins involved in BCR signaling. Toxicol Appl Pharmacol 2023; 474:116607. [PMID: 37348680 PMCID: PMC10534200 DOI: 10.1016/j.taap.2023.116607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/09/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
Epidemiological studies link exposure to mercury with autoimmune disease. Unfortunately, in spite of considerable effort, no generally accepted mechanistic understanding of how mercury functions with respect to the etiology of autoimmune disease is currently available. Nevertheless, autoimmune disease often arises because of defective B cell signaling. Because B cell signaling is dependent on phosphorylation cascades, in this report, we have focused on how mercury intoxication alters phosphorylation of B cell proteins in antigen-non stimulated (tonic) mouse (BALB/c) splenic B cells. Specifically, we utilized mass spectrometric techniques to conduct a comprehensive unbiased global analysis of the effect of inorganic mercury (Hg2+) on the entire B cell phosphoproteome. We found that the effects were pleotropic in the sense that large numbers of pathways were impacted. However, confirming our earlier work, we found that the B cell signaling pathway stood out from the rest, in that phosphoproteins which had sites which were affected by Hg2+, exhibited a much higher degree of connectivity, than components of other pathways. Further analysis showed that many of these BCR pathway proteins had been previously linked to autoimmune disease. Finally, dose response analysis of these BCR pathway proteins showed STIM1_S575, and NFAT2_S259 are the two most Hg2+ sensitive of these sites. Because STIM1_S575 controls the ability of STIM1 to regulate internal Ca2+, we speculate that STIM1 may be the initial point of disruption, where Hg2+ interferes with B cell signaling leading to systemic autoimmunity, with the molecular effects pleiotropically propagated throughout the cell by virtue of Ca2+ dysregulation.
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Affiliation(s)
- N J Carruthers
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, United States of America
| | - C Guo
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, United States of America
| | - R Gill
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, United States of America
| | - P M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, United States of America
| | - A J Rosenspire
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, United States of America.
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4
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Kirkpatrick J, Stemmer PM, Searle BC, Herring LE, Martin L, Midha MK, Phinney BS, Shan B, Palmblad M, Wang Y, Jagtap PD, Neely BA. 2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Proteomics Study. J Biomol Tech 2023; 34:3fc1f5fe.9b78d780. [PMID: 37435391 PMCID: PMC10332336 DOI: 10.7171/3fc1f5fe.9b78d780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Despite the advantages of fewer missing values by collecting fragment ion data on all analytes in the sample as well as the potential for deeper coverage, the adoption of data-independent acquisition (DIA) in proteomics core facility settings has been slow. The Association of Biomolecular Resource Facilities conducted a large interlaboratory study to evaluate DIA performance in proteomics laboratories with various instrumentation. Participants were supplied with generic methods and a uniform set of test samples. The resulting 49 DIA datasets act as benchmarks and have utility in education and tool development. The sample set consisted of a tryptic HeLa digest spiked with high or low levels of 4 exogenous proteins. Data are available in MassIVE MSV000086479. Additionally, we demonstrate how the data can be analyzed by focusing on 2 datasets using different library approaches and show the utility of select summary statistics. These data can be used by DIA newcomers, software developers, or DIA experts evaluating performance with different platforms, acquisition settings, and skill levels.
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Affiliation(s)
- Joanna Kirkpatrick
- Leibniz Institute on AgingFritz Lipmann Institute07745JenaGermany
- The Francis Crick InstituteLondonNW1 1ATUnited Kingdom
| | | | - Brian C. Searle
- Department of Biomedical InformaticsThe Ohio State UniversityColumbusOhio43210USA
- Pelotonia Institute for Immuno-OncologyThe Ohio State University Comprehensive Cancer CenterColumbusOhio43210USA
| | - Laura E. Herring
- UNC Proteomics Core FacilityDepartment of PharmacologyUniversity of North Carolina at Chapel HillChapel HillNorth Carolina27514USA
| | | | | | | | - Baozhen Shan
- Bioinformatics Solutions Inc.WaterlooON N2L 3K8Canada
| | - Magnus Palmblad
- Center for Proteomics and MetabolomicsLeiden University Medical Center2333 ZC LeidenThe Netherlands
| | - Yan Wang
- National Institute of Dental and Craniofacial ResearchNational Institutes of HealthBethesdaMaryland20892USA
| | - Pratik D. Jagtap
- Department of BiochemistryMolecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMinnesota55455USA
| | - Benjamin A. Neely
- National Institute of Standards and TechnologyCharlestonSouth Carolina29412USA
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5
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Maxwell A, Adzibolosu N, Hu A, You Y, Stemmer PM, Ruden DM, Petriello MC, Sadagurski M, Debarba LK, Koshko L, Ramadoss J, Nguyen AT, Richards D, Liao A, Mor G, Ding J. Intrinsic sexual dimorphism in the placenta determines the differential response to benzene exposure. iScience 2023; 26:106287. [PMID: 37153445 PMCID: PMC10156617 DOI: 10.1016/j.isci.2023.106287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/09/2022] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Maternal immune activation (MIA) by environmental challenges is linked to severe developmental complications, such as neurocognitive disorders, autism, and even fetal/maternal death. Benzene is a major toxic compound in air pollution that affects the mother as well as the fetus and has been associated with reproductive complications. Our objective was to elucidate whether benzene exposure during gestation triggers MIA and its impact on fetal development. We report that benzene exposure during pregnancy leads MIA associated with increased fetal resorptions, fetal growth, and abnormal placenta development. Furthermore, we demonstrate the existence of a sexual dimorphic response to benzene exposure in male and female placentas. The sexual dimorphic response is a consequence of inherent differences between male and female placenta. These data provide crucial information on the origins or sexual dimorphism and how exposure to environmental factors can have a differential impact on the development of male and female offspring.
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Affiliation(s)
- Anthony Maxwell
- C.S Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Nicholas Adzibolosu
- C.S Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Anna Hu
- C.S Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Yuan You
- C.S Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - Douglas M. Ruden
- C.S Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Michael C. Petriello
- Institute of Environmental Health Sciences and Department of Pharmacology, Wayne State University, Detroit, MI, USA
| | - Marianna Sadagurski
- Department of Biological Sciences, Integrative Biosciences Center, Wayne State University, Detroit, MI, USA
| | - Lucas K. Debarba
- Department of Biological Sciences, Integrative Biosciences Center, Wayne State University, Detroit, MI, USA
| | - Lisa Koshko
- Department of Biological Sciences, Integrative Biosciences Center, Wayne State University, Detroit, MI, USA
| | - Jayanth Ramadoss
- C.S Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | | | - Darby Richards
- School of Medicine, Wayne State University, Detroit, MI, USA
| | - Aihua Liao
- Institute of Reproductive Health, Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China
| | - Gil Mor
- C.S Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Jiahui Ding
- C.S Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
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6
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Baek J, Sas K, He C, Nair V, Giblin W, Inoki A, Zhang H, Yingbao Y, Hodgin J, Nelson RG, Brosius FC, Kretzler M, Stemmer PM, Lombard DB, Pennathur S. The deacylase sirtuin 5 reduces malonylation in nonmitochondrial metabolic pathways in diabetic kidney disease. J Biol Chem 2023; 299:102960. [PMID: 36736426 PMCID: PMC9996370 DOI: 10.1016/j.jbc.2023.102960] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 01/14/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 02/05/2023] Open
Abstract
Early diabetic kidney disease (DKD) is marked by dramatic metabolic reprogramming due to nutrient excess, mitochondrial dysfunction, and increased renal energy requirements from hyperfiltration. We hypothesized that changes in metabolism in DKD may be regulated by Sirtuin 5 (SIRT5), a deacylase that removes posttranslational modifications derived from acyl-coenzyme A and has been demonstrated to regulate numerous metabolic pathways. We found decreased malonylation in the kidney cortex (∼80% proximal tubules) of type 2 diabetic BKS db/db mice, associated with increased SIRT5 expression. We performed a proteomics analysis of malonylated peptides and found that proteins with significantly decreased malonylated lysines in the db/db cortex were enriched in nonmitochondrial metabolic pathways: glycolysis and peroxisomal fatty acid oxidation. To confirm relevance of these findings in human disease, we analyzed diabetic kidney transcriptomic data from a cohort of Southwestern American Indians, which revealed a tubulointerstitial-specific increase in Sirt5 expression. These data were further corroborated by immunofluorescence data of SIRT5 from nondiabetic and DKD cohorts. Furthermore, overexpression of SIRT5 in cultured human proximal tubules demonstrated increased aerobic glycolysis. Conversely, we observed reduced glycolysis with decreased SIRT5 expression. These findings suggest that SIRT5 may lead to differential nutrient partitioning and utilization in DKD. Taken together, our findings highlight a previously unrecognized role for SIRT5 in metabolic reprogramming in DKD.
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Affiliation(s)
- Judy Baek
- Department of Internal Medicine-Nephrology, University of Michigan, Ann Arbor, Michigan, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kelli Sas
- Department of Internal Medicine-Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Chenchen He
- Department of Internal Medicine-Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Viji Nair
- Department of Internal Medicine-Nephrology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - William Giblin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Ayaka Inoki
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hongyu Zhang
- Department of Internal Medicine-Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yang Yingbao
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jeffrey Hodgin
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Robert G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona, USA
| | - Frank C Brosius
- Department of Internal Medicine-Nephrology, University of Michigan, Ann Arbor, Michigan, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA; Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Matthias Kretzler
- Department of Internal Medicine-Nephrology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan, USA
| | - David B Lombard
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA; Institute of Gerontology, University of Michigan, Ann Arbor, Michigan, USA
| | - Subramaniam Pennathur
- Department of Internal Medicine-Nephrology, University of Michigan, Ann Arbor, Michigan, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA.
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7
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Burton JB, Carruthers NJ, Stemmer PM. Enriching extracellular vesicles for mass spectrometry. Mass Spectrom Rev 2023; 42:779-795. [PMID: 34632607 DOI: 10.1002/mas.21738] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Extracellular vesicles from plasma, other body fluids and cell culture media hold great promise in the search for biomarkers. Exosomes in particular, the vesicle type that is secreted after being produced in the endocytic pathway and having a diameter of 30-150 nm, are considered to be a conveyance for signaling molecules and, therefore, to hold valuable information regarding the health and activity status of the cells from which they are released. The vesicular nature of exosomes is central to all methods used to separate them from the highly abundant proteins in plasma and other fluids. The enrichment of the vesicles is essential for mass spectrometry-based analysis as they represent only a very small component of all plasma proteins. The progression of isolation techniques for exosomes from ultracentrifugation through chromatographic separation using hydrophobic packing materials shows that effective enrichment is possible and that high throughput approaches to exosome enrichment are achievable.
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Affiliation(s)
- Jordan B Burton
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan, USA
| | | | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan, USA
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8
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Cala SE, Carruthers NJ, Stemmer PM, Chen Z, Chen X. Activation of Ca transport in cardiac microsomes enriches functional sets of ER and SR proteins. Res Sq 2023:rs.3.rs-2557992. [PMID: 36798315 PMCID: PMC9934757 DOI: 10.21203/rs.3.rs-2557992/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The importance of sarcoplasmic reticulum (SR) Ca-handling in heart has led to detailed understanding of Ca-release and re-uptake protein complexes, while less is known about other endoplasmic reticulum (ER) functions in the heart. To more fully understand cardiac SR and ER functions, we analyzed cardiac microsomes based on their increased density through the actions of the SR Ca-ATPase (SERCA) and the ryanodine receptor that are highly active in cardiomyocytes. Crude cardiac microsomal vesicles loaded with Ca oxalate produced two higher density subfractions, MedSR and HighSR. Analyses of protein enrichments from the 3 membrane preparations (crude microsomes, MedSR, and HighSR), showed that only a third of microsomal proteins in heart, or 354 proteins, were enriched ≥2.0-fold in SR. Previously studied SR proteins were all enriched, as were proteins associated with canonical ER functions. Contractile, mitochondrial, and sarcolemmal proteins were not enriched. Comparing the levels of SERCA-positive SR proteins in MedSR versus HighSR vesicles produced a range of SR subfraction enrichments signifying differing levels of Ca leak (ryanodine receptor) co-localized in the same membrane patch. All known junctional SR proteins were more enriched in MedSR, while canonical ER proteins were more enriched in HighSR membrane. Proteins from other putative ER/SR subdomains also showed characteristic distributions among SR subpopulations. We conclude that active Ca loading of cardiac microsomes, reflecting the combined activities of Ca uptake by SERCA, and Ca leak by RyR, permits evaluation of multiple functional ER/SR subdomains. Sets of proteins from these subdomains exhibited similar enrichment patterns across membrane subfractions, reflecting the relative levels of SERCA and RyR present within individual patches of cardiac ER and SR.
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9
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Guo C, Mattingly RR, Stemmer PM, Rosenspire AJ. At low levels, inorganic mercury interference with antigen signaling is associated with modifications to a panel of novel phosphoserine sites in B cell receptor pathway proteins. Toxicol In Vitro 2023; 89:105564. [PMID: 36736710 DOI: 10.1016/j.tiv.2023.105564] [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: 10/11/2022] [Revised: 12/23/2022] [Accepted: 01/29/2023] [Indexed: 02/04/2023]
Abstract
Epidemiological studies indicate that human and animal exposure to environmental mercury (Hg) disrupts normal immune system function, but the molecular mechanism responsible for this is still unresolved. We have previously utilized phospho-proteomic mass spectrometry to demonstrate that in the absence of B Cell Receptor (BCR) stimulation, exposure of B cells to Hg induces significant changes to a great many elements of the BCR signaling pathway in a concentration dependent manner. In this report, we have extended those initial findings by utilizing mass spectrometry to evaluate in detail the effect of low-level Hg exposure on BCR induced phospho-proteomic changes. Specifically, murine WEHI-231 B lymphoma cells were exposed to environmentally relevant levels of Hg with or without concomitant BCR stimulation. The cellular phospho-proteomes were then profiled by LC-MS/MS. We found that for low-level exposures, Hg interference with signal transduction across the BCR pathway was predominantly associated with modification of phosphorylation of 12 phosphosites located on seven different proteins. Nine sites were serine, two sites tyrosine and one site threonine. Most of these sites are novel, in the sense that only the two tyrosine and one of the serine sites have previously been reported to be associated with BCR signaling.
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Affiliation(s)
- Chunna Guo
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, USA
| | - Raymond R Mattingly
- Department of Pharmacology & Toxicology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA.
| | - Allen J Rosenspire
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, USA.
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10
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Thakur C, Qiu Y, Zhang Q, Carruthers NJ, Yu M, Bi Z, Fu Y, Wadgaonkar P, Almutairy B, Seno A, Stemmer PM, Chen F. Deletion of mdig enhances H3K36me3 and metastatic potential of the triple negative breast cancer cells. iScience 2022; 25:105057. [PMID: 36124233 PMCID: PMC9482110 DOI: 10.1016/j.isci.2022.105057] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/06/2022] [Accepted: 08/26/2022] [Indexed: 11/25/2022] Open
Abstract
In this report, we provide evidence showing diminished expression of the mineral dust-induced gene (mdig), a previously identified oncogenic gene, in human triple negative breast cancer (TNBC). Using a mouse model of orthotopic xenograft of the TNBC MDA-MB-231 cells, we demonstrate that mdig promotes the growth of primary tumors but inhibits metastasis of these cells in vivo. Knockout of mdig resulted in an enhancement of H3K36me3 in the genome and upregulation of some X chromosome-linked genes for cell motility, invasion, and metastasis. Silencing MAGED2, one of the most upregulated and H3K36me3-enriched genes resulted from mdig depletion, can partially reverse the invasive migration of the mdig knockout cells. The anti-metastatic and inhibitory role of mdig on H3K36me3 was cross-validated in another cell line, A549 lung cancer cells. Together, our data suggest that mdig is antagonist against H3K36me3 that enforces expression of genes, such as MAGED2, for cell invasion and metastasis. Loss of mdig expression in TNBC and metastatic breast cancer Knockout of mdig enforces metastasis of the TNBC cells Mdig antagonizes H3K36me3 that promotes expression of X-linked metastatic genes Silencing MAGED2 reduces invasive migration of the mdig knockout cells
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Affiliation(s)
- Chitra Thakur
- Stony Brook Cancer Center and Department of Pathology, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY 11794, USA
| | - Yiran Qiu
- Stony Brook Cancer Center and Department of Pathology, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY 11794, USA
| | - Qian Zhang
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Nicholas J Carruthers
- Institute of Environmental Health Sciences, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Miaomiao Yu
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA.,Cancer Hospital of China Medical University, 44 Xiaoheyan Road, Dadong District, Shenyang, 110042 Liaoning Province, China
| | - Zhuoyue Bi
- Stony Brook Cancer Center and Department of Pathology, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY 11794, USA
| | - Yao Fu
- Stony Brook Cancer Center and Department of Pathology, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY 11794, USA
| | - Priya Wadgaonkar
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Bandar Almutairy
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA.,College of Pharmacy, Al-Dawadmi Campus, Shaqra University, P.O. Box 11961, Riyadh, Saudi Arabia
| | - Akimasa Seno
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA.,Faculty of Engineering, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama 700-8530, Japan
| | - Paul M Stemmer
- Institute of Environmental Health Sciences, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Fei Chen
- Stony Brook Cancer Center and Department of Pathology, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY 11794, USA.,Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
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11
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Ghandour M, Yamin JB, Arnetz JE, Lumley MA, Stemmer PM, Burghardt P, Jamil H, Arnetz BB. Association Between Inflammatory Biomarkers and Mental Health Symptoms in Middle Eastern Refugees in the US. Cureus 2022; 14:e28246. [PMID: 36158450 PMCID: PMC9498960 DOI: 10.7759/cureus.28246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2022] [Indexed: 11/30/2022] Open
Abstract
Introduction: Refugees are at increased risk for trauma-related mental health disorders, including anxiety, depression, and post-traumatic stress disorder (PTSD). The underlying biological mechanisms linking trauma to mental disorders need additional study, and the possible pathophysiological role of the immune system is attracting increasing interest. In this study, we investigated whether two well-known pro-inflammatory cytokines (interleukin (IL-8) and IL-6) are associated with mental health symptoms in Middle Eastern refugees displaced to the United States. Methods: Refugees (n=64, mean age=37.6 years) ages ranged from 21 to 74 years (mean=37.62, SD=11.84) were interviewed one month after arrival in Michigan, United States, using a validated survey in Arabic. Questions covered pre-displacement trauma, current anxiety, depression, and PTSD symptoms. Blood, collected immediately following the interview, was analyzed for the levels of interleukins. Multivariate linear regression was used to determine the association between mental health symptoms and IL-6 and IL-8. Results: In multivariate modeling, older age (β=0.37; p<0.01) and anxiety (β=0.31; p<0.05) were positively associated with IL-8. Age (β=0.28; p<0.05) and pre-displacement trauma (β=0.40; p<0.05) were positively associated with IL-6. Depression (β=-0.38) was negatively associated with IL-6. Conclusion/relevance: This study of inflammatory biomarkers suggests the possibility of differential associations between mental health symptoms (anxiety and depression) and pro-inflammatory markers (IL-6 and IL-8). To enhance our ability to prevent and more effectively treat trauma-exposed refugees, we need to better understand the neuroinflammatory mechanisms contributing to mental disorders.
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12
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Thakur C, Carruthers NJ, Zhang Q, Xu L, Fu Y, Bi Z, Qiu Y, Zhang W, Wadgaonkar P, Almutairy B, Guo C, Stemmer PM, Chen F. Depletion of Mdig Changes Proteomic Profiling in Triple Negative Breast Cancer Cells. Biomedicines 2022; 10:biomedicines10082021. [PMID: 36009568 PMCID: PMC9405604 DOI: 10.3390/biomedicines10082021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Triple-negative breast cancers are highly aggressive with an overall poor prognosis and limited therapeutic options. We had previously investigated the role of mdig, an oncogenic gene induced by some environmental risk factors, on the pathogenesis of breast cancer. However, a comprehensive analysis of the proteomic profile affected by mdig in triple-negative breast cancer has not been determined yet. Using label-free bottom-up quantitative proteomics, we compared wildtype control and mdig knockout MDA-MB-231 cells and identified the proteins and pathways that are significantly altered with mdig deletion. A total of 904 differentially expressed (p < 0.005) proteins were identified in the KO cells. Approximately 30 pathways and networks linked to the pathogenicity of breast cancer were either up- or downregulated, such as EIF2 signaling, the unfolded protein response, and isoleucine degradation I. Ingenuity Pathway Analysis established that the differentially expressed proteins have relevant biological actions in cell growth, motility, and malignancy. These data provide the first insight into protein expression patterns in breast cancer associated with a complete disruption of the mdig gene and yielded substantial information on the key proteins, biological processes, and pathways modulated by mdig that contribute to breast cancer tumorigenicity and invasiveness.
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Affiliation(s)
- Chitra Thakur
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, The State University of New York, Lauterbur Drive, Stony Brook, NY 11794, USA
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, 101 Nicolls Road, Stony Brook, NY 11794, USA
- Correspondence: (C.T.); (F.C.)
| | - Nicholas J. Carruthers
- Institute of Environmental Health Sciences, Wayne State University, 2309 Scott Hall, 540 E Canfield Ave, Detroit, MI 48202, USA
| | - Qian Zhang
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Liping Xu
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Yao Fu
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, The State University of New York, Lauterbur Drive, Stony Brook, NY 11794, USA
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Zhuoyue Bi
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, The State University of New York, Lauterbur Drive, Stony Brook, NY 11794, USA
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Yiran Qiu
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, The State University of New York, Lauterbur Drive, Stony Brook, NY 11794, USA
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Wenxuan Zhang
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, The State University of New York, Lauterbur Drive, Stony Brook, NY 11794, USA
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Priya Wadgaonkar
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Bandar Almutairy
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
| | - Chunna Guo
- Department of Immunology and Microbiology, Wayne State University, Detroit, MI 48201, USA
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University, 2309 Scott Hall, 540 E Canfield Ave, Detroit, MI 48202, USA
| | - Fei Chen
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, The State University of New York, Lauterbur Drive, Stony Brook, NY 11794, USA
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Avenue, Detroit, MI 48201, USA
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, 101 Nicolls Road, Stony Brook, NY 11794, USA
- Correspondence: (C.T.); (F.C.)
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13
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Burton JB, Carruthers NJ, Hou Z, Matherly LH, Stemmer PM. Pattern Analysis of Organellar Maps for Interpretation of Proteomic Data. Proteomes 2022; 10:18. [PMID: 35645376 PMCID: PMC9149908 DOI: 10.3390/proteomes10020018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 03/23/2022] [Revised: 05/07/2022] [Accepted: 05/17/2022] [Indexed: 12/13/2022] Open
Abstract
Localization of organelle proteins by isotope tagging (LOPIT) maps are a coordinate-directed representation of proteome data that can aid in biological interpretation. Analysis of organellar association for proteins as displayed using LOPIT is evaluated and interpreted for two types of proteomic data sets. First, test and control group protein abundances and fold change data obtained in a proximity labeling experiment are plotted on a LOPIT map to evaluate the likelihood of true protein interactions. Selection of true positives based on co-localization of proteins in the organellar space is shown to be consistent with carboxylase enrichment which serves as a positive control for biotinylation in streptavidin affinity selected proteome data sets. The mapping in organellar space facilitates discrimination between the test and control groups and aids in identification of proteins of interest. The same representation of proteins in organellar space is used in the analysis of extracellular vesicle proteomes for which protein abundance and fold change data are evaluated. Vesicular protein organellar localization patterns provide information about the subcellular origin of the proteins in the samples which are isolates from the extracellular milieu. The organellar localization patterns are indicative of the provenance of the vesicular proteome origin and allow discrimination between proteomes prepared using different enrichment methods. The patterns in LOPIT displays are easy to understand and compare which aids in the biological interpretation of proteome data.
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Affiliation(s)
- Jordan B. Burton
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA;
| | | | - Zhanjun Hou
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48202, USA; (Z.H.); (L.H.M.)
| | - Larry H. Matherly
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48202, USA; (Z.H.); (L.H.M.)
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA;
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14
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Zhang K, Grossman LI, Stemmer PM, Kim H, Carruthers N. Inhalation Exposure to Airborne PM
2.5
Induces Integrated Organelle Stress Response in the Liver. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.l7647] [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: 11/11/2022]
Affiliation(s)
- Kezhong Zhang
- Center for Molecular Medicine and GeneticsWayne State UniversityDetroitMI
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15
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Lash LH, Mathieu P, Stemmer PM, Rosati R, Hu X, Jones DP. Secreted Proteins, Lipids and Low‐Molecular‐Weight Metabolites as Early Biomarkers of Human Proximal Tubular Cell Exposure to Nephrotoxic Agents. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r4468] [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: 11/11/2022]
Affiliation(s)
| | | | - Paul M. Stemmer
- Institute of Environmental Health SciencesWayne State UniversityDetroitMI
| | - Rita Rosati
- Institute of Environmental Health SciencesWayne State UniversityDetroitMI
| | - Xin Hu
- Pulmonary MedicineEmory University School of MedicineAtlantaGA
| | - Dean P. Jones
- Pulmonary MedicineEmory University School of MedicineAtlantaGA
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16
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Yang Z, Stemmer PM, Petriello MC. Proteomics-Based Identification of Interaction Partners of the Xenobiotic Detoxification Enzyme FMO3 Reveals Involvement in Urea Cycle. Toxics 2022; 10:60. [PMID: 35202247 PMCID: PMC8877285 DOI: 10.3390/toxics10020060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/18/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023]
Abstract
The hepatic xenobiotic metabolizing enzyme flavin-containing monooxygenase 3 (FMO3) has been implicated in the development of cardiometabolic disease primarily due to its enzymatic product trimethylamine-N oxide (TMAO), which has recently been shown to be associated with multiple chronic diseases, including kidney and coronary artery diseases. Although TMAO may have causative roles as a pro-inflammatory mediator, the possibility for roles in metabolic disease for FMO3, irrespective of TMAO formation, does exist. We hypothesized that FMO3 may interact with other proteins known to be involved in cardiometabolic diseases and that modulating the expression of FMO3 may impact on these interaction partners. Here, we combine a co-immunoprecipitation strategy coupled to unbiased proteomic workflow to report a novel protein:protein interaction network for FMO3. We identified 51 FMO3 protein interaction partners, and through gene ontology analysis, have identified urea cycle as an enriched pathway. Using mice deficient in FMO3 on two separate backgrounds, we validated and further investigated expressional and functional associations between FMO3 and the identified urea cycle genes. FMO3-deficient mice showed hepatic overexpression of carbamoylphosphate synthetase (CPS1), the rate-limiting gene of urea cycle, and increased hepatic urea levels, especially in mice of FVB (Friend leukemia virus B strain) background. Finally, overexpression of FMO3 in murine AML12 hepatocytes led to downregulation of CPS1. Although there is past literature linking TMAO to urea cycle, this is the first published work showing that FMO3 and CPS1 may directly interact, implicating a role for FMO3 in chronic kidney disease irrespective of TMAO formation.
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Affiliation(s)
- Zhao Yang
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA; (Z.Y.); (P.M.S.)
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA; (Z.Y.); (P.M.S.)
- Department of Pharmaceutical Sciences, College of Pharmacy, Wayne State University, Detroit, MI 48202, USA
| | - Michael C. Petriello
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA; (Z.Y.); (P.M.S.)
- Department of Pharmacology, School of Medicine, Wayne State University, Detroit, MI 48202, USA
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17
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Keaton SA, Arnetz J, Jamil H, Dhalimi A, Stemmer PM, Ruden DM, Yamin J, Achtyes E, Smart L, Brundin L, Arnetz BB. IL-10: A possible immunobiological component of positive mental health in refugees. Comprehensive Psychoneuroendocrinology 2021; 8:100097. [PMID: 35757662 PMCID: PMC9216633 DOI: 10.1016/j.cpnec.2021.100097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 06/28/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 01/23/2023] Open
Abstract
Objective As the number of refugees continues to rise, there is growing concern about the impact from trauma exposures on their mental health. However, there is a limited understanding of possible biological mechanisms contributing to the substantial inter-individual differences in trauma-related outcomes, especially as it relates to positive mental health. Only sparse work has focused on the biology of positive mental health, including energy and sleep, in trauma-exposed persons. In this study, we analyzed cytokines in blood from newly arrived refugees with differential trauma exposures in relationship to self-reported energy, as a key marker of positive mental health. Methods Within the first month of arrival in the USA, 64 refugees from Iraq and Syria were interviewed. Refugees completed the clinical DSM-IV PTSD-Checklist Civilian Version (PCL-C), the Beck Anxiety Inventory (BAI), and the Hospital Anxiety and Depression Scale (HADS). Ten psychiatrically healthy non-refugee persons were used as healthy controls to compare levels of cytokines. Blood samples were collected at the time of the interview and subsequently analyzed for IL-1β, IL-6, IL-8, IL-10, and TNF-α concentrations. Results Energy correlated positively with current concentration ability and sleep quality, and negatively with stress, PCL-C, BAI and HADS scores (Spearman correlations, all p<0.05). Refugees had lower levels of IL-10 compared to controls (p<0.05). IL-10 levels in refugees correlated with higher energy levels (p<0.01). Conclusions Results suggest that self-reported energy is a key component of positive mental health in newly arrived traumatized refugees. Additionally, the anti-inflammatory cytokine IL-10 could be a marker of, or causally associated with positive mental health. A better understanding of the balance between pro- and anti-inflammatory states in highly traumatized individuals has the potential to create more targeted and effective treatments with implications for long-term health outcomes. Energy is a key component to positive mental health in traumatized refugees. IL-10 could be associated with positive mental health in refugees. Energy levels correlated positively with concentration ability and sleep quality.
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Affiliation(s)
- Sarah A. Keaton
- Department of Physiology, Michigan State University, East Lansing, MI, USA
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
- Corresponding author. Department of Physiology, Michigan State University, Center for Neurodegenerative Science, Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI, 49503, USA.
| | - Judy Arnetz
- Department of Family Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Hikmet Jamil
- Department of Family Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Abir Dhalimi
- Department of Family Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Paul M. Stemmer
- Institute of Environmental Health Science, Wayne State University, Detroit, MI, USA
| | - Douglas M. Ruden
- Institute of Environmental Health Science, Wayne State University, Detroit, MI, USA
| | - Jolin Yamin
- Institute of Environmental Health Science, Wayne State University, Detroit, MI, USA
| | - Eric Achtyes
- Pine Rest Christian Mental Health, Grand Rapids, MI, USA
- Division of Psychiatry & Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - LeAnn Smart
- Pine Rest Christian Mental Health, Grand Rapids, MI, USA
| | - Lena Brundin
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
- Division of Psychiatry & Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Bengt B. Arnetz
- Department of Family Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
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18
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Carruthers NJ, Strieder-Barboza C, Caruso JA, Flesher CG, Baker NA, Kerk SA, Ky A, Ehlers AP, Varban OA, Lyssiotis CA, Lumeng CN, Stemmer PM, O'Rourke RW. The human type 2 diabetes-specific visceral adipose tissue proteome and transcriptome in obesity. Sci Rep 2021; 11:17394. [PMID: 34462518 PMCID: PMC8405693 DOI: 10.1038/s41598-021-96995-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 12/05/2020] [Accepted: 08/11/2021] [Indexed: 01/21/2023] Open
Abstract
Dysfunctional visceral adipose tissue (VAT) in obesity is associated with type 2 diabetes (DM) but underlying mechanisms remain unclear. Our objective in this discovery analysis was to identify genes and proteins regulated by DM to elucidate aberrant cellular metabolic and signaling mediators. We performed label-free proteomics and RNA-sequencing analysis of VAT from female bariatric surgery subjects with DM and without DM (NDM). We quantified 1965 protein groups, 23 proteins, and 372 genes that were differently abundant in DM vs. NDM VAT. Proteins downregulated in DM were related to fatty acid synthesis and mitochondrial function (fatty acid synthase, FASN; dihydrolipoyl dehydrogenase, mitochondrial, E3 component, DLD; succinate dehydrogenase-α, SDHA) while proteins upregulated in DM were associated with innate immunity and transcriptional regulation (vitronectin, VTN; endothelial protein C receptor, EPCR; signal transducer and activator of transcription 5B, STAT5B). Transcriptome indicated defects in innate inflammation, lipid metabolism, and extracellular matrix (ECM) function, and components of complement classical and alternative cascades. The VAT proteome and transcriptome shared 13 biological processes impacted by DM, related to complement activation, cell proliferation and migration, ECM organization, lipid metabolism, and gluconeogenesis. Our data revealed a marked effect of DM in downregulating FASN. We also demonstrate enrichment of complement factor B (CFB), coagulation factor XIII A chain (F13A1), thrombospondin 1 (THBS1), and integrins at mRNA and protein levels, albeit with lower q-values and lack of Western blot or PCR confirmation. Our findings suggest putative mechanisms of VAT dysfunction in DM.
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Affiliation(s)
- Nicholas J Carruthers
- Proteomics Core Facility, Wayne State University, 42 W. Warren Ave, Detroit, MI, 48202, USA
| | - Clarissa Strieder-Barboza
- Department of Surgery, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA
| | - Joseph A Caruso
- Department of Chemistry, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA
| | - Carmen G Flesher
- Department of Surgery, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA
| | - Nicki A Baker
- Department of Surgery, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA
| | - Samuel A Kerk
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA.,Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA.,Rogel Cancer Center, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA
| | - Alexander Ky
- Department of Surgery, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA
| | - Anne P Ehlers
- Department of Surgery, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA.,Department of Surgery, Veterans Affairs Ann Arbor Healthcare System, 2215 Fuller Rd, Ann Arbor, MI, 48105, USA
| | - Oliver A Varban
- Department of Surgery, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA.,Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA.,Rogel Cancer Center, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA
| | - Carey N Lumeng
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA.,Graduate Program in Immunology, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA.,Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA
| | - Paul M Stemmer
- Proteomics Core Facility, Wayne State University, 42 W. Warren Ave, Detroit, MI, 48202, USA
| | - Robert W O'Rourke
- Department of Surgery, University of Michigan Medical School, 1301 Catherine St, Ann Arbor, MI, 48109, USA. .,Department of Surgery, Veterans Affairs Ann Arbor Healthcare System, 2215 Fuller Rd, Ann Arbor, MI, 48105, USA. .,Section of General Surgery, Department of Surgery, University of Michigan, 2210 Taubman Center-5343, 1500 E. Medical Center Drive, Ann Arbor, MI, 48109-5343, USA.
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19
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Yamin JB, Sudan S, Lumley MA, Dhalimi A, Arnetz JE, Stemmer PM, Burghardt PR, Jamil H, Arnetz BB. The Development of Posttraumatic Stress Disorder and Depression Symptoms in Iraqi Refugees: Associations with Acculturation and C-reactive Protein. J Nerv Ment Dis 2021; 209:585-591. [PMID: 33958551 PMCID: PMC8544132 DOI: 10.1097/nmd.0000000000001360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
ABSTRACT Refugees experience distress from premigration trauma, often exacerbated by postmigration difficulties. To develop effective interventions, risk factors for mental health symptoms need to be determined. Male Iraqi refugees (N = 53) to the United States provided background information and reported predisplacement trauma and psychological health within 1 month of their arrival. An inflammatory biomarker-C-reactive protein (CRP) was assessed approximately 1.5 years after arrival, and a contextual factor-acculturation-and psychological health were assessed 2 years after arrival. We tested whether acculturation and CRP were associated with posttraumatic stress disorder (PTSD) and depression symptoms at the 2-year follow-up, controlling for baseline symptoms, age, body mass index, and predisplacement trauma. Acculturation was inversely related to depression, and CRP was positively related to both PTSD and depression at the 2-year follow-up. Interventions targeting acculturation could help reduce the development of depression symptoms in refugees. The role of CRP in the development of PTSD and depression symptoms warrants further research.
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Affiliation(s)
- Jolin B. Yamin
- Department of Psychology, Wayne State University, Detroit, MI, US
| | - Sukhesh Sudan
- Department of Family Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, US
| | - Mark A. Lumley
- Department of Psychology, Wayne State University, Detroit, MI, US
| | - Abir Dhalimi
- Department of Family Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, US
| | - Judith E. Arnetz
- Department of Family Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, US
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, US
| | - Paul R. Burghardt
- Department of Food and Nutrition Science, Wayne State University, Detroit, MI, US
| | - Hikmet Jamil
- Department of Family Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, US
| | - Bengt B. Arnetz
- Department of Family Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, US
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20
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Cukovic D, Bagla S, Ukasik D, Stemmer PM, Jena BP, Naik AR, Sood S, Asano E, Luat A, Chugani DC, Dombkowski AA. Exosomes in Epilepsy of Tuberous Sclerosis Complex: Carriers of Pro-Inflammatory MicroRNAs. Noncoding RNA 2021; 7:ncrna7030040. [PMID: 34287356 PMCID: PMC8293460 DOI: 10.3390/ncrna7030040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 05/25/2021] [Revised: 06/30/2021] [Accepted: 07/03/2021] [Indexed: 01/14/2023] Open
Abstract
Exosomes are a class of small, secreted extracellular vesicles (EV) that have recently gained considerable attention for their role in normal cellular function, disease processes and potential as biomarkers. Exosomes serve as intercellular messengers and carry molecular cargo that can alter gene expression and the phenotype of recipient cells. Here, we investigated alterations of microRNA cargo in exosomes secreted by epileptogenic tissue in tuberous sclerosis complex (TSC), a multi-system genetic disorder that includes brain lesions known as tubers. Approximately 90% of TSC patients suffer from seizures that originate from tubers, and ~60% are resistant to antiseizure drugs. It is unknown why some tubers cause seizures while others do not, and the molecular basis of drug-resistant epilepsy is not well understood. It is believed that neuroinflammation is involved, and characterization of this mechanism may be key to disrupting the "vicious cycle" between seizures, neuroinflammation, and increased seizure susceptibility. We isolated exosomes from epileptogenic and non-epileptogenic TSC tubers, and we identified differences in their microRNA cargo using small RNA-seq. We identified 12 microRNAs (including miR-142-3p, miR-223-3p and miR-21-5p) that are significantly increased in epileptogenic tubers and contain nucleic acid motifs that activate toll-like receptors (TLR7/8), initiating a neuroinflammatory cascade. Exosomes from epileptogenic tissue caused induction of key pathways in cultured cells, including innate immune signaling (TLR), inflammatory response and key signaling nodes SQSTM1 (p62) and CDKN1A (p21). Genes induced in vitro were also significantly upregulated in epileptogenic tissue. These results provide new evidence on the role of exosomes and non-coding RNA cargo in the neuroinflammatory cascade of epilepsy and may help advance the development of novel biomarkers and therapeutic approaches for the treatment of drug-resistant epilepsy.
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Affiliation(s)
- Daniela Cukovic
- Department of Pediatrics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (D.C.); (S.B.); (E.A.)
| | - Shruti Bagla
- Department of Pediatrics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (D.C.); (S.B.); (E.A.)
| | - Dylan Ukasik
- Translational Neurosciences Program, Wayne State University, Detroit, MI 48201, USA;
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA;
| | - Bhanu P. Jena
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (B.P.J.); (A.R.N.)
| | - Akshata R. Naik
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (B.P.J.); (A.R.N.)
| | - Sandeep Sood
- Department of Neurosurgery, School of Medicine, Wayne State University, Detroit, MI 48201, USA;
| | - Eishi Asano
- Department of Pediatrics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (D.C.); (S.B.); (E.A.)
- Translational Neurosciences Program, Wayne State University, Detroit, MI 48201, USA;
- Department of Neurology, School of Medicine, Wayne State University, Detroit, MI 48201, USA;
| | - Aimee Luat
- Department of Neurology, School of Medicine, Wayne State University, Detroit, MI 48201, USA;
- Department of Pediatrics, Central Michigan University, Mt Pleasant, MI 48858, USA
| | - Diane C. Chugani
- Departments of Communication Sciences and Disorders, and Chemistry and Biochemistry, University of Delaware, Newark, DE 19713, USA;
| | - Alan A. Dombkowski
- Department of Pediatrics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (D.C.); (S.B.); (E.A.)
- Translational Neurosciences Program, Wayne State University, Detroit, MI 48201, USA;
- Correspondence: ; Tel.: +1-(313)-745-6381
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21
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Paul J, Templin TN, Carruthers NJ, Burghardt PR, Ivanics C, Stemmer PM, Pieper B. C-reactive Protein Levels in Plasma and Chronic Venous Ulcer Exudate of Persons Who Inject Drugs: A Pilot Study. Wounds 2021:WNDS20210331-1. [PMID: 33913822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
BACKGROUND Persons who inject drugs (PWID) in the groin, legs, and/or feet are at high risk for chronic venous ulcers (CVUs). The plasma C-reactive protein (CRP) level is a marker of systemic inflammation. OBJECTIVE This pilot study examined CRP levels in plasma and CVU exudate of PWID. The aims were to (1) compare levels of CRP in plasma and exudate; (2) examine if the CRP level in exudate changed over 4 weeks with wound treatment; and (3) examine the relationship of the exudate CRP level with CVU area, CVU age, number of CVUs, and number of comorbidities. MATERIALS AND METHODS Persons who inject drugs seeking wound care were enrolled in this Institutional Review Board approved prospective, longitudinal, descriptive study. A blood sample was collected on the first visit (week 1); the plasma was then separated. Wound exudate was collected on swabs during the first visit (week 1) and 4 weeks later (week 4). All samples were stored at -80° C. Samples were eluted from swabs using mass spectrometry grade water then aliquoted for CRP analysis. RESULTS The participants of the study included 14 PWID (mean age, 62.14 ± 4.52 years; mean number of comorbidities, 5.71 ± 1.90; and mean number of ulcers 2.07 ± 1.07 that were present for a mean of 7.96 ± 11.91 years without healing). C-reactive protein level in plasma was a mean of 6.47 ± 8.56 mg/L, with lower levels found in wound exudate but highly correlated (rho = .925). Exudate CRP levels decreased from week 1 to week 4, and the 2 were highly correlated (rho = .895). Exudate CRP level week 1 was not significantly related to wound area, wound age, number of ulcers, or number of comorbidities. CONCLUSIONS Plasma and exudate CRP levels were highly correlated. Exudate CRP levels decreased across time. Future large-scale wound healing studies should examine CRP levels over a longer duration and as they correlate to wound healing.
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Affiliation(s)
- Julia Paul
- School of Nursing, Oakland University, Rochester, Michigan;William Beaumont Hospital, Royal Oak, Michigan
| | | | - Nicholas J Carruthers
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan
| | - Paul R Burghardt
- Department of Nutrition and Food Sciences, Wayne State University, Detroit, Michigan
| | - Ciara Ivanics
- School of Medicine, Wayne State University, Detroit, Michigan
| | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan
| | - Barbara Pieper
- College of Nursing, Wayne State University, Detroit, Michigan
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22
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Pan G, Deshpande M, Pang H, Stemmer PM, Carruthers NJ, Shearn CT, Backos DS, Palaniyandi SS. 4-Hydroxy-2-nonenal attenuates 8-oxoguanine DNA glycosylase 1 activity. J Cell Biochem 2020; 121:4887-4897. [PMID: 32628320 PMCID: PMC7935017 DOI: 10.1002/jcb.29814] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 12/18/2019] [Revised: 02/18/2020] [Accepted: 05/11/2020] [Indexed: 02/06/2023]
Abstract
Elevated cellular oxidative stress and oxidative DNA damage are key contributors to impaired cardiac function in diabetes. During chronic inflammation, reactive oxygen species (ROS)-induced lipid peroxidation results in the formation of reactive aldehydes, foremost of which is 4-hydroxy-2-nonenal (4HNE). 4HNE forms covalent adducts with proteins, negatively impacting cellular protein function. During conditions of elevated oxidative stress, oxidative DNA damage such as modification by 8-hydroxydeoxyguanosine (8OHdG) is repaired by 8-oxoguanine glycosylase-1 (OGG-1). Based on these facts, we hypothesized that 4HNE forms adducts with OGG-1 inhibiting its activity, and thus, increases the levels of 8OHG in diabetic heart tissues. To test our hypothesis, we evaluated OGG-1 activity, 8OHG and 4HNE in the hearts of leptin receptor deficient db/db mice, a type-2 diabetic model. We also treated the recombinant OGG-1 with 4HNE to measure direct adduction. We found decreased OGG-1 activity (P > .05), increased 8OHG (P > .05) and increased 4HNE adducts (P > .05) along with low aldehyde dehydrogenase-2 activity (P > .05). The increased colocalization of OGG-1 and 4HNE in cardiomyocytes suggest 4HNE adduction on OGG-1. Furthermore, colocalization of 8OHG and OGG-1 with mitochondrial markers TOM 20 and aconitase, respectively, indicated significant levels of oxidatively-induced mtDNA damage and implicated a role for mitochondrial OGG-1 function. In vitro exposure of recombinant OGG-1 (rOGG-1) with increasing concentrations of 4HNE resulted in a concentration-dependent decrease in OGG-1 activity. Mass spectral analysis of trypsin digests of 4HNE-treated rOGG-1 identified 4HNE adducts on C28, C75, C163, H179, H237, C241, K249, H270, and H282. In silico molecular modeling of 4HNE-K249 OGG-1 and 4HNE-H270 OGG-1 mechanistically supported 4HNE-mediated enzymatic inhibition of OGG-1. In conclusion, these data support the hypothesis that inhibition of OGG-1 by direct modification by 4HNE contributes to decreased OGG-1 activity and increased 8OHG-modified DNA that are present in the diabetic heart.
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Affiliation(s)
- Guodong Pan
- Division of Hypertension and Vascular Research, Department of Internal Medicine, Henry Ford Health System, Detroit, MI 48202
| | - Mandar Deshpande
- Division of Hypertension and Vascular Research, Department of Internal Medicine, Henry Ford Health System, Detroit, MI 48202
| | - Haiyan Pang
- Division of Hypertension and Vascular Research, Department of Internal Medicine, Henry Ford Health System, Detroit, MI 48202
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences & Proteomics Facility Core, Wayne State University, Detroit, MI, USA, 48201
| | - Nicholas J Carruthers
- Institute of Environmental Health Sciences & Proteomics Facility Core, Wayne State University, Detroit, MI, USA, 48201
| | - Colin T. Shearn
- Department of Pediatrics Division of Pediatric Gastroenterology, Hepatology and Nutrition, School of Medicine, University of Colorado Anschutz Medical Center, Aurora, CO 80045
| | - Donald S. Backos
- School of Pharmacy, University of Colorado Anschutz Medical Center, Aurora, CO 80045
| | - Suresh Selvaraj Palaniyandi
- Division of Hypertension and Vascular Research, Department of Internal Medicine, Henry Ford Health System, Detroit, MI 48202
- Department of Physiology, Wayne State University, Detroit, MI, 48202
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23
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Carruthers NJ, McClellan SA, Somayajulu M, Pitchaikannu A, Bessert D, Peng X, Huitsing K, Stemmer PM, Hazlett LD. Effects of Glycyrrhizin on Multi-Drug Resistant Pseudomonas aeruginosa. Pathogens 2020; 9:pathogens9090766. [PMID: 32962036 PMCID: PMC7557769 DOI: 10.3390/pathogens9090766] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 09/02/2020] [Accepted: 09/16/2020] [Indexed: 02/06/2023] Open
Abstract
The effects of glycyrrhizin (GLY) on multi-drug resistant (MDR) systemic (MDR9) vs. ocular (B1045) Pseudomonas aeruginosa clinical isolates were determined. Proteomes of each isolate with/without GLY treatment were profiled using liquid chromatography mass spectrometry (LC-MS/MS). The effect of GLY on adherence of MDR isolates to immortalized human (HCET) and mouse (MCEC) corneal epithelial cells, and biofilm and dispersal was tested. Both isolates were treated with GLY (0.25 minimum inhibitory concentration (MIC), 10 mg/mL for MDR9 and 3.75 mg/mL for B1045) and subjected to proteomic analysis. MDR9 had a greater response to GLY (51% of identified proteins affected vs. <1% in B1045). In MDR9 vs. controls, GLY decreased the abundance of proteins for: antibiotic resistance, biofilm formation, and type III secretion. Further, antibiotic resistance and type III secretion proteins had higher control abundances in MDR9 vs. B1045. GLY (5 and 10 mg/mL) significantly reduced binding of both isolates to MCEC, and B1045 to HCET. MDR9 binding to HCET was only reduced at 10 mg/mL GLY. GLY (5 and 10 mg/mL) enhanced dispersal for both isolates, at early (6.5 h) but not later times (24–72 h). This study provides evidence that GLY has a greater effect on the proteome of MDR9 vs. B1045, yet it was equally effective at disrupting adherence and early biofilm dispersal.
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Affiliation(s)
- Nicholas J. Carruthers
- Institute of Environmental Health Sciences, Wayne State University School of Medicine, 540 E. Canfield Avenue, Detroit, MI 48201, USA; (N.J.C.); (P.M.S.)
| | - Sharon A. McClellan
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, School of Medicine, Detroit, MI 48201, USA; (S.A.M.); (M.S.); (A.P.); (D.B.); (K.H.)
| | - Mallika Somayajulu
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, School of Medicine, Detroit, MI 48201, USA; (S.A.M.); (M.S.); (A.P.); (D.B.); (K.H.)
| | - Ahalya Pitchaikannu
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, School of Medicine, Detroit, MI 48201, USA; (S.A.M.); (M.S.); (A.P.); (D.B.); (K.H.)
| | - Denise Bessert
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, School of Medicine, Detroit, MI 48201, USA; (S.A.M.); (M.S.); (A.P.); (D.B.); (K.H.)
| | - Xudong Peng
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao 266071, China;
| | - Kylie Huitsing
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, School of Medicine, Detroit, MI 48201, USA; (S.A.M.); (M.S.); (A.P.); (D.B.); (K.H.)
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University School of Medicine, 540 E. Canfield Avenue, Detroit, MI 48201, USA; (N.J.C.); (P.M.S.)
| | - Linda D. Hazlett
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, School of Medicine, Detroit, MI 48201, USA; (S.A.M.); (M.S.); (A.P.); (D.B.); (K.H.)
- Correspondence: ; Tel.: +1-313-577-1079; Fax: +1-313-577-3125
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24
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Arnetz BB, Sudan S, Arnetz JE, Yamin JB, Lumley MA, Beck JS, Stemmer PM, Burghardt P, Counts SE, Jamil H. Dysfunctional neuroplasticity in newly arrived Middle Eastern refugees in the U.S.: Association with environmental exposures and mental health symptoms. PLoS One 2020; 15:e0230030. [PMID: 32142533 PMCID: PMC7059916 DOI: 10.1371/journal.pone.0230030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/19/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Psychological war trauma among displaced refugees is an established risk factor for mental health disorders, especially post-traumatic stress disorder (PTSD). Persons with trauma-induced disorders have heightened neuroplastic restructuring of limbic brain circuits (e.g., amygdala and hippocampus), which are critical factors in the pathophysiology of PTSD. Civilians in war are exposed to both psychological trauma and environmental hazards, such as metals. Little is known about the possible mental health impact from such environmental exposures, alone or in combination with trauma. It is of special interest to determine whether war exposures contribute to dysfunctional neuroplasticity; that is, an adverse outcome from sustained stress contributing to mental health disorders. The current study examined Middle Eastern refugees in the United States to determine the relationships among pre-displacement trauma and environmental exposures, brain derived neurotrophic growth factor (BDNF) and nerve growth factor (NGF)-two neurotrophins reported to mediate neuroplasticity responses to stress-related exposures-and mental health. METHODS Middle Eastern refugees (n = 64; 33 men, 31 women) from Syria (n = 40) or Iraq (n = 24) were assessed 1 month after arrival to Michigan, US. Participants were interviewed in Arabic using a semi-structured survey to assess pre-displacement trauma and environmental exposure, PTSD, depression, anxiety, and self-rated mental health. Whole blood was collected, and concentrations of six heavy metals as well as BDNF and NGF levels were determined. Because these two neurotrophins have similar functions in neuroplasticity, we combined them to create a neuroplasticity index. Linear regression tested whether psychosocial trauma, environmental exposures and biomarkers were associated with mental health symptoms. FINDINGS The neuroplasticity index was associated with PTSD (standardized beta, β = 0.25, p < 0.05), depression (0.26, < 0.05) and anxiety (0.32, < 0.01) after controlling for pre-displacement trauma exposures. In addition, pre-displacement environmental exposure was associated with PTSD (0.28, < 0.05) and anxiety (0.32, < 0.05). Syrian refugees and female gender were associated with higher scores on depression (0.25, < 0.05; 0.30, < 0.05) and anxiety scales (0.35, < 0.01; 0.27, < 0.05), and worse on self-rated mental health (0.32, < 0.05; 0.34, < 0.05). In bivariate analysis, the neuroplasticity index was related to blood lead levels (r = 0.40; p < 0.01). CONCLUSIONS The current study confirms the adverse effects of war trauma on mental health. Higher levels of biomarkers of neuroplasticity correlated with worse mental health and higher blood lead levels. Higher neurotrophin levels in refugees might indicate dysfunctional neuroplasticity with increased consolidation of adverse war memories in the limbic system. Such a process may contribute to psychiatric symptoms. Further research is needed to clarify the pathobiological mechanisms linking war trauma and environmental exposures to adverse mental health.
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Affiliation(s)
- Bengt B. Arnetz
- Department of Family medicine, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, United States of America
| | - Sukhesh Sudan
- Department of Family medicine, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, United States of America
| | - Judith E. Arnetz
- Department of Family medicine, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, United States of America
| | - Jolin B. Yamin
- Department of Psychology, Wayne State University, Detroit, Michigan, United States of America
| | - Mark A. Lumley
- Department of Psychology, Wayne State University, Detroit, Michigan, United States of America
| | - John S. Beck
- Department of Translational Neuroscience, Grand Rapids, Michigan, United States of America
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Paul Burghardt
- Department of Nutrition and Food Science, Wayne State University, Detroit, Michigan, United States of America
| | - Scott E. Counts
- Department of Family medicine, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, United States of America
- Department of Translational Neuroscience, Grand Rapids, Michigan, United States of America
| | - Hikmet Jamil
- Department of Family medicine, College of Human Medicine, Michigan State University, Grand Rapids, Michigan, United States of America
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25
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Tan Z, Zhu J, Stemmer PM, Sun L, Yang Z, Schultz K, Gaffrey MJ, Cesnik AJ, Yi X, Hao X, Shortreed MR, Shi T, Lubman DM. Comprehensive Detection of Single Amino Acid Variants and Evaluation of Their Deleterious Potential in a PANC-1 Cell Line. J Proteome Res 2020; 19:1635-1646. [PMID: 32058723 DOI: 10.1021/acs.jproteome.9b00840] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Identifying single amino acid variants (SAAVs) in cancer is critical for precision oncology. Several advanced algorithms are now available to identify SAAVs, but attempts to combine different algorithms and optimize them on large data sets to achieve a more comprehensive coverage of SAAVs have not been implemented. Herein, we report an expanded detection of SAAVs in the PANC-1 cell line using three different strategies, which results in the identification of 540 SAAVs in the mass spectrometry data. Among the set of 540 SAAVs, 79 are evaluated as deleterious SAAVs based on analysis using the novel AssVar software in which one of the driver mutations found in each protein of KRAS, TP53, and SLC37A4 is further validated using independent selected reaction monitoring (SRM) analysis. Our study represents the most comprehensive discovery of SAAVs to date and the first large-scale detection of deleterious SAAVs in the PANC-1 cell line. This work may serve as the basis for future research in pancreatic cancer and personal immunotherapy and treatment.
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Affiliation(s)
- Zhijing Tan
- Department of Surgery, The University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jianhui Zhu
- Department of Surgery, The University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan 48202, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Zhichang Yang
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Kendall Schultz
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Matthew J Gaffrey
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Anthony J Cesnik
- Department of Genetics, Stanford University, Stanford, California 94305, United States
| | - Xinpei Yi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Xiaohu Hao
- Shanghai Institutes for Biological Science, Chinese Academy of Science, Shanghai 200031, China
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Tujin Shi
- Integrative Omics Group, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - David M Lubman
- Department of Surgery, The University of Michigan, Ann Arbor, Michigan 48109, United States
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Carruthers NJ, Stemmer PM, Media J, Swartz K, Wang X, Aube N, Hamann MT, Valeriote F, Shaw J. The anti-MRSA compound 3-O-alpha-L-(2″,3″-di-p-coumaroyl)rhamnoside (KCR) inhibits protein synthesis in Staphylococcus aureus. J Proteomics 2019; 210:103539. [PMID: 31629958 DOI: 10.1016/j.jprot.2019.103539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/05/2019] [Accepted: 09/27/2019] [Indexed: 11/16/2022]
Abstract
Methicillin-resistant S aureus (MRSA) contributes to patient mortality and extended hospital stays. 3-O-alpha-L-(2″,3″-di-p-coumaroyl)rhamnoside (KCR) is a natural product antibiotic that is effective against MRSA but has no known mechanism of action (MOA). We used proteomics to identify the MOA for KCR. Methicillin sensitive S aureus and a mixture of four KCR stereoisomers were tested. A time-kill assay was used to choose a 4 h treatment using KCR at 5× its MIC for proteomic analysis. S aureus was treated in triplicate with KCR, oxacillin or vehicle and quantitative proteomic analysis was carried out using isobaric tags and mass spectrometry. 1190 proteins were identified and 552 were affected by KCR (q < 0.01). Ontology analysis identified 6 distinct translation-related categories that were affected by KCR (PIANO, 10% false-discovery rate) including structural constituent of ribosome, translation, rRNA binding, tRNA binding, tRNA processing and aminoacyl-tRNA ligase activity. Median fold changes (KCR vs Control) for small and large ribosomal components were 1.46 and 1.43 respectively. KCR inhibited the production of luciferase protein in an in vitro assay (IC50 39.6 μg/ml). Upregulation of translation-related proteins in response to KCR indicates that KCR acts to disrupt S aureus protein synthesis. This was confirmed with an in vitro transcription/translation assay. SIGNIFICANCE: Methicillin-resistant S aureus (MRSA) contributes to patient mortality and extended hospital stays. 3-O-alpha-L-(2″,3″-di-p-coumaroyl)rhamnoside (KCR) is a natural product antibiotic that is effective against MRSA but has no known mechanism of action (MOA). Using proteomic analysis we determined that KCR acts by inhibiting protein synthesis. KCR is an exciting novel antibiotic and this work represents an important step in its development towards clinical use.
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Affiliation(s)
- Nicholas J Carruthers
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA; Wayne State University, Institute of Environmental Health Sciences, 2309 Scott Hall, 540 E Canfield Ave, Detroit, MI 48202, United States of America.
| | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA.
| | - Joe Media
- Department of Internal Medicine, Henry Ford Hospital, Detroit, MI 48201, USA.
| | - Ken Swartz
- Department of Internal Medicine, Henry Ford Hospital, Detroit, MI 48201, USA.
| | - Xiaojuan Wang
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Nicholas Aube
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Mark T Hamann
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Frederick Valeriote
- Department of Internal Medicine, Henry Ford Hospital, Detroit, MI 48201, USA.
| | - Jiajiu Shaw
- Henry Ford Health System, Detroit, MI, USA; 21st Century Therapeutics, Detroit, MI 48201, USA
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27
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Benjamins JA, Nedelkoska L, Touil H, Stemmer PM, Carruthers NJ, Jena BP, Naik AR, Bar-Or A, Lisak RP. Exosome-enriched fractions from MS B cells induce oligodendrocyte death. Neurol Neuroimmunol Neuroinflamm 2019; 6:e550. [PMID: 31044144 PMCID: PMC6467686 DOI: 10.1212/nxi.0000000000000550] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/16/2019] [Indexed: 12/21/2022]
Abstract
Objective To identify whether factors toxic to oligodendrocytes (OLs), released by B cells from patients with MS, are found in extracellular microvesicles enriched in exosomes. Methods Conditioned medium (Sup) was obtained from cultures of blood B cells of patients with MS and normal controls (NCs). Exosome-enriched (Ex-En) fractions were prepared by solvent precipitation from Sup containing bovine serum and from serum-free Sup by ultracentrifugation (UC) or immunoprecipitation (IP) with antibodies to CD9. Ex-En fractions were diluted 1:4 with OL culture medium and screened for toxic effects on cultured rat OLs as measured by trypan blue uptake. Proteomic analysis was performed on Sup fractions. Results MS B cell–derived Ex-En fractions prepared from Sup by solvent extraction, UC, or IP induced OL death, whereas corresponding Ex-En fractions from NC showed little toxicity. Proteomic analysis of Sup demonstrated enrichment of proteins characteristic of exosomes from both NC and MS B-cell Sup. Ontology enrichment analysis suggested differences in the types and cargo of exosomes from MS Sup compared with NC, with proteins related to cell surface, extracellular plasma membrane, and gliogenesis enriched in MS. Conclusions Much of the in vitro toxicity of Sup from B cells of patients with relapsing-remitting MS is found in Ex-En fractions, as confirmed by 3 methods. Proteomic analysis of B-cell Sup indicates multiple differences between MS and NC.
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Affiliation(s)
- Joyce A Benjamins
- Departments of Neurology and Biochemistry, Immunology and Microbiology (J.A.B., R.P.L.), Wayne State University School of Medicine; Department of Neurology (L.N.), Wayne State University School of Medicine, Detroit, Michigan; Department of Neurology and Center for Neuroinflammation and Experimental Therapeutics (H.T., A.B.-O.), Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Neurology (H.T., A.B.-O.), McGill University, Montreal Neurological Institute, Montreal, Quebec, Canada; Institute of Environmental Health Sciences (P.M.S., N.J.C.), Wayne State University; and Department of Physiology (B.P.J., A.R.N.), Wayne State University School of Medicine, Detroit, Michigan
| | - Liljana Nedelkoska
- Departments of Neurology and Biochemistry, Immunology and Microbiology (J.A.B., R.P.L.), Wayne State University School of Medicine; Department of Neurology (L.N.), Wayne State University School of Medicine, Detroit, Michigan; Department of Neurology and Center for Neuroinflammation and Experimental Therapeutics (H.T., A.B.-O.), Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Neurology (H.T., A.B.-O.), McGill University, Montreal Neurological Institute, Montreal, Quebec, Canada; Institute of Environmental Health Sciences (P.M.S., N.J.C.), Wayne State University; and Department of Physiology (B.P.J., A.R.N.), Wayne State University School of Medicine, Detroit, Michigan
| | - Hanane Touil
- Departments of Neurology and Biochemistry, Immunology and Microbiology (J.A.B., R.P.L.), Wayne State University School of Medicine; Department of Neurology (L.N.), Wayne State University School of Medicine, Detroit, Michigan; Department of Neurology and Center for Neuroinflammation and Experimental Therapeutics (H.T., A.B.-O.), Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Neurology (H.T., A.B.-O.), McGill University, Montreal Neurological Institute, Montreal, Quebec, Canada; Institute of Environmental Health Sciences (P.M.S., N.J.C.), Wayne State University; and Department of Physiology (B.P.J., A.R.N.), Wayne State University School of Medicine, Detroit, Michigan
| | - Paul M Stemmer
- Departments of Neurology and Biochemistry, Immunology and Microbiology (J.A.B., R.P.L.), Wayne State University School of Medicine; Department of Neurology (L.N.), Wayne State University School of Medicine, Detroit, Michigan; Department of Neurology and Center for Neuroinflammation and Experimental Therapeutics (H.T., A.B.-O.), Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Neurology (H.T., A.B.-O.), McGill University, Montreal Neurological Institute, Montreal, Quebec, Canada; Institute of Environmental Health Sciences (P.M.S., N.J.C.), Wayne State University; and Department of Physiology (B.P.J., A.R.N.), Wayne State University School of Medicine, Detroit, Michigan
| | - Nicholas J Carruthers
- Departments of Neurology and Biochemistry, Immunology and Microbiology (J.A.B., R.P.L.), Wayne State University School of Medicine; Department of Neurology (L.N.), Wayne State University School of Medicine, Detroit, Michigan; Department of Neurology and Center for Neuroinflammation and Experimental Therapeutics (H.T., A.B.-O.), Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Neurology (H.T., A.B.-O.), McGill University, Montreal Neurological Institute, Montreal, Quebec, Canada; Institute of Environmental Health Sciences (P.M.S., N.J.C.), Wayne State University; and Department of Physiology (B.P.J., A.R.N.), Wayne State University School of Medicine, Detroit, Michigan
| | - Bhanu P Jena
- Departments of Neurology and Biochemistry, Immunology and Microbiology (J.A.B., R.P.L.), Wayne State University School of Medicine; Department of Neurology (L.N.), Wayne State University School of Medicine, Detroit, Michigan; Department of Neurology and Center for Neuroinflammation and Experimental Therapeutics (H.T., A.B.-O.), Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Neurology (H.T., A.B.-O.), McGill University, Montreal Neurological Institute, Montreal, Quebec, Canada; Institute of Environmental Health Sciences (P.M.S., N.J.C.), Wayne State University; and Department of Physiology (B.P.J., A.R.N.), Wayne State University School of Medicine, Detroit, Michigan
| | - Akshata R Naik
- Departments of Neurology and Biochemistry, Immunology and Microbiology (J.A.B., R.P.L.), Wayne State University School of Medicine; Department of Neurology (L.N.), Wayne State University School of Medicine, Detroit, Michigan; Department of Neurology and Center for Neuroinflammation and Experimental Therapeutics (H.T., A.B.-O.), Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Neurology (H.T., A.B.-O.), McGill University, Montreal Neurological Institute, Montreal, Quebec, Canada; Institute of Environmental Health Sciences (P.M.S., N.J.C.), Wayne State University; and Department of Physiology (B.P.J., A.R.N.), Wayne State University School of Medicine, Detroit, Michigan
| | - Amit Bar-Or
- Departments of Neurology and Biochemistry, Immunology and Microbiology (J.A.B., R.P.L.), Wayne State University School of Medicine; Department of Neurology (L.N.), Wayne State University School of Medicine, Detroit, Michigan; Department of Neurology and Center for Neuroinflammation and Experimental Therapeutics (H.T., A.B.-O.), Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Neurology (H.T., A.B.-O.), McGill University, Montreal Neurological Institute, Montreal, Quebec, Canada; Institute of Environmental Health Sciences (P.M.S., N.J.C.), Wayne State University; and Department of Physiology (B.P.J., A.R.N.), Wayne State University School of Medicine, Detroit, Michigan
| | - Robert P Lisak
- Departments of Neurology and Biochemistry, Immunology and Microbiology (J.A.B., R.P.L.), Wayne State University School of Medicine; Department of Neurology (L.N.), Wayne State University School of Medicine, Detroit, Michigan; Department of Neurology and Center for Neuroinflammation and Experimental Therapeutics (H.T., A.B.-O.), Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Neurology (H.T., A.B.-O.), McGill University, Montreal Neurological Institute, Montreal, Quebec, Canada; Institute of Environmental Health Sciences (P.M.S., N.J.C.), Wayne State University; and Department of Physiology (B.P.J., A.R.N.), Wayne State University School of Medicine, Detroit, Michigan
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Naik AR, Pernal S, Lewis KT, Wu Y, Wu H, Carruthers NJ, Stemmer PM, Jena BP. Human Skeletal Muscle Cells on Engineered 3D Platform Express Key Growth and Developmental Proteins. ACS Biomater Sci Eng 2019; 5:970-976. [PMID: 33405788 DOI: 10.1021/acsbiomaterials.8b01338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Current approaches in regenerative medicine to develop human skeletal muscle replicating native tissue for engrafts and high-throughput drug screening and gene therapy are still in their infancy and have not proven to recapitulate the behavior and regulatory processes present in endogenous skeletal muscle tissue. This stems at least in part from the lack of a comprehensive understanding of the emergent properties of in vitro skeletal muscle growth and development. To address this gap in our current knowledge, we have developed a stretchable micropatterned 3D human skeletal muscle platform that recapitulates organized and parallel growth of muscle cells and fibers as opposed to the randomly oriented cells growth on a 2D glass surface. Mass spectrometry of the muscle cells growing on the 3D platform express key myogenic proteins such as myoferlin for myoblast fusion required in the formation of muscle tissue, and proteins involved in mitochondrial health and biogenesis, in contrast to cells growing on 2D glass surface. These results demonstrate that the engineered human muscle cells grown on the 3D platform holds great promise to further establish the emergent properties of in vitro skeletal muscle growth and development for a wide range of biomedical applications.
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Affiliation(s)
| | | | | | - Yaobin Wu
- Department of Chemistry, Hong Kong University of Science & Technology, Hong Kong, China
| | - Hongkai Wu
- Department of Chemistry, Hong Kong University of Science & Technology, Hong Kong, China
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Abstract
We have performed deep proteomic profiling down to as few as 9 Panc-1 cells using sample fractionation, TMT multiplexing, and a carrier/reference strategy. Off line fractionation of the TMT-labeled sample pooled with TMT-labeled carrier Panc-1 whole cell proteome was achieved using alkaline reversed phase spin columns. The fractionation in conjunction with the carrier/reference (C/R) proteome allowed us to detect 47 414 unique peptides derived from 6261 proteins, which provided a sufficient coverage to search for single amino acid variants (SAAVs) related to cancer. This high sample coverage is essential in order to detect a significant number of SAAVs. In order to verify genuine SAAVs versus false SAAVs, we used the SAVControl pipeline and found a total of 79 SAAVs from the 9-cell Panc-1 sample and 174 SAAVs from the 5000-cell Panc-1 C/R proteome. The SAAVs as sorted into high confidence and low confidence SAAVs were checked manually. All the high confidence SAAVs were found to be genuine SAAVs, while half of the low confidence SAAVs were found to be false SAAVs mainly related to PTMs. We identified several cancer-related SAAVs including KRAS, which is an important oncoprotein in pancreatic cancer. In addition, we were able to detect sites involved in loss or gain of glycosylation due to the enhanced coverage available in these experiments where we can detect both sites of loss and gain of glycosylation.
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Affiliation(s)
- Zhijing Tan
- Department of Surgery , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Xinpei Yi
- NCMIS, RCSDS, Academy of Mathematics and Systems Science , Chinese Academy of Sciences , Beijing 100190 , China.,School of Mathematical Sciences , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Nicholas J Carruthers
- Institute of Environmental Health Sciences , Wayne State University , Detroit , Michigan 48202 , United States
| | - Paul M Stemmer
- Institute of Environmental Health Sciences , Wayne State University , Detroit , Michigan 48202 , United States
| | - David M Lubman
- Department of Surgery , University of Michigan , Ann Arbor , Michigan 48109 , United States
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Li Y, Maleki M, Carruthers NJ, Stemmer PM, Ngom A, Rueda L. The predictive performance of short-linear motif features in the prediction of calmodulin-binding proteins. BMC Bioinformatics 2018; 19:410. [PMID: 30453876 PMCID: PMC6245490 DOI: 10.1186/s12859-018-2378-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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] [Indexed: 04/21/2023] Open
Abstract
Background The prediction of calmodulin-binding (CaM-binding) proteins plays a very important role in the fields of biology and biochemistry, because the calmodulin protein binds and regulates a multitude of protein targets affecting different cellular processes. Computational methods that can accurately identify CaM-binding proteins and CaM-binding domains would accelerate research in calcium signaling and calmodulin function. Short-linear motifs (SLiMs), on the other hand, have been effectively used as features for analyzing protein-protein interactions, though their properties have not been utilized in the prediction of CaM-binding proteins. Results We propose a new method for the prediction of CaM-binding proteins based on both the total and average scores of known and new SLiMs in protein sequences using a new scoring method called sliding window scoring (SWS) as features for the prediction module. A dataset of 194 manually curated human CaM-binding proteins and 193 mitochondrial proteins have been obtained and used for testing the proposed model. The motif generation tool, Multiple EM for Motif Elucidation (MEME), has been used to obtain new motifs from each of the positive and negative datasets individually (the SM approach) and from the combined negative and positive datasets (the CM approach). Moreover, the wrapper criterion with random forest for feature selection (FS) has been applied followed by classification using different algorithms such as k-nearest neighbors (k-NN), support vector machines (SVM), naive Bayes (NB) and random forest (RF). Conclusions Our proposed method shows very good prediction results and demonstrates how information contained in SLiMs is highly relevant in predicting CaM-binding proteins. Further, three new CaM-binding motifs have been computationally selected and biologically validated in this study, and which can be used for predicting CaM-binding proteins. Electronic supplementary material The online version of this article (10.1186/s12859-018-2378-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yixun Li
- School of Computer Science, University of Windsor, Windsor, Ontario, Canada
| | - Mina Maleki
- School of Computer Science, University of Windsor, Windsor, Ontario, Canada
| | | | - Paul M Stemmer
- Inst. of Env. Health Sci., Wayne State University, Detroit, MI, USA
| | - Alioune Ngom
- School of Computer Science, University of Windsor, Windsor, Ontario, Canada
| | - Luis Rueda
- School of Computer Science, University of Windsor, Windsor, Ontario, Canada.
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31
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Caruso JA, Carruthers NJ, Thibodeau B, Geddes TJ, Dombkowski AA, Stemmer PM. Global Signaling Profiling in a Human Model of Tumorigenic Progression Indicates a Role for Alternative RNA Splicing in Cellular Reprogramming. Int J Mol Sci 2018; 19:ijms19102847. [PMID: 30241319 PMCID: PMC6213538 DOI: 10.3390/ijms19102847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 12/13/2022] Open
Abstract
Intracellular signaling is controlled to a large extent by the phosphorylation status of proteins. To determine how human breast cells can be reprogrammed during tumorigenic progression, we profiled cell lines in the MCF10A lineage by phosphoproteomic analyses. A large cluster of proteins involved in RNA splicing were hypophosphorylated as cells progressed to a hyperplastic state, and then hyperphosphorylated after progression to a fully metastatic phenotype. A comprehensive transcriptomic approach was used to determine whether alterations in splicing factor phosphorylation status would be reflected in changes in mRNA splicing. Results indicated that the degree of mRNA splicing trended with the degree of tumorigenicity of the 4 cell lines tested. That is, highly metastatic cell cultures had the greatest number of genes with splice variants, and these genes had greater fluctuations in expression intensities. Genes with high splicing indices were mapped against gene ontology terms to determine whether they have known roles in cancer. This group showed highly significant associations for angiogenesis, cytokine-mediated signaling, cell migration, programmed cell death and epithelial cell differentiation. In summary, data from global profiling of a human model of breast cancer development suggest that therapeutics should be developed which target signaling pathways that regulate RNA splicing.
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Affiliation(s)
- Joseph A Caruso
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA.
| | - Nicholas J Carruthers
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA.
| | - Bryan Thibodeau
- Beaumont BioBank and Molecular Core Laboratory, Royal Oak, MI 48073, USA.
| | - Timothy J Geddes
- Beaumont BioBank and Molecular Core Laboratory, Royal Oak, MI 48073, USA.
| | - Alan A Dombkowski
- Department of Pediatrics, Wayne State University, Detroit, MI 48201, USA.
| | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA.
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Abstract
Petroleum coke (PC) is a coal-like product that is produced during the refinement of crude oil and bituminous sand. Fugitive dust from open storage of PC in urban areas is a potential human health concern. Animal inhalation studies suggest that PC leads to an adverse pulmonary histopathology, including areas of fibrosis and chronic inflammation; however, little is known about its impact on human health. In order to identify biomarkers and cellular pathways that are associated with exposure, we performed two-dimensional liquid chromatography-mass spectrometric analyses on secreted proteins from two human lung culture models. A total of 2795 proteins were identified and relatively quantified from an immortalized cell line and 2406 proteins from primary cultures that were either mock treated or exposed to particulate matter with a diameter of 2.5-10 μm PC or filtered urban air particulates for 16 h. Pathway analysis on secretomes from primary lung cultures indicated that PC exposure suppressed the secretion of proteins involved in the organization of the extracellular matrix and epithelial differentiation. Because these cellular processes could facilitate fibrosis, we performed chronic 12-day exposure studies on three-dimensional human lung cultures consisting of epithelia and stromal fibroblasts. Relative to mock-treated cells, matrix metallopeptidase 9 levels in the conditioned media were lower by 4 days postexposure and remained suppressed for the duration of the experiment. Immunocytochemical staining of collagen III, a marker associated with fibrosis, showed increased accumulation in the epithelial layer and at the air-liquid interface.
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Affiliation(s)
- J A Caruso
- 1 Proteomics Core Facility, Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - P M Stemmer
- 2 Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
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Carruthers NJ, Rosenspire AJ, Caruso JA, Stemmer PM. Low level Hg 2+ exposure modulates the B-cell cytoskeletal phosphoproteome. J Proteomics 2017; 173:107-114. [PMID: 29199152 DOI: 10.1016/j.jprot.2017.11.026] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/31/2017] [Accepted: 11/28/2017] [Indexed: 10/18/2022]
Abstract
Exposure of Wehi-231 B-cells to Hg2+ for 5min resulted in concentration dependent changes in protein phosphorylations. Phosphorylation was quantified using mass spectrometry to analyze TiO2 and anti-pTyr antibody selected phosphopeptides from Wehi-231 digests. The most frequent and largest amplitude responses to Hg2+ exposure were increased phosphorylation although a decrease was observed for 1% of phosphoproteins detected in the untreated cells. A subset of proteins responded with an increase in phosphorylation to Hg2+ exposure at low micromolar concentrations. The majority of proteins required Hg2+ over 20μM in order to increase phosphorylation. Ser/Thr phosphorylations are prominent in the cytoskeletal organization and the GTPase signaling systems and these systems are notable as the primary ones responding to the lowest concentrations of Hg2+. Systems that required higher concentrations of Hg2+ to increase phosphorylation included immune receptor signaling. The proteins for which an increase in phosphorylation occurred at Hg2+ above 20μM have a higher proportion of pTyr sites. Anti Ig stimulation of Wehi-231 cells confirmed that cytoskeletal protein phosphorylation and GTPase signaling are modulated in physiologically relevant B-cell receptor activation. Candidate kinases that respond to Hg2+ exposure at the low μM concentrations include MAP Kinase 1, CaM Kinase II delta and PAK2. SIGNIFICANCE Mercury (Hg) is a wide spread environmental toxicant. Epidemiological and laboratory studies suggest that exposure to environmental Hg at current levels, which have been perceived to be non-toxic, may contribute to immune system dysfunction and autoimmune disease in humans and animals respectively. While we have previously shown that exposure of B lymphocytes to low levels of mercury interferes with B-cell receptor signaling mediated by post transcriptional phosphorylation events, overall the mechanism that is responsible for increased autoimmunity in mercury exposed human or animal populations is not well understood. The current study evaluated the dose dependent actions of mercury to change phosphorylation in the Wehi-231 cell line, an immature B-cell model in which actions of mercury on development of cell function can be evaluated. The study identified the cytoskeletal proteins as the most sensitive to modulation by mercury with changes in Ser/Thr phosphorylation being observed at the lowest concentrations of mercury. These findings indicate that the actions of mercury on B-cell immune function and development are at least in part likely mediated through changes in cytoskeletal protein phosphorylation.
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Affiliation(s)
- Nicholas J Carruthers
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - Allen J Rosenspire
- Department of Immunology and Microbiology, Wayne State University, Detroit, MI, USA
| | - Joseph A Caruso
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA.
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Carruthers NJ, Stemmer PM, Chen B, Valeriote F, Gao X, Guatam SC, Shaw J. Phosphoproteome and transcription factor activity profiling identify actions of the anti-inflammatory agent UTL-5g in LPS stimulated RAW 264.7 cells including disrupting actin remodeling and STAT-3 activation. Eur J Pharmacol 2017; 811:66-73. [PMID: 28576409 PMCID: PMC5581996 DOI: 10.1016/j.ejphar.2017.05.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 08/27/2016] [Revised: 05/24/2017] [Accepted: 05/29/2017] [Indexed: 11/25/2022]
Abstract
UTL-5g is a novel small-molecule TNF-alpha modulator. It reduces cisplatin-induced side effects by protecting kidney, liver, and platelets, thereby increasing tolerance for cisplatin. UTL-5g also reduces radiation-induced acute liver toxicity. The mechanism of action for UTL-5g is not clear at the present time. A phosphoproteomic analysis to a depth of 4943 phosphopeptides and a luminescence-based transcription factor activity assay were used to provide complementary analyses of signaling events that were disrupted by UTL-5g in RAW 264.7 cells. Transcriptional activity downstream of the interferon gamma, IL-6, type 1 Interferon, TGF-β, PKC/Ca2+ and the glucocorticoid receptor pathways were disrupted by UTL-5g. Phosphoproteomic analysis indicated that hyperphosphorylation of proteins involved in actin remodeling was suppressed by UTL-5g (gene set analysis, FDR < 1%) as was phosphorylation of Stat3, consistent with the IL-6 results in the transcription factor assay. Neither analysis indicated that LPS-induced activation of the NF-kB, cAMP/PKA and JNK signaling pathways were affected by UTL-5g. This global characterization of UTL-5g activity in a macrophage cell line discovered that it disrupts selected aspects of LPS signaling including Stat3 activation and actin remodeling providing new insight on how UTL-5g acts to reduce cisplatin-induced side effects.
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Affiliation(s)
- Nicholas J Carruthers
- Wayne State University, Institute of Environmental Health Sciences, 540 East Canfield Ave., Room 2105, Detroit, MI 48202, United States.
| | - Paul M Stemmer
- Wayne State University, Institute of Environmental Health Sciences, 540 East Canfield Ave., Room 2105, Detroit, MI 48202, United States.
| | - Ben Chen
- 21st Century Therapeutics, Inc., 440 Burroughs, Suite 447, Detroit, MI 48202, United States.
| | - Frederick Valeriote
- Henry Ford Health System, Internal Medicine, 440 Burroughs, Suite 415, Detroit, MI 48202, United States.
| | - Xiaohua Gao
- Henry Ford Health System, Department of Surgery, One Ford Place, Oncology Research Laboratory, 4D, Detroit, MI 48202, United States.
| | - Subhash C Guatam
- Henry Ford Health System, Department of Surgery, One Ford Place, Oncology Research Laboratory, 4D, Detroit, MI 48202, United States.
| | - Jiajiu Shaw
- 21st Century Therapeutics, Inc., 440 Burroughs, Suite 447, Detroit, MI 48202, United States; Henry Ford Health System, Internal Medicine, 440 Burroughs, Suite 415, Detroit, MI 48202, United States.
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35
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Caruso JA, Carruthers N, Shin N, Gill R, Stemmer PM, Rosenspire A. Mercury alters endogenous phosphorylation profiles of SYK in murine B cells. BMC Immunol 2017; 18:37. [PMID: 28716125 PMCID: PMC5514489 DOI: 10.1186/s12865-017-0221-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/07/2017] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Epidemiological evidence and animal models suggest that exposure to low and non-neurotoxic concentrations of mercury may contribute to idiosyncratic autoimmune disease. Since defects in function and signaling in B cells are often associated with autoimmunity, we investigated whether mercury exposure might alter B cell responsiveness to self-antigens by interfering with B cell receptor (BCR) signal transduction. In this study we determined the effects of mercury on the protein tyrosine kinase SYK, a critical protein involved in regulation of the BCR signaling pathway. METHODS Phosphorylation sites of murine SYK were mapped before and after treatment of WEHI cell cultures with mercury, or with anti-IgM antibody (positive control) or pervanadate (a potent phosphatase inhibitor). Phosphopeptides were enriched by either titanium dioxide chromatography or anti-phosphotyrosine immunoaffinity, and analyzed by liquid chromatography-mass spectrometry. Select SYK phosphosite cluster regions were profiled for responsiveness to treatments using multiple reaction monitoring (MRM) methodology. RESULTS A total of 23 phosphosites were identified with high probability in endogenous SYK, including 19 tyrosine and 4 serine residues. For 10 of these sites phosphorylation levels were increased following BCR activation. Using MRM to profile changes in phosphorylation status we found that 4 cluster regions, encompassing 8 phosphosites, were activated by mercury and differentially responsive to all 3 treatments. Phosphorylation of tyrosine-342 and -346 residues were most sensitive to mercury exposure. This cluster is known to propagate normal BCR signal transduction by recruiting adaptor proteins such as PLC-γ and Vav-1 to SYK during formation of the BCR signalosome. CONCLUSIONS Our data shows that mercury alters the phosphorylation status of SYK on tyrosine sites known to have a role in promoting BCR signals. Considering the importance of SYK in the BCR signaling pathway, these data suggest that mercury can alter BCR signaling in B cells, which might affect B cell responsiveness to self-antigen and have implications with respect to autoimmunity and autoimmune disease.
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Affiliation(s)
- Joseph A Caruso
- Institute of Environmental Health Sciences, Center for Urban Responses to Environmental Stressors (CURES), Wayne State University, Detroit, MI, 48201, USA.
| | - Nicholas Carruthers
- Institute of Environmental Health Sciences, Center for Urban Responses to Environmental Stressors (CURES), Wayne State University, Detroit, MI, 48201, USA
| | - Namhee Shin
- Institute of Environmental Health Sciences, Center for Urban Responses to Environmental Stressors (CURES), Wayne State University, Detroit, MI, 48201, USA
| | - Randal Gill
- Department of Immunology and Microbiology, Center for Urban Responses to Environmental Stressors (CURES), Wayne State University, Detroit, MI, 48201, USA
| | - Paul M Stemmer
- Institute of Environmental Health Sciences, Center for Urban Responses to Environmental Stressors (CURES), Wayne State University, Detroit, MI, 48201, USA
| | - Allen Rosenspire
- Department of Immunology and Microbiology, Center for Urban Responses to Environmental Stressors (CURES), Wayne State University, Detroit, MI, 48201, USA
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Abstract
In the past 50 years, isolated blood platelets have had restricted use in wound healing, cancer therapy, and organ and tissue transplant, to name a few. The major obstacle for its unrestricted use has been, among others, the presence of ultrahigh concentrations of growth factors and the presence of both pro-angiogenic and anti-angiogenic proteins. To overcome this problem requires the isolation and separation of the membrane bound secretory vesicles containing the different factors. In the current study, high-resolution imaging of isolated secretory vesicles from human platelets using atomic force microscopy (AFM) and mass spectrometry enabled characterization of the remaining vesicles size and composition following their immunoseparation. The remaining vesicles obtained following osmotic lysis, when subjected to immunoseparation employing antibody to different vesicle-associated membrane proteins (VAMPs), demonstrate for the first time that VAMP-3-, VAMP-7-, and VAMP-8-specific vesicles each possesses distinct size range and composition. These results provide a window into our understanding of the heterogeneous population of vesicles in human platelets and their stability following both physical manipulation using AFM and osmotic lysis of the platelet. This study further provides a platform for isolation and the detailed characterization of platelet granules, with promise for their future use in therapy. Additionally, results from the study demonstrate that secretory vesicles of different size found in cells reflect their unique and specialized composition and function.
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Affiliation(s)
- Bhanu P Jena
- Department of Physiology, School of Medicine, ‡Department of Chemical Engineering & Materials Science, College of Engineering, and §Institute of Environment Health Sciences, Wayne State University , Detroit, Michigan 48201, United States
| | - Paul M Stemmer
- Department of Physiology, School of Medicine, ‡Department of Chemical Engineering & Materials Science, College of Engineering, and §Institute of Environment Health Sciences, Wayne State University , Detroit, Michigan 48201, United States
| | - Sunxi Wang
- Department of Physiology, School of Medicine, ‡Department of Chemical Engineering & Materials Science, College of Engineering, and §Institute of Environment Health Sciences, Wayne State University , Detroit, Michigan 48201, United States
| | - Guangzhao Mao
- Department of Physiology, School of Medicine, ‡Department of Chemical Engineering & Materials Science, College of Engineering, and §Institute of Environment Health Sciences, Wayne State University , Detroit, Michigan 48201, United States
| | - Kenneth T Lewis
- Department of Physiology, School of Medicine, ‡Department of Chemical Engineering & Materials Science, College of Engineering, and §Institute of Environment Health Sciences, Wayne State University , Detroit, Michigan 48201, United States
| | - Daniel A Walz
- Department of Physiology, School of Medicine, ‡Department of Chemical Engineering & Materials Science, College of Engineering, and §Institute of Environment Health Sciences, Wayne State University , Detroit, Michigan 48201, United States
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37
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Li Y, Maleki M, Carruthers NJ, Rueda L, Stemmer PM, Ngom A. Prediction of Calmodulin-Binding Proteins Using Short-Linear Motifs. Bioinformatics and Biomedical Engineering 2017. [DOI: 10.1007/978-3-319-56154-7_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Wang W, Lu Y, Stemmer PM, Zhang X, Bi Y, Yi Z, Chen F. The proteomic investigation reveals interaction of mdig protein with the machinery of DNA double-strand break repair. Oncotarget 2016; 6:28269-81. [PMID: 26293673 PMCID: PMC4695059 DOI: 10.18632/oncotarget.4961] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/03/2015] [Indexed: 12/28/2022] Open
Abstract
To investigate how mineral dust-induced gene (mdig, also named as mina53, MINA, or NO52) promotes carcinogenesis through inducing active chromatin, we performed proteomics analyses for the interacting proteins that were co-immunoprecipitated by anti-mdig antibody from either the lung cancer cell line A549 cells or the human bronchial epithelial cell line BEAS-2B cells. On SDS-PAGE gels, three to five unique protein bands were consistently observed in the complexes pulled-down by mdig antibody, but not the control IgG. In addition to the mdig protein, several DNA repair or chromatin binding proteins, including XRCC5, XRCC6, RBBP4, CBX8, PRMT5, and TDRD, were identified in the complexes by the proteomics analyses using both Orbitrap Fusion and Orbitrap XL nanoESI-MS/MS in four independent experiments. The interaction of mdig with some of these proteins was further validated by co-immunoprecipitation using antibodies against mdig and its partner proteins, respectively. These data, thus, provide evidence suggesting that mdig accomplishes its functions on chromatin, DNA repair and cell growth through interacting with the partner proteins.
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Affiliation(s)
- Wei Wang
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA.,School of Public Health, Wuhan University, Wuhan, Hubei, P.R. China
| | - Yongju Lu
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA
| | - Paul M Stemmer
- The Proteomics Core and Institute of Environmental Health Sciences, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Xiangmin Zhang
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA
| | - Yongyi Bi
- School of Public Health, Wuhan University, Wuhan, Hubei, P.R. China
| | - Zhengping Yi
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA
| | - Fei Chen
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA
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39
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Carruthers NJ, Parker GC, Gratsch T, Caruso JA, Stemmer PM. Protein Mobility Shifts Contribute to Gel Electrophoresis Liquid Chromatography Analysis. J Biomol Tech 2016; 26:103-12. [PMID: 26229520 DOI: 10.7171/jbt.15-2603-003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Profiling of cellular and subcellular proteomes by liquid chromatography with tandem mass spectrometry (MS) after fractionation by SDS-PAGE is referred to as GeLC (gel electrophoresis liquid chromatography)-MS. The GeLC approach decreases complexity within individual MS analyses by size fractionation with SDS-PAGE. SDS-PAGE is considered an excellent fractionation technique for intact proteins because of good resolution for proteins of all sizes, isoelectric points, and hydrophobicities. Additional information derived from the mobility of the intact proteins is available after an SDS-PAGE fractionation, but that information is usually not incorporated into the proteomic analysis. Any chemical or proteolytic modification of a protein that changes the mobility of that protein in the gel can be detected. The ability of SDS-PAGE to resolve proteins with chemical modifications has not been widely utilized within profiling experiments. In this work, we examined the ability of the GeLC-MS approach to help identify proteins that were modified after a small hairpin RNA-dependent knockdown in an experiment using stable isotope labeling by amino acids in cell culture-based quantitation.
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Affiliation(s)
- Nicholas J Carruthers
- 1 Institute of Environmental Health Sciences and 2 Carman and Ann Adam Department of Pediatrics, Wayne State University, Detroit, Michigan 48201, USA
| | - Graham C Parker
- 1 Institute of Environmental Health Sciences and 2 Carman and Ann Adam Department of Pediatrics, Wayne State University, Detroit, Michigan 48201, USA
| | - Theresa Gratsch
- 1 Institute of Environmental Health Sciences and 2 Carman and Ann Adam Department of Pediatrics, Wayne State University, Detroit, Michigan 48201, USA
| | - Joseph A Caruso
- 1 Institute of Environmental Health Sciences and 2 Carman and Ann Adam Department of Pediatrics, Wayne State University, Detroit, Michigan 48201, USA
| | - Paul M Stemmer
- 1 Institute of Environmental Health Sciences and 2 Carman and Ann Adam Department of Pediatrics, Wayne State University, Detroit, Michigan 48201, USA
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40
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Parker GC, Carruthers NJ, Gratsch T, Caruso JA, Stemmer PM. Proteomic profile of embryonic stem cells with low survival motor neuron protein is consistent with developmental dysfunction. J Neural Transm (Vienna) 2016; 124:13-23. [PMID: 27145767 DOI: 10.1007/s00702-016-1520-y] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 02/01/2016] [Indexed: 12/22/2022]
Abstract
Spinal muscular atrophy is an autosomal recessive motor neuron disease caused by a genetic defect carried by as many as one in 75 people. Unlike most neurological disorders, we know exactly what the genetic basis is of the disorder, but in spite of this, have little understanding of why the low levels of one protein, survival motor neuron protein, results in the specific progressive die back of only one cell type in the body, the motor neuron. Given the fact that all cells in the body of a patient with spinal muscular atrophy share the same low abundance of the protein throughout development, an appropriate approach is to ask how lower levels of survival motor neuron protein affects the proteome of embryonic stem cells prior to development. Convergent biostatistical analyses of a discovery proteomic analysis of these cells provide results that are consistent with the pathomechanistic fate of the developed motor neuron.
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Affiliation(s)
- Graham C Parker
- Carman and Ann Adam Department of Pediatrics, Wayne State University, Detroit, USA.
- iBio, 6135 Woodward Ave., Suite 2128 CURES H208, Detroit, MI, 48202, USA.
| | - Nicholas J Carruthers
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - Theresa Gratsch
- Carman and Ann Adam Department of Pediatrics, Wayne State University, Detroit, USA
| | - Joseph A Caruso
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
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41
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Li L, Lu Y, Stemmer PM, Chen F. Filamin A phosphorylation by Akt promotes cell migration in response to arsenic. Oncotarget 2016; 6:12009-19. [PMID: 25944616 PMCID: PMC4494919 DOI: 10.18632/oncotarget.3617] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/14/2015] [Indexed: 12/19/2022] Open
Abstract
We had previously reported that trivalent arsenic (As3+), a well-known environmental carcinogen, induces phosphorylation of several putative Akt substrates. In the present report, we characterized one of these substrates by immunoprecipitation and proteomics analysis. The results indicate that a cytoskeleton remodeling protein, filamin A, with a molecular weight around 280 kDa, is phosphorylated by Akt in HEK-293 cells treated with As3+, which was also confirmed in human bronchial epithelial cell line, BEAS-2B cells. Additional biochemical and biological studies revealed that serine 2152 (S2152) of filamin A is phosphorylated by activated Akt in the cells treated with As3+. To further confirm the importance of Akt-dependent filamin A S2152 phosphorylation in As3+-induced cell migration, we over-expressed either wild type filamin A or the mutated filamin A in which the S2152 was substituted with alanine (S2152A). The capability of cell migration was reduced significantly in the cells expressing the mutated filamin A (S2152A). Clinically, we found that increased expression of filamin A predicts poorer overall survival of the lung cancer patients with adenocarcinoma. Thus, these data suggest that Akt dependent filamin A phosphorylation is one of the key events in mediating As3+-induced carcinogenesis. Antagonizing Akt signaling can ameliorate As3+-induced filamin A phosphorylation and cell migration, which may serve as a molecular targeting strategy for malignancies associated with environmental As3+ exposure.
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Affiliation(s)
- Lingzhi Li
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Yongju Lu
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Paul M Stemmer
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA.,The Proteomics Core and Institute of Environmental Health Sciences, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Fei Chen
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
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42
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Trimpin S, Thawoos S, Foley CD, Woodall DW, Li J, Inutan ED, Stemmer PM. Rapid high mass resolution mass spectrometry using matrix-assisted ionization. Methods 2016; 104:63-8. [PMID: 26835606 DOI: 10.1016/j.ymeth.2016.01.019] [Citation(s) in RCA: 16] [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: 12/08/2015] [Accepted: 01/29/2016] [Indexed: 11/18/2022] Open
Abstract
Matrix-assisted ionization (MAI) is demonstrated to be a robust and sensitive analytical method capable of analyzing proteins such as cholera toxin B-subunit and pertussis toxin mutant from conditions containing relatively high amounts of inorganic salts, buffers, and preservatives without the need for prior sample clean-up or concentration. By circumventing some of the sample preparation steps, MAI simplifies and accelerates the analytical workflow for biological samples in complex media. The benefits of multiply charged ions characteristic of electrospray ionization (ESI) and the robustness of matrix-assisted laser desorption/ionization (MALDI) can be obtained from a single method, making it well suited for analysis of proteins and other biomolecules at ultra-high resolution as demonstrated on an Orbitrap Fusion where protein subunits were resolved for which MALDI-time-of-flight failed. MAI results are compared with those obtained with ESI, MALDI, and laserspray ionization methods and fundamental commonalities discussed.
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Affiliation(s)
- Sarah Trimpin
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA; Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, MI 48202, USA.
| | - Shameemah Thawoos
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Casey D Foley
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Daniel W Woodall
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Jing Li
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Ellen D Inutan
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Paul M Stemmer
- Proteomics Core Facility, Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA
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43
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Lee JS, Wu Y, Schnepp P, Fang J, Zhang X, Karnovsky A, Woods J, Stemmer PM, Liu M, Zhang K, Chen X. Proteomics analysis of rough endoplasmic reticulum in pancreatic beta cells. Proteomics 2016; 15:1508-11. [PMID: 25546123 DOI: 10.1002/pmic.201400345] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 07/22/2014] [Revised: 11/02/2014] [Accepted: 12/18/2014] [Indexed: 12/20/2022]
Abstract
Pancreatic beta cells have well-developed ER to accommodate for the massive production and secretion of insulin. ER homeostasis is vital for normal beta cell function. Perturbation of ER homeostasis contributes to beta cell dysfunction in both type 1 and type 2 diabetes. To systematically identify the molecular machinery responsible for proinsulin biogenesis and maintenance of beta cell ER homeostasis, a widely used mouse pancreatic beta cell line, MIN6 cell was used to purify rough ER. Two different purification schemes were utilized. In each experiment, the ER pellets were solubilized and analyzed by 1D SDS-PAGE coupled with HPLC-MS/MS. A total of 1467 proteins were identified in three experiments with ≥95% confidence, among which 1117 proteins were found in at least two separate experiments and 737 proteins found in all three experiments. GO analysis revealed a comprehensive profile of known and novel players responsible for proinsulin biogenesis and ER homeostasis. Further bioinformatics analysis also identified potential beta cell specific ER proteins as well as ER proteins present in the risk genetic loci of type 2 diabetes. This dataset defines a molecular environment in the ER for proinsulin synthesis, folding and export and laid a solid foundation for further characterizations of altered ER homeostasis under diabetes-causing conditions. All MS data have been deposited in the ProteomeXchange with identifier PXD001081 (http://proteomecentral.proteomexchange.org/dataset/PXD001081).
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Affiliation(s)
- Jin-sook Lee
- Department of Physiology, Wayne State University, Detroit, MI, USA
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44
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Dombkowski AA, Batista CE, Cukovic D, Carruthers NJ, Ranganathan R, Shukla U, Stemmer PM, Chugani HT, Chugani DC. Cortical Tubers: Windows into Dysregulation of Epilepsy Risk and Synaptic Signaling Genes by MicroRNAs. Cereb Cortex 2014; 26:1059-71. [PMID: 25452577 DOI: 10.1093/cercor/bhu276] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is a multisystem genetic disorder caused by mutations in the TSC1 and TSC2 genes. Over 80% of TSC patients are affected by epilepsy, but the molecular events contributing to seizures in TSC are not well understood. Recent reports have demonstrated that the brain is enriched with microRNA activity, and they are critical in neural development and function. However, little is known about the role of microRNAs in TSC. Here, we report the characterization of aberrant microRNA activity in cortical tubers resected from 5 TSC patients surgically treated for medically intractable epilepsy. By comparing epileptogenic tubers with adjacent nontuber tissue, we identified a set of 4 coordinately overexpressed microRNAs (miRs 23a, 34a, 34b*, 532-5p). We used quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic profiling to investigate the combined effect of the 4 microRNAs on target proteins. The proportion of repressed proteins among the predicted targets was significantly greater than in the overall proteome and was highly enriched for proteins involved in synaptic signal transmission. Among the combinatorial targets were TSC1, coding for the protein hamartin, and several epilepsy risk genes. We found decreased levels of hamartin in epileptogenic tubers and confirmed targeting of the TSC1 3' UTR by miRs-23a and 34a.
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Affiliation(s)
| | | | | | - Nicholas J Carruthers
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | | | | | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - Harry T Chugani
- Carman and Ann Adams Department of Pediatrics Department of Neurology, Wayne State University School of Medicine, Children's Hospital of Michigan, Detroit Medical Center, Detroit, MI, USA
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45
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Zhou X, Mester C, Stemmer PM, Reid GE. Oxidation-induced conformational changes in calcineurin determined by covalent labeling and tandem mass spectrometry. Biochemistry 2014; 53:6754-65. [PMID: 25286016 PMCID: PMC4222536 DOI: 10.1021/bi5009744] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [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] [Indexed: 11/29/2022]
Abstract
![]()
The Ca2+/calmodulin activated
phosphatase, calcineurin,
is inactivated by H2O2 or superoxide-induced
oxidation, both in vivo and in vitro. However, the potential for global and/or local conformation changes
occurring within calcineurin as a function of oxidative modification,
that may play a role in the inactivation process, has not been examined.
Here, the susceptibility of calcineurin methionine residues toward
H2O2-induced oxidation were determined using
a multienzyme digestion strategy coupled with capillary HPLC–electrospray
ionization mass spectrometry and tandem mass spectrometry analysis.
Then, regions within the protein complex that underwent significant
conformational perturbation upon oxidative modification were identified
by monitoring changes in the modification rates of accessible lysine
residues between native and oxidized forms of calcineurin, using an
amine-specific covalent labeling reagent, S,S′-dimethylthiobutanoylhydroxysuccinimide ester (DMBNHS),
and tandem mass spectrometry. Importantly, methionine residues found
to be highly susceptible toward oxidation, and the lysine residues
exhibiting large increases in accessibility upon oxidation, were all
located in calcineurin functional domains involved in Ca2+/CaM binding regulated calcineurin stimulation. These findings therefore
provide initial support for the novel mechanistic hypothesis that
oxidation-induced global and/or local conformational changes within
calcineurin contribute to inactivation via (i) impairing the interaction
between calcineurin A and calcineurin B, (ii) altering the low-affinity
Ca2+ binding site in calcineurin B, (iii) inhibiting calmodulin
binding to calcineurin A, and/or (iv) by altering the affinity between
the calcineurin A autoinhibitory domain and the catalytic center.
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Affiliation(s)
- Xiao Zhou
- Department of Chemistry, and §Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States
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46
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Caruthers NJ, Stemmer PM, Shin N, Dombkowski A, Caruso JA, Gill R, Rosenspire A. Mercury alters B-cell protein phosphorylation profiles. J Proteome Res 2014; 13:496-505. [PMID: 24224561 DOI: 10.1021/pr400657k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Environmental exposure to mercury is suggested to contribute to human immune dysfunction. To shed light on the mechanism, we identified changes in the phosphoproteomic profile of the WEHI-231 B cell line after intoxication with Hg(2+). These changes were compared to changes in the phosphoproteome that were induced by pervanadate or okadaic acid exposure. Both 250 μM HgCl2 and pervanadate, a known phosphotyrosine phosphatase inhibitor, caused an increase in the number of proteins identified after TiO2 affinity selection and LC-MS/MS analysis. Pervanadate treatment had a larger effect than Hg(2+) on the number of Scansite motifs that were tyrosine-phosphorylated, 17, and Ingenuity canonical signaling pathways activated, 4, with score >5.0. However, Hg(2+) had a more focused effect, primarily causing tyrosine-phosphorylation in src homology 2 domains in proteins that are in the B cell receptor signaling pathway. The finding that many of the changes induced by Hg(2+) overlap with those of pervanadate, indicates that at high concentrations Hg(2+) inhibits protein tyrosine phosphatases.
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Affiliation(s)
- Nicholas J Caruthers
- Institute of Environmental Health Sciences, ‡Department of Pediatrics, and §Department of Immunology and Microbiology, Wayne State University , Detroit, Michigan 48201, United States
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47
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Caruso JA, Stemmer PM, Dombkowski A, Caruthers NJ, Gill R, Rosenspire AJ. A systems toxicology approach identifies Lyn as a key signaling phosphoprotein modulated by mercury in a B lymphocyte cell model. Toxicol Appl Pharmacol 2014; 276:47-54. [PMID: 24440445 DOI: 10.1016/j.taap.2014.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 12/24/2013] [Accepted: 01/04/2014] [Indexed: 01/10/2023]
Abstract
Network and protein-protein interaction analyses of proteins undergoing Hg²⁺-induced phosphorylation and dephosphorylation in Hg²⁺-intoxicated mouse WEHI-231 B cells identified Lyn as the most interconnected node. Lyn is a Src family protein tyrosine kinase known to be intimately involved in the B cell receptor (BCR) signaling pathway. Under normal signaling conditions the tyrosine kinase activity of Lyn is controlled by phosphorylation, primarily of two well known canonical regulatory tyrosine sites, Y-397 and Y-508. However, Lyn has several tyrosine residues that have not yet been determined to play a major role under normal signaling conditions, but are potentially important sites for phosphorylation following mercury exposure. In order to determine how Hg²⁺ exposure modulates the phosphorylation of additional residues in Lyn, a targeted MS assay was developed. Initial mass spectrometric surveys of purified Lyn identified 7 phosphorylated tyrosine residues. A quantitative assay was developed from these results using the multiple reaction monitoring (MRM) strategy. WEHI-231 cells were treated with Hg²⁺, pervanadate (a phosphatase inhibitor), or anti-Ig antibody (to stimulate the BCR). Results from these studies showed that the phosphoproteomic profile of Lyn after exposure of the WEHI-231 cells to a low concentration of Hg²⁺ closely resembled that of anti-Ig antibody stimulation, whereas exposure to higher concentrations of Hg²⁺ led to increases in the phosphorylation of Y-193/Y-194, Y-501 and Y-508 residues. These data indicate that mercury can disrupt a key regulatory signal transduction pathway in B cells and point to phospho-Lyn as a potential biomarker for mercury exposure.
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Affiliation(s)
- Joseph A Caruso
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - Alan Dombkowski
- Department of Pediatrics, Wayne State University, Detroit, MI, USA
| | - Nicholas J Caruthers
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - Randall Gill
- Department of Immunology and Microbiology, Wayne State University, Detroit, MI, USA
| | - Allen J Rosenspire
- Department of Immunology and Microbiology, Wayne State University, Detroit, MI, USA.
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48
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Lu Y, Zhou X, Stemmer PM, Reid GE. Sulfonium ion derivatization, isobaric stable isotope labeling and data dependent CID- and ETD-MS/MS for enhanced phosphopeptide quantitation, identification and phosphorylation site characterization. J Am Soc Mass Spectrom 2012; 23:577-93. [PMID: 21952753 PMCID: PMC4228788 DOI: 10.1007/s13361-011-0190-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/03/2011] [Accepted: 06/03/2011] [Indexed: 05/12/2023]
Abstract
An amine specific peptide derivatization strategy involving the use of novel isobaric stable isotope encoded 'fixed charge' sulfonium ion reagents, coupled with an analysis strategy employing capillary HPLC, ESI-MS, and automated data dependent ion trap CID-MS/MS, -MS(3), and/or ETD-MS/MS, has been developed for the improved quantitative analysis of protein phosphorylation, and for identification and characterization of their site(s) of modification. Derivatization of 50 synthetic phosphopeptides with S,S'-dimethylthiobutanoylhydroxysuccinimide ester iodide (DMBNHS), followed by analysis using capillary HPLC-ESI-MS, yielded an average 2.5-fold increase in ionization efficiencies and a significant increase in the presence and/or abundance of higher charge state precursor ions compared to the non-derivatized phosphopeptides. Notably, 44% of the phosphopeptides (22 of 50) in their underivatized states yielded precursor ions whose maximum charge states corresponded to +2, while only 8% (4 of 50) remained at this maximum charge state following DMBNHS derivatization. Quantitative analysis was achieved by measuring the abundances of the diagnostic product ions corresponding to the neutral losses of 'light' (S(CH(3))(2)) and 'heavy' (S(CD(3))(2)) dimethylsulfide exclusively formed upon CID-MS/MS of isobaric stable isotope labeled forms of the DMBNHS derivatized phosphopeptides. Under these conditions, the phosphate group stayed intact. Access for a greater number of peptides to provide enhanced phosphopeptide sequence identification and phosphorylation site characterization was achieved via automated data-dependent CID-MS(3) or ETD-MS/MS analysis due to the formation of the higher charge state precursor ions. Importantly, improved sequence coverage was observed using ETD-MS/MS following introduction of the sulfonium ion fixed charge, but with no detrimental effects on ETD fragmentation efficiency.
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Affiliation(s)
- Yali Lu
- Department of Chemistry, Michigan State University, 229 Chemistry Building, Michigan State University, East Lansing, MI, 48824, USA
| | - Xiao Zhou
- Department of Chemistry, Michigan State University, 229 Chemistry Building, Michigan State University, East Lansing, MI, 48824, USA
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - Gavin E. Reid
- Department of Chemistry, Michigan State University, 229 Chemistry Building, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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49
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Palumbo AM, Smith SA, Kalcic CL, Dantus M, Stemmer PM, Reid GE. Tandem mass spectrometry strategies for phosphoproteome analysis. Mass Spectrom Rev 2011; 30:600-25. [PMID: 21294150 DOI: 10.1002/mas.20310] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is involved in nearly all essential biochemical pathways and the deregulation of phosphorylation events has been associated with the onset of numerous diseases. A multitude of tandem mass spectrometry (MS/MS) and multistage MS/MS (i.e., MS(n) ) strategies have been developed in recent years and have been applied toward comprehensive phosphoproteomic analysis, based on the interrogation of proteolytically derived phosphopeptides. However, the utility of each of these MS/MS and MS(n) approaches for phosphopeptide identification and characterization, including phosphorylation site localization, is critically dependant on the properties of the precursor ion (e.g., polarity and charge state), the specific ion activation method that is employed, and the underlying gas-phase ion chemistries, mechanisms and other factors that influence the gas-phase fragmentation behavior of phosphopeptide ions. This review therefore provides an overview of recent studies aimed at developing an improved understanding of these issues, and highlights the advantages and limitations of both established (e.g., CID) and newly maturing (e.g., ECD, ETD, photodissociation, etc.) yet complementary, ion activation techniques. This understanding is expected to facilitate the continued refinement of existing MS/MS strategies, and the development of novel MS/MS techniques for phosphopeptide analysis, with great promise in providing new insights into the role of protein phosphorylation on normal biological function, and in the onset and progression of disease. © 2011 Wiley Periodicals, Inc., Mass Spec Rev 30:600-625, 2011.
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Affiliation(s)
- Amanda M Palumbo
- Department of Chemistry, Michigan State University, East Lansing, USA
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50
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Lee DC, Hassan SS, Romero R, Tarca AL, Bhatti G, Gervasi MT, Caruso JA, Stemmer PM, Kim CJ, Hansen LK, Becher N, Uldbjerg N. Protein profiling underscores immunological functions of uterine cervical mucus plug in human pregnancy. J Proteomics 2011; 74:817-28. [PMID: 21362502 DOI: 10.1016/j.jprot.2011.02.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 02/18/2011] [Accepted: 02/22/2011] [Indexed: 10/18/2022]
Abstract
The cervical mucus plug (CMP) differs from the cervical secretions of non-pregnant women, and is the ultimate sealant of the uterine cavity during pregnancy. Although several studies have analyzed biochemical properties of large glycoproteins in the CMP, comprehensive information about its protein composition is yet unavailable. We hypothesized that protein profiling of the CMP could provide key clues to its physiological functions in pregnancy. For this purpose, five CMPs obtained from women in labor at term were analyzed by LC-MS/MS. Out of 291 total proteins identified, 137 were detected in two or more samples, which included S100A8, S100A9, and complement proteins (C3, C4a, C4b, C6, and C8g). Several proteins, which have not been described in the cervical mucus of non-pregnant women or in cervicovaginal fluids, such as CD81 antigen and pregnancy zone protein, were also identified. Gene ontology analysis of identified proteins showed significant enrichment of 28 biological processes such as 'activation of plasma proteins involved in acute inflammatory response' and 'positive regulation of cholesterol esterification'. We report the proteome of CMPs from pregnant women at term for the first time, and the overall findings strongly suggest an important role for the CMP in the maintenance of pregnancy and parturition.
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Affiliation(s)
- Deug-Chan Lee
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, MI, USA
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