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Macdonald JK, Clift CL, Saunders J, Zambrzycki SC, Mehta AS, Drake RR, Angel PM. Differential Protease Specificity by Collagenase as a Novel Approach to Serum Proteomics That Includes Identification of Extracellular Matrix Proteins without Enrichment. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:487-497. [PMID: 38329320 PMCID: PMC10921462 DOI: 10.1021/jasms.3c00366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/09/2024]
Abstract
Circulating extracellular matrix (ECM) proteins are serological biomarkers of interest due to their association with pathologies involving disease processes such as fibrosis and cancers. In this study, we investigate the potential for serum biomarker research using differential protease specificity (DPS), leveraging alternate protease specificity as a targeting mechanism to selectively digest circulating ECM protein serum proteins. A proof-of-concept study is presented using serum from patients with cirrhotic liver or hepatocellular carcinoma. The approach uses collagenase DPS for digestion of deglycosylated serum and liquid-chromatography-trapped ion mobility-tandem mass spectrometry (LC-TIMS-MS/MS) to enhance the detection of ECM proteins in serum. It requires no sample enrichment and minimizes the albumin average precursor intensity readout to less than 1.2%. We further demonstrate the capabilities for using the method as a high-throughput matrix-assisted laser/desorption ionization mass spectrometry (MALDI-MS) assay coupled with reference library searching. A goal is to improve the depth and breadth of biofluid proteomics for noninvasive assays.
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Affiliation(s)
- Jade K. Macdonald
- Department of Cell and Molecular
Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | | | | | - Stephen C. Zambrzycki
- Department of Cell and Molecular
Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Anand S. Mehta
- Department of Cell and Molecular
Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Richard R. Drake
- Department of Cell and Molecular
Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Peggi M. Angel
- Department of Cell and Molecular
Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, United States
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2
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Kumar Barik A, Mathew C, Sanoop PM, John RV, Adigal SS, Bhat S, Pai KM, Bhandary SV, Devasia T, Upadhya R, Kartha VB, Chidangil S. Protein profile pattern analysis: A multifarious, in vitro diagnosis technique for universal screening. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1232:123944. [PMID: 38056315 DOI: 10.1016/j.jchromb.2023.123944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
Universal health care is attracting increased attention nowadays, because of the large increase in population all over the world, and a similar increase in life expectancy, leading to an increase in the incidence of non-communicable (various cancers, coronary diseases, neurological and old-age-related diseases) and communicable diseases/pandemics like SARS-COVID 19. This has led to an immediate need for a healthcare technology that should be cost-effective and accessible to all. A technology being considered as a possible one at present is liquid biopsy, which looks for markers in readily available samples like body fluids which can be accessed non- or minimally- invasive manner. Two approaches are being tried now towards this objective. The first involves the identification of suitable, specific markers for each condition, using established methods like various Mass Spectroscopy techniques (Surface-Enhanced Laser Desorption/Ionization Mass Spectroscopy (SELDI-MS), Matrix-Assisted Laser Desorption/Ionization (MALDI-MS), etc., immunoassays (Enzyme-Linked Immunoassay (ELISA), Proximity Extension Assays, etc.) and separation methods like 2-Dimensional Polyacrylamide Gel Electrophoresis (2-D PAGE), Sodium Dodecyl-Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE), Capillary Electrophoresis (CE), etc. In the second approach, no attempt is made the identification of specific markers; rather an efficient separation method like High-Performance Liquid Chromatography/ Ultra-High-Performance Liquid Chromatography (HPLC/UPLC) is used to separate the protein markers, and a profile of the protein pattern is recorded, which is analysed by Artificial Intelligence (AI)/Machine Learning (MI) methods to derive characteristic patterns and use them for identifying the disease condition. The present report gives a summary of the current status of these two approaches and compares the two in the use of their suitability for universal healthcare.
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Affiliation(s)
- Ajaya Kumar Barik
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Clint Mathew
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Pavithran M Sanoop
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Reena V John
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Sphurti S Adigal
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Sujatha Bhat
- Division of Microbiology, Department of Basic Medical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Keerthilatha M Pai
- Department of Dental Surgery, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Gangtok, Sikkim 737102, India
| | - Sulatha V Bhandary
- Department of Ophthalmology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Tom Devasia
- Department of Cardiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Rekha Upadhya
- Department of Obstetrics and Gynecology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - V B Kartha
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Santhosh Chidangil
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.
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3
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Hou Z, Xu D, Deng N, Li Y, Yang L, Li S, Zhou H, Huang Q, Wang X. Comparative Proteomics of Mulberry Leaves at Different Developmental Stages Identify Novel Proteins Function Related to Photosynthesis. FRONTIERS IN PLANT SCIENCE 2021; 12:797631. [PMID: 35003187 PMCID: PMC8739898 DOI: 10.3389/fpls.2021.797631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Mulberry leaves at different positions are different in photosynthetic rate, nutrient substance and feeding impact to silkworms. Here, we investigated the proteomic differences of the first (L1), sixth (L6), and twentieth (L20) mulberry leaves at different stem positions (from top to the base) using a label-free quantitative proteomics approach. L1 contained less developed photosynthetic apparatus but was more active in protein synthesis. L20 has more channel proteins and oxidoreductases relative to L6. Proteins that detected in all measured leaves were classified into three groups according to their expression patterns in L1, L6, and L20. The protein group that displayed the maximum amount in L6 has the highest possibility that function related to photosynthesis. Nine function unknown proteins belong to this group were further analyzed in the light responsive expression, evolutionary tree and sub-cellular localization analysis. Based on the results, five proteins were suggested to be involved in photosynthesis. Taken together, these results reveal the molecular details of different roles of mulberry leaves at different developmental stages and contribute to the identification of five proteins that might function related to photosynthesis.
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Affiliation(s)
- Zhiwei Hou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Dashun Xu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Na Deng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Yan Li
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Luoling Yang
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Shuxuan Li
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Hong Zhou
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Qintao Huang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Xiling Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
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4
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Okai CA, Wölter M, Russ M, Koy C, Petre BA, Rath W, Pecks U, Glocker MO. Profiling of intact blood proteins by matrix-assisted laser desorption/ionization mass spectrometry without the need for freezing - Dried serum spots as future clinical tools for patient screening. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9121. [PMID: 33955049 DOI: 10.1002/rcm.9121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/30/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE To open up new ways for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS)-based patient screening, blood serum is the most preferred specimen because of its richness in patho-physiological information and due to ease of collection. To overcome deleterious freeze/thaw cycles and to reduce high costs for shipping and storage, we sought to develop a procedure which enables MALDI-MS protein profiling of blood serum proteins without the need for serum freezing. METHODS Blood sera from patients/donors were divided into portions which after pre-incubation were fast frozen. Thawed aliquots were deposited on filter paper discs and air-dried at room temperature. Intact serum proteins were eluted with acid-labile detergent-containing solutions and were desalted by employing a reversed-phase bead system. Purified protein solutions were screened by MALDI-MS using standardized instrument settings. RESULTS MALDI mass spectra from protein solutions which were eluted from filter paper discs and desalted showed on average 25 strong ion signals (mass range m/z 6000 to 10,000) from intact serum proteins (apolipoproteins, complement proteins, transthyretin and hemoglobin) and from proteolytic processing products. Semi-quantitative analysis of three ion pairs: m/z 6433 and 6631, m/z 8205 and 8916, as well as m/z 9275 and 9422, indicated that the mass spectra from either pre-incubated fast-frozen serum or pre-incubated dried serum spot eluted serum contained the same information on protein composition. CONCLUSIONS A workflow that avoids the conventional cold-chain and yet enables the investigation of intact serum proteins and/or serum proteolysis products by MALDI-MS profiling was developed. The presented protocol tremendously broadens the clinical application of MALDI-MS and simultaneously allows a reduction in the costs for storage and shipping of serum samples. This will pave the way for clinical screening of patients also in areas with limited access to health care systems, and/or specialized laboratories.
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Affiliation(s)
- Charles A Okai
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, Rostock, 18057, Germany
| | - Manja Wölter
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, Rostock, 18057, Germany
- Department of Obstetrics and Gynecology, Medical Faculty, University of Rostock, Clinic Südstadt, Rostock, 18059, Germany
| | - Manuela Russ
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, Rostock, 18057, Germany
| | - Cornelia Koy
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, Rostock, 18057, Germany
| | - Brindusa A Petre
- Department of Chemistry, Alexandru Ioan Cuza University, Bd. Carol I, No.11, Iasi, 700506, Romania
- Transcend Research Center, Regional Institute of Oncology, General Henri Mathias, No.2-4, Iasi, 700483, Romania
| | - Werner Rath
- Department of Obstetrics and Gynecology, Medical Faculty, RWTH Aachen University, Aachen, 52062, Germany
| | - Ulrich Pecks
- Department of Obstetrics and Gynecology, Medical Faculty, University of Schleswig-Holstein, Campus Kiel, Arnold-Heller-Straße 3, Kiel, 24105, Germany
| | - Michael O Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, Rostock, 18057, Germany
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5
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Petito V, Greco V, Laterza L, Graziani C, Fanali C, Lucchetti D, Barbaro MR, Bugli F, Pieroni L, Lopetuso LR, Sgambato A, Sanguinetti M, Scaldaferri F, Urbani A, Gasbarrini A. Impact of the Trophic Effects of the Secretome From a Multistrain Probiotic Preparation on the Intestinal Epithelia. Inflamm Bowel Dis 2021; 27:902-913. [PMID: 33300553 DOI: 10.1093/ibd/izaa298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Probiotics are defined as live, nonpathogenic bacteria that confer health benefits beyond their nutritional value. In particular, VSL#3 exhibits demonstrated efficacy in the management of diseases characterized by an increased intestinal permeability. Our study aimed to understand how VSL#3 promotes gut health by secreting bioactive factors and identify which human pathways are modulated by secretome derived from the VSL#3 formula. METHODS Two different lots of VSL#3 were used, and Caco-2 cell line was treated with conditioned media (CM) prepared using 1 g of the probiotic formula. We evaluated the effects of the probiotics on cellular proliferation and apoptosis by cytometry and the expression of tight junction proteins by western blotting. A proteomics analysis of both culture media and the whole proteome of Caco-2 cells treated with VSL#3-CM was performed by nano-ultra performance liquid chromatography - tandem mass (nUPLC MS/MS) spectrometry. RESULTS The probiotic formula increased cell proliferation, decreased cellular apoptosis cells, and increased re-epithelialization in the scratch assay. Several peptides specifically synthetized by all the species within the probiotic preparation were recognized in the proteomics analysis. Human proteins synthesized by CaCo-2 cells were also identified. CONCLUSIONS To our knowledge, this manuscript describes the first evaluation of the probiotic secretome, and the results showed that the improvement in intestinal barrier functions induced by probiotics seems to be accompanied by the modulation of some human cellular pathways.
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Affiliation(s)
- Valentina Petito
- Università Cattolica del Sacro Cuore, Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Rome, Italy
| | - Viviana Greco
- Università Cattolica del Sacro Cuore, Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Rome, Italy.,Università Cattolica del Sacro Cuore, Dipartimento Universitario di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Rome, Italy
| | - Lucrezia Laterza
- Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, Rome, Italy
| | - Cristina Graziani
- Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, Rome, Italy
| | - Caterina Fanali
- Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, Rome, Italy
| | - Donatella Lucchetti
- Università Cattolica del Sacro Cuore, Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Rome, Italy
| | - Maria Raffaella Barbaro
- Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Dipartimento di Scienze Mediche e Chirurgiche, Rome, Italy
| | - Francesca Bugli
- Policlinico Sant'Orsola- Malpighi, Università di Bologna, Dipartimento di Scienze Mediche e Chirurgiche, Bologna, Italia
| | - Luisa Pieroni
- Fondazione Santa Lucia IRCCS, Unitá di Proteomica e Metabolomica, Rome, Italy
| | - Loris Riccardo Lopetuso
- Università Cattolica del Sacro Cuore, Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Rome, Italy.,Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, Rome, Italy
| | - Alessandro Sgambato
- Università Cattolica del Sacro Cuore, Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Rome, Italy
| | - Maurizio Sanguinetti
- Università Cattolica del Sacro Cuore, Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Rome, Italy.,Università Cattolica del Sacro Cuore, Dipartimento Universitario di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Rome, Italy
| | - Franco Scaldaferri
- Università Cattolica del Sacro Cuore, Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Rome, Italy.,Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, Rome, Italy
| | - Andrea Urbani
- Università Cattolica del Sacro Cuore, Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Rome, Italy.,Università Cattolica del Sacro Cuore, Dipartimento Universitario di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Rome, Italy
| | - Antonio Gasbarrini
- Università Cattolica del Sacro Cuore, Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Rome, Italy.,Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Dipartimento di Scienze di Laboratorio e Infettivologiche, Rome, Italy
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6
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Proteomics Study of Peripheral Blood Mononuclear Cells in Down Syndrome Children. Antioxidants (Basel) 2020; 9:antiox9111112. [PMID: 33187268 PMCID: PMC7696178 DOI: 10.3390/antiox9111112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/22/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023] Open
Abstract
Down syndrome (DS) is the most common chromosomal disorder and the leading genetic cause of intellectual disability in humans, which results from the triplication of chromosome 21. To search for biomarkers for the early detection and exploration of the disease mechanisms, here, we investigated the protein expression signature of peripheral blood mononuclear cells (PBMCs) in DS children compared with healthy donors (HD) by using an in-depth label-free shotgun proteomics approach. Identified proteins are found associated with metabolic pathways, cellular trafficking, DNA structure, stress response, cytoskeleton network, and signaling pathways. The results showed that a well-defined number of dysregulated pathways retain a prominent role in mediating DS pathological features. Further, proteomics results are consistent with published study in DS and provide evidences that increased oxidative stress and the increased induction of stress related response, is a participant in DS pathology. In addition, the expression levels of some key proteins have been validated by Western blot analysis while protein carbonylation, as marker of protein oxidation, was investigated. The results of this study propose that PBMCs from DS children might be in an activated state where endoplasmic reticulum stress and increased production of radical species are one of the primary events contributing to multiple DS pathological features.
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7
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Glucocerebrosidase: Functions in and Beyond the Lysosome. J Clin Med 2020; 9:jcm9030736. [PMID: 32182893 PMCID: PMC7141376 DOI: 10.3390/jcm9030736] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 02/07/2023] Open
Abstract
Glucocerebrosidase (GCase) is a retaining β-glucosidase with acid pH optimum metabolizing the glycosphingolipid glucosylceramide (GlcCer) to ceramide and glucose. Inherited deficiency of GCase causes the lysosomal storage disorder named Gaucher disease (GD). In GCase-deficient GD patients the accumulation of GlcCer in lysosomes of tissue macrophages is prominent. Based on the above, the key function of GCase as lysosomal hydrolase is well recognized, however it has become apparent that GCase fulfills in the human body at least one other key function beyond lysosomes. Crucially, GCase generates ceramides from GlcCer molecules in the outer part of the skin, a process essential for optimal skin barrier property and survival. This review covers the functions of GCase in and beyond lysosomes and also pays attention to the increasing insight in hitherto unexpected catalytic versatility of the enzyme.
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8
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Marini F, Carregari VC, Greco V, Ronci M, Iavarone F, Persichilli S, Castagnola M, Urbani A, Pieroni L. Exploring the HeLa Dark Mitochondrial Proteome. Front Cell Dev Biol 2020; 8:137. [PMID: 32195257 PMCID: PMC7066081 DOI: 10.3389/fcell.2020.00137] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/18/2020] [Indexed: 12/04/2022] Open
Abstract
In the framework of the Human Proteome Project initiative, we aim to improve mapping and characterization of mitochondrial proteome. In this work we implemented an experimental workflow, combining classical biochemical enrichments and mass spectrometry, to pursue a much deeper definition of mitochondrial proteome and possibly mine mitochondrial uncharacterized dark proteins. We fractionated in two compartments mitochondria enriched from HeLa cells in order to annotate 4230 proteins in both fraction by means of a multiple-enzyme digestion (trypsin, chymotrypsin and Glu-C) followed by mass spectrometry analysis using a combination of Data Dependent Acquisition (DDA) and Data Independent Acquisition (DIA). We detected 22 mitochondrial dark proteins not annotated for their function and we provide their relative abundance inside the mitochondrial organelle. Considering this work as a pilot study we expect that the same approach, in different biological system, could represent an advancement in the characterization of the human mitochondrial proteome providing uncharted ground to explore the mitonuclear phenotypic relationships. All spectra have been deposited to ProteomeXchange with PXD014201 and PXD014200 identifier.
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Affiliation(s)
- Federica Marini
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, Rome, Italy.,Department of Laboratory Diagnostic and Infectious Diseases, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Victor Corasolla Carregari
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, Rome, Italy.,Department of Laboratory Diagnostic and Infectious Diseases, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Viviana Greco
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, Rome, Italy.,Department of Laboratory Diagnostic and Infectious Diseases, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Maurizio Ronci
- Department of Pharmacy, University G. D'Annunzio Chieti, Chieti, Italy
| | - Federica Iavarone
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, Rome, Italy.,Department of Laboratory Diagnostic and Infectious Diseases, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Silvia Persichilli
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, Rome, Italy.,Department of Laboratory Diagnostic and Infectious Diseases, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Massimo Castagnola
- Proteomics and Metabonomics Unit, IRCCS-Fondazione Santa Lucia, Rome, Italy
| | - Andrea Urbani
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, Rome, Italy.,Department of Laboratory Diagnostic and Infectious Diseases, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Luisa Pieroni
- Proteomics and Metabonomics Unit, IRCCS-Fondazione Santa Lucia, Rome, Italy
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9
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Aerts JMFG, Artola M, van Eijk M, Ferraz MJ, Boot RG. Glycosphingolipids and Infection. Potential New Therapeutic Avenues. Front Cell Dev Biol 2019; 7:324. [PMID: 31867330 PMCID: PMC6908816 DOI: 10.3389/fcell.2019.00324] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
Glycosphingolipids (GSLs), the main topic of this review, are a subclass of sphingolipids. With their glycans exposed to the extracellular space, glycosphingolipids are ubiquitous components of the plasma membrane of cells. GSLs are implicated in a variety of biological processes including specific infections. Several pathogens use GSLs at the surface of host cells as binding receptors. In addition, lipid-rafts in the plasma membrane of host cells may act as platform for signaling the presence of pathogens. Relatively common in man are inherited deficiencies in lysosomal glycosidases involved in the turnover of GSLs. The associated storage disorders (glycosphingolipidoses) show lysosomal accumulation of substrate(s) of the deficient enzyme. In recent years compounds have been identified that allow modulation of GSLs levels in cells. Some of these agents are well tolerated and already used to treat lysosomal glycosphingolipidoses. This review summarizes present knowledge on the role of GSLs in infection and subsequent immune response. It concludes with the thought to apply glycosphingolipid-lowering agents to prevent and/or combat infections.
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Affiliation(s)
| | - M Artola
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - M van Eijk
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - M J Ferraz
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - R G Boot
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
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10
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Aerts JMFG, Kuo CL, Lelieveld LT, Boer DEC, van der Lienden MJC, Overkleeft HS, Artola M. Glycosphingolipids and lysosomal storage disorders as illustrated by gaucher disease. Curr Opin Chem Biol 2019; 53:204-215. [PMID: 31783225 DOI: 10.1016/j.cbpa.2019.10.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/02/2019] [Accepted: 10/24/2019] [Indexed: 02/06/2023]
Abstract
Glycosphingolipids are important building blocks of the outer leaflet of the cell membrane. They are continuously recycled, involving fragmentation inside lysosomes by glycosidases. Inherited defects in degradation cause lysosomal glycosphingolipid storage disorders. The relatively common glycosphingolipidosis Gaucher disease is highlighted here to discuss new insights in the molecular basis and pathophysiology of glycosphingolipidoses reached by fundamental research increasingly using chemical biology tools. We discuss improvements in the detection of glycosphingolipid metabolites by mass spectrometry and review new developments in laboratory diagnosis and disease monitoring as well as therapeutic interventions.
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Affiliation(s)
- Johannes M F G Aerts
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, the Netherlands.
| | - Chi-Lin Kuo
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, the Netherlands
| | - Lindsey T Lelieveld
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, the Netherlands
| | - Daphne E C Boer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, the Netherlands
| | | | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, the Netherlands
| | - Marta Artola
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA, Leiden, the Netherlands
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11
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Kuot A, Ronci M, Mills R, Klebe S, Snibson G, Wiffen S, Loh R, Corbett M, Zhou T, Chataway T, Burdon KP, Craig JE, Urbani A, Sharma S. Reduced expression of apolipoprotein E and immunoglobulin heavy constant gamma 1 proteins in Fuchs endothelial corneal dystrophy. Clin Exp Ophthalmol 2019; 47:1028-1042. [PMID: 31206232 DOI: 10.1111/ceo.13569] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 05/30/2019] [Accepted: 06/05/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Fuchs endothelial corneal dystrophy (FECD) is a progressive and potentially a sight threatening disease, and a common indication for corneal grafting in the elderly. Aberrant thickening of Descemet's membrane, formation of microscopic excrescences (guttae) and gradual loss of corneal endothelial cells are the hallmarks of the disease. The aim of this study was to identify differentially abundant proteins between FECD-affected and unaffected Descemet's membrane. METHODS Label-free quantitative proteomics using nanoscale ultra-performance liquid chromatography-mass spectrometry (nUPLC-MSE ) was employed on affected and unaffected Descemet's membrane extracts, and interesting findings were further investigated using quantitative reverse transcription-polymerase chain reaction and immunohistochemical techniques. RESULTS Quantitative proteomics revealed significantly lower abundance of apolipoprotein E (APOE) and immunoglobulin heavy constant gamma 1 protein (IGHG1) in affected Descemet's membrane. The difference in the distribution of APOE between affected and unaffected Descemet's membrane and of IGHG1 detected by immunohistochemistry support their down-regulation in the disease. Comparative gene expression analysis showed significantly lower APOE mRNA levels in FECD-affected than unaffected corneal endothelium. IGHG1 gene is expressed at extremely low levels in the corneal endothelium, precluding relative expression analysis. CONCLUSIONS This is the first study to report comparative proteomics of Descemet's membrane tissue, and implicates dysregulation of APOE and IGHG1 proteins in the pathogenesis of Fuchs endothelial corneal dystrophy.
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Affiliation(s)
- Abraham Kuot
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Maurizio Ronci
- Department of Medical, Oral and Biotechnological Sciences, University of G. d'Annunzio Chieti Pescara, Pescara, Italy
| | - Richard Mills
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Sonja Klebe
- Department of Anatomical Pathology, Flinders University, Adelaide, South Australia, Australia
| | - Grant Snibson
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Steven Wiffen
- The Lions Eye Bank of Western Australia, Lions Eye Institute, Perth, Western Australia, Australia
| | - Raymond Loh
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Mark Corbett
- Discipline of Paediatrics, School of Medicine and Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Tiger Zhou
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Tim Chataway
- Department of Human Physiology, Proteomics Laboratory, Flinders University, Adelaide, South Australia, Australia
| | - Kathryn P Burdon
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia.,Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Andrea Urbani
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, Rome, Italy.,Department of Laboratory Diagnostic and Infectious Diseases, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy
| | - Shiwani Sharma
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
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12
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Pellegrini D, Del Grosso A, Angella L, Giordano N, Dilillo M, Tonazzini I, Caleo M, Cecchini M, McDonnell LA. Quantitative Microproteomics Based Characterization of the Central and Peripheral Nervous System of a Mouse Model of Krabbe Disease. Mol Cell Proteomics 2019; 18:1227-1241. [PMID: 30926673 PMCID: PMC6553931 DOI: 10.1074/mcp.ra118.001267] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/15/2019] [Indexed: 11/06/2022] Open
Abstract
Krabbe disease is a rare, childhood lysosomal storage disorder caused by a deficiency of galactosylceramide beta-galactosidase (GALC). The major effect of GALC deficiency is the accumulation of psychosine in the nervous system and widespread degeneration of oligodendrocytes and Schwann cells, causing rapid demyelination. The molecular mechanisms of Krabbe disease are not yet fully elucidated and a definite cure is still missing. Here we report the first in-depth characterization of the proteome of the Twitcher mouse, a spontaneous mouse model of Krabbe disease, to investigate the proteome changes in the Central and Peripheral Nervous System. We applied a TMT-based workflow to compare the proteomes of the corpus callosum, motor cortex and sciatic nerves of littermate homozygous Twitcher and wild-type mice. More than 400 protein groups exhibited differences in expression and included proteins involved in pathways that can be linked to Krabbe disease, such as inflammatory and defense response, lysosomal proteins accumulation, demyelination, reduced nervous system development and cell adhesion. These findings provide new insights on the molecular mechanisms of Krabbe disease, representing a starting point for future functional experiments to study the molecular pathogenesis of Krabbe disease. Data are available via ProteomeXchange with identifier PXD010594.
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Affiliation(s)
- Davide Pellegrini
- From ‡NEST, Scuola Normale Superiore, Pisa 56127, Italy
- §Fondazione Pisana per la Scienza ONLUS, 56107 San Giuliano Terme, Pisa, Italy
| | - Ambra Del Grosso
- From ‡NEST, Scuola Normale Superiore, Pisa 56127, Italy
- ¶NEST, Istituto Nanoscienze-CNR, Pisa, Italy
| | | | | | - Marialaura Dilillo
- §Fondazione Pisana per la Scienza ONLUS, 56107 San Giuliano Terme, Pisa, Italy
| | | | | | - Marco Cecchini
- From ‡NEST, Scuola Normale Superiore, Pisa 56127, Italy
- ¶NEST, Istituto Nanoscienze-CNR, Pisa, Italy
| | - Liam A McDonnell
- §Fondazione Pisana per la Scienza ONLUS, 56107 San Giuliano Terme, Pisa, Italy;
- **Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
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13
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Acioglu C, Tuzuner MB, Serhatli M, Acilan C, Sahin B, Akgun E, Adiguzel Z, Gurel B, Baykal AT. A Proteomic Analysis of Mitochondrial Complex III Inhibition in SH-SY5Y Human Neuroblastoma Cell Line. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164615666180713110139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background and Objective: Antimycin A (AntA) is a potent Electron Transport System (ETS) inhibitor exerting its effect through inhibiting the transfer of the electrons by binding to the quinone reduction site of the cytochrome bc1 complex (Complex III), which is known to be impaired in Huntington’s Disease (HD). The current studies were undertaken to investigate the effect of complex III inhibition in the SH-SY5Y cell line to delineate the molecular and cellular processes, which may play a role in the pathogenesis of HD.
Methods:
We treated SH-SY5Y neuroblastoma cells with AntA in order to establish an in vitro mitochondrial dysfunction model for HD. Differential proteome analysis was performed by the nLCMS/ MS system. Protein expression was assessed by western blot analysis.
Results:
Thirty five differentially expressed proteins as compared to the vehicle-treated controls were detected. Functional pathway analysis indicated that proteins involved in ubiquitin-proteasomal pathway were up-regulated in AntA-treated SH-SY5Y neuroblastoma cells and the ubiquitinated protein accumulation was confirmed by immunoblotting. We found that Prothymosin α (ProT α) was downregulated. Furthermore, we demonstrated that nuclear factor erythroid 2-related factor 2 (Nrf2) protein expression was co-regulated with ProT α expression, hence knockdown of ProT α in SH-SY5Y cells decreased Nrf2 protein level.
Conclusion:
Our findings suggest that complex III impairment might downregulate ubiquitinproteasome function and NRF2/Keap1 antioxidant response. In addition, it is likely that downregulation of Nrf2 is due to the decreased expression of ProT α in AntA-treated SH-SY5Y cells. Our results could advance the understanding of mechanisms involved in neurodegenerative diseases.
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Affiliation(s)
- Cigdem Acioglu
- Department of Neurological Surgery, Reynolds Family Spine Laboratory, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, United States
| | - Mete Bora Tuzuner
- Research and Development Center, Acibadem Labmed Medical Laboratories, Istanbul, Turkey
| | - Muge Serhatli
- TUBITAK, Marmara Research Center, Genetic Engineering and Biotechnology Institute, 41470, Gebze, Kocaeli, Turkey
| | - Ceyda Acilan
- School of Medicine, Research Center for Translational Medicine, Koc University, Istanbul, Turkey
| | - Betul Sahin
- Research and Development Center, Acibadem Labmed Medical Laboratories, Istanbul, Turkey
| | - Emel Akgun
- Research and Development Center, Acibadem Labmed Medical Laboratories, Istanbul, Turkey
| | - Zelal Adiguzel
- TUBITAK, Marmara Research Center, Genetic Engineering and Biotechnology Institute, 41470, Gebze, Kocaeli, Turkey
| | - Busra Gurel
- Department of Medical Biochemistry, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
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14
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Li Y, Liu K, Chen F, Cheng Y. Comparative proteomics analysis reveals the effect of germination and selenium enrichment on the quality of brown rice during storage. Food Chem 2018; 269:220-227. [DOI: 10.1016/j.foodchem.2018.07.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/21/2018] [Accepted: 07/02/2018] [Indexed: 01/07/2023]
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15
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Greco V, Spalloni A, Corasolla Carregari V, Pieroni L, Persichilli S, Mercuri NB, Urbani A, Longone P. Proteomics and Toxicity Analysis of Spinal-Cord Primary Cultures upon Hydrogen Sulfide Treatment. Antioxidants (Basel) 2018; 7:antiox7070087. [PMID: 29996549 PMCID: PMC6070951 DOI: 10.3390/antiox7070087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/05/2018] [Accepted: 07/07/2018] [Indexed: 12/25/2022] Open
Abstract
Hydrogen sulfide (H2S) is an endogenous gasotransmitter recognized as an essential body product with a dual, biphasic action. It can function as an antioxidant and a cytoprotective, but also as a poison with a high probability of causing brain damage when present at noxious levels. In a previous study, we measured toxic liquoral levels of H2S in sporadic amyotrophic lateral sclerosis (ALS) patients and in the familial ALS (fALS) mouse model, SOD1G93A. In addition, we experimentally demonstrated that H2S is extremely and selectively toxic to motor neurons, and that it is released by glial cells and increases Ca2+ concentration in motor neurons due to a lack of ATP. The presented study further examines the effect of toxic concentrations of H2S on embryonic mouse spinal-cord cultures. We performed a proteomic analysis that revealed a significant H2S-mediated activation of pathways related to oxidative stress and cell death, particularly the Nrf-2-mediated oxidative stress response and peroxiredoxins. Furthermore, we report that Na2S (a stable precursor of H2S) toxicity is, at least in part, reverted by the Bax inhibitor V5 and by necrostatin, a potent necroptosis inhibitor.
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Affiliation(s)
- Viviana Greco
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, 00168 Rome, Italy.
- Department of Laboratory Diagnostic and Infectious Diseases, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, 00168 Rome, Italy.
| | - Alida Spalloni
- Department of Experimental Neuroscience, Molecular Neurobiology Unit, Fondazione Santa Lucia, 00143 Rome, Italy.
| | - Victor Corasolla Carregari
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, 00168 Rome, Italy.
- Department of Laboratory Diagnostic and Infectious Diseases, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, 00168 Rome, Italy.
| | - Luisa Pieroni
- Department of Experimental Neuroscience, Proteomics and Metabonomics Unit, Fondazione Santa Lucia-IRCCS, 00143 Rome, Italy.
| | - Silvia Persichilli
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, 00168 Rome, Italy.
- Department of Laboratory Diagnostic and Infectious Diseases, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, 00168 Rome, Italy.
| | - Nicola B Mercuri
- Department of Systems Medicine, Policlinico Universitario "Tor Vergata", University of Rome "Tor Vergata", 00133 Rome, Italy.
- Department of Experimental Neuroscience, Experimental Neurology Unit, 00143 Rome, Italy.
| | - Andrea Urbani
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, 00168 Rome, Italy.
- Department of Laboratory Diagnostic and Infectious Diseases, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, 00168 Rome, Italy.
| | - Patrizia Longone
- Department of Experimental Neuroscience, Molecular Neurobiology Unit, Fondazione Santa Lucia, 00143 Rome, Italy.
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16
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Chen Y, Sud N, Hettinghouse A, Liu CJ. Molecular regulations and therapeutic targets of Gaucher disease. Cytokine Growth Factor Rev 2018; 41:65-74. [PMID: 29699937 DOI: 10.1016/j.cytogfr.2018.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 04/09/2018] [Indexed: 02/07/2023]
Abstract
Gaucher disease (GD) is the most common lysosomal storage disease caused by deficiency of beta-glucocerebrosidase (GCase) resulting in lysosomal accumulation of its glycolipid substrate glucosylceramide. The activity of GCase depends on many factors such as proper folding and lysosomal localization, which are influenced by mutations in GCase encoding gene, and regulated by various GCase-binding partners including Saposin C, progranulin and heat shock proteins. In addition, proinflammatory molecules also contribute to pathogenicity of GD. In this review, we summarize the molecules that are known to be important for the pathogenesis of GD, particularly those modulating GCase lysosomal appearance and activity. In addition, small molecules that inhibit inflammatory mediators, calcium ion channels and other factors associated with GD are also described. Discovery and characterization of novel molecules that impact GD are not only important for deciphering the pathogenic mechanisms of the disease, but they also provide new targets for drug development to treat the disease.
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Affiliation(s)
- Yuehong Chen
- Department of Orthopaedic Surgery, New York University Medical Center, New York, NY 10003, USA; Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Neetu Sud
- Department of Orthopaedic Surgery, New York University Medical Center, New York, NY 10003, USA
| | - Aubryanna Hettinghouse
- Department of Orthopaedic Surgery, New York University Medical Center, New York, NY 10003, USA
| | - Chuan-Ju Liu
- Department of Orthopaedic Surgery, New York University Medical Center, New York, NY 10003, USA; Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.
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17
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Piras C, Guo Y, Soggiu A, Chanrot M, Greco V, Urbani A, Charpigny G, Bonizzi L, Roncada P, Humblot P. Changes in protein expression profiles in bovine endometrial epithelial cells exposed to E. coli LPS challenge. MOLECULAR BIOSYSTEMS 2017; 13:392-405. [PMID: 28070584 DOI: 10.1039/c6mb00723f] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
E. coli is one of the most frequently involved bacteria in uterine diseases. Lipopolysaccharide (LPS) is a component of the outer membrane of Gram-negative bacteria involved in pathogenic processes leading to post-partum metritis and endometritis in cattle. It also causes inflammation of the endometrium. The increase of cell proliferation by LPS is part of the inflammatory process. The aim of this study was to investigate possible changes in protein expression in relation to the proliferative response of bEECs after challenge with E. coli-LPS. In vitro culture of bEECs was performed from cow genital tracts collected at a slaughterhouse. In passage 5, bEECs from each of 9 cows (3 series of 3 cows) were exposed to 0, 8, and 16 μg ml-1 LPS for 72 h. At time 0 and 72 h later, attached cells/living cells were counted and for each time and LPS dosage, cells were frozen for proteomic analyses. All samples from the 3 series were analyzed by 2-D gel electrophoresis coupled to MALDI-TOF/TOF mass spectrometry. The samples from the first series were subjected to shotgun nLC-MS/MS analysis. From the whole differential proteomics analysis, 38 proteins were differentially expressed (p < 0.05 to p < 0.001) following exposure to LPS. Among them, twenty-eight were found to be up-regulated in the LPS groups in comparison to control groups and ten were down-regulated. Differentially expressed proteins were associated with cell proliferation and apoptosis, transcription, destabilization of cell structure, oxidative stress, regulation of histones, allergy and general cell metabolism pathways. The de-regulations induced by LPS were consistent with the proliferative phenotype and indicated strong alterations of several cell functions. In addition, some of the differentially expressed proteins relates to pathways activated at the time of implantation. The specific changes induced through those signals may have negative consequences for the establishment of pregnancy.
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Affiliation(s)
- Cristian Piras
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milano, Italy
| | - Yongzhi Guo
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, SLU, Sweden
| | - Alessio Soggiu
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milano, Italy
| | - Metasu Chanrot
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, SLU, Sweden and Rajamangala University of Srivijaya (RMUTSV), Thungyai, Thailand
| | - Viviana Greco
- Proteomics and Metabonomics Unit Fondazione Santa Lucia - IRCCS, Rome, Italy
| | - Andrea Urbani
- Istituto di Biochimica e Biochimica Clinica, Università Cattolica, Roma, Italy
| | - Gilles Charpigny
- INRA, Biologie du Développement et Reproduction, 78350, Jouy en Josas, France
| | - Luigi Bonizzi
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milano, Italy
| | - Paola Roncada
- Dipartimento di Medicina Veterinaria, Università degli studi di Milano, Milano, Italy and Istituto Sperimentale Italiano L. Spallanzani, Milano and TechnologieS srl, via Celoria 10, 20133 Milano, Italy.
| | - Patrice Humblot
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, SLU, Sweden
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18
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Quesada-Calvo F, Massot C, Bertrand V, Longuespée R, Blétard N, Somja J, Mazzucchelli G, Smargiasso N, Baiwir D, De Pauw-Gillet MC, Delvenne P, Malaise M, Coimbra Marques C, Polus M, De Pauw E, Meuwis MA, Louis E. OLFM4, KNG1 and Sec24C identified by proteomics and immunohistochemistry as potential markers of early colorectal cancer stages. Clin Proteomics 2017; 14:9. [PMID: 28344541 PMCID: PMC5364649 DOI: 10.1186/s12014-017-9143-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/21/2017] [Indexed: 12/17/2022] Open
Abstract
Background Despite recent advances in colorectal cancer (CRC) diagnosis and population screening programs, the identification of patients with preneoplastic lesions or with early CRC stages remains challenging and is important for reducing CRC incidence and increasing patient’s survival.
Methods We analysed 76 colorectal tissue samples originated from early CRC stages, normal or inflamed mucosa by label-free proteomics. The characterisation of three selected biomarker candidates was performed by immunohistochemistry on an independent set of precancerous and cancerous lesions harbouring increasing CRC stages. Results Out of 5258 proteins identified, we obtained 561 proteins with a significant differential distribution among groups of patients and controls. KNG1, OLFM4 and Sec24C distributions were validated in tissues and showed different expression levels especially in the two early CRC stages compared to normal and preneoplastic tissues. Conclusion We highlighted three proteins that require further investigations to better characterise their role in early CRC carcinogenesis and their potential as early CRC markers. Electronic supplementary material The online version of this article (doi:10.1186/s12014-017-9143-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Florence Quesada-Calvo
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Charlotte Massot
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Virginie Bertrand
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Rémi Longuespée
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Noëlla Blétard
- Department of Anatomy and Pathology, GIGA-R, Liège University Hospital CHU, ULg, 4000 Liège, Belgium
| | - Joan Somja
- Department of Anatomy and Pathology, GIGA-R, Liège University Hospital CHU, ULg, 4000 Liège, Belgium
| | - Gabriel Mazzucchelli
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Nicolas Smargiasso
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | | | - Marie-Claire De Pauw-Gillet
- Mammalian Cell Culture Laboratory, Department of Preclinical and Biomedical Sciences, GIGA-R, ULg, 4000 Liège, Belgium
| | - Philippe Delvenne
- Department of Anatomy and Pathology, GIGA-R, Liège University Hospital CHU, ULg, 4000 Liège, Belgium
| | - Michel Malaise
- Department of Clinical Sciences, Rheumatology, Liège University Hospital CHU, 4000 Liège, Belgium
| | | | - Marc Polus
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Marie-Alice Meuwis
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Edouard Louis
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
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Proteomic Profiling of Skin Fibroblasts as a Model of Schizophrenia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 974:305-311. [DOI: 10.1007/978-3-319-52479-5_29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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20
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Kramer G, Wegdam W, Donker-Koopman W, Ottenhoff R, Gaspar P, Verhoek M, Nelson J, Gabriel T, Kallemeijn W, Boot RG, Laman JD, Vissers JPC, Cox T, Pavlova E, Moran MT, Aerts JM, van Eijk M. Elevation of glycoprotein nonmetastatic melanoma protein B in type 1 Gaucher disease patients and mouse models. FEBS Open Bio 2016; 6:902-13. [PMID: 27642553 PMCID: PMC5011488 DOI: 10.1002/2211-5463.12078] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/18/2016] [Accepted: 04/27/2016] [Indexed: 12/23/2022] Open
Abstract
Gaucher disease is caused by inherited deficiency of lysosomal glucocerebrosidase. Proteome analysis of laser‐dissected splenic Gaucher cells revealed increased amounts of glycoprotein nonmetastatic melanoma protein B (gpNMB). Plasma gpNMB was also elevated, correlating with chitotriosidase and CCL18, which are established markers for human Gaucher cells. In Gaucher mice, gpNMB is also produced by Gaucher cells. Correction of glucocerebrosidase deficiency in mice by gene transfer or pharmacological substrate reduction reverses gpNMB abnormalities. In conclusion, gpNMB acts as a marker for glucosylceramide‐laden macrophages in man and mouse and gpNMB should be considered as candidate biomarker for Gaucher disease in treatment monitoring.
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Affiliation(s)
- Gertjan Kramer
- Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands; European Molecular Biology Laboratory Germany
| | - Wouter Wegdam
- Department of Gynecology Academic Medical Center Amsterdam The Netherlands
| | - Wilma Donker-Koopman
- Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands
| | - Roelof Ottenhoff
- Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands
| | - Paulo Gaspar
- Organelle Biogenesis & Function Group Instituto de Investigação e Inovação em Saúde (I3S) Porto Portugal; Institute of Molecular and Cell Biology (IBMC) Universidade do Porto Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS) Universidade do Porto Portugal
| | - Marri Verhoek
- Department of Medical Biochemistry Leiden Institute of Chemistry Leiden University The Netherlands
| | - Jessica Nelson
- Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands
| | - Tanit Gabriel
- Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands
| | - Wouter Kallemeijn
- Department of Medical Biochemistry Leiden Institute of Chemistry Leiden University The Netherlands
| | - Rolf G Boot
- Department of Medical Biochemistry Leiden Institute of Chemistry Leiden University The Netherlands
| | - Jon D Laman
- Department of Neuroscience University Medical Center Groningen The Netherlands
| | | | - Timothy Cox
- Department of Internal Medicine Addenbrooke's Hospital Cambridge UK
| | - Elena Pavlova
- Department of Internal Medicine Addenbrooke's Hospital Cambridge UK
| | | | - Johannes M Aerts
- Department of Medical Biochemistry Leiden Institute of Chemistry Leiden University The Netherlands
| | - Marco van Eijk
- Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands; Department of Medical Biochemistry Leiden Institute of Chemistry Leiden University The Netherlands
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21
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Brioschi M, Baetta R, Ghilardi S, Gianazza E, Guarino A, Parolari A, Polvani G, Tremoli E, Banfi C. Normal human mitral valve proteome: A preliminary investigation by gel-based and gel-free proteomic approaches. Electrophoresis 2016; 37:2633-2643. [PMID: 27450324 DOI: 10.1002/elps.201600081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/27/2016] [Accepted: 07/14/2016] [Indexed: 12/24/2022]
Abstract
The mitral valve is a highly complex structure which regulates blood flow from the left atrium to the left ventricle (LV) avoiding a significant forward gradient during diastole or regurgitation during systole. The integrity of the mitral valve is also essential for the maintenance of normal LV size, geometry, and function. Significant advances in the comprehension of the biological, functional, and mechanical behavior of the mitral valve have recently been made. However, current knowledge of protein components in the normal human mitral valve is still limited and complicated by the low cellularity of this tissue and the presence of high abundant proteins from the extracellular matrix. We employed here an integrated proteomic approach to analyse the protein composition of the normal human mitral valve and reported confident identification of 422 proteins, some of which have not been previously described in this tissue. In particular, we described the ability of pre-MS separation technique based on liquid-phase IEF and SDS-PAGE to identify the largest number of proteins. We also demonstrated that some of these proteins, e.g. αB-Crystallin, septin-11, four-and-a-half LIM domains protein 1, and dermatopontin, are synthesised by interstitial cells isolated from human mitral valves. These initial results provide a valuable basis for future studies aimed at analysing in depth the mitral valve protein composition and at investigating potential pathogenetic molecular mechanisms. Data are available via ProteomeXchange with identifier PXD004397.
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Affiliation(s)
| | | | | | | | - Anna Guarino
- Centro Cardiologico Monzino, IRCCS, Milan, Italy.,Banca Tessuti Cardiovascolari Regione Lombardia, Centro Cardiologico Monzino IRCCS Milan, Milan, Italy
| | - Alessandro Parolari
- Dipartimento di Chirurgia cardiaca, IRCCS Policlinico San Donato, Milan, Italy
| | - Gianluca Polvani
- Centro Cardiologico Monzino, IRCCS, Milan, Italy.,Università degli Studi di Milano, Dipartimento di Scienze Cliniche e di Comunità, Sezione Cardiovascolare, Milan, Italy
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Cevik O, Baykal AT, Sener A. Platelets Proteomic Profiles of Acute Ischemic Stroke Patients. PLoS One 2016; 11:e0158287. [PMID: 27336623 PMCID: PMC4919045 DOI: 10.1371/journal.pone.0158287] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 06/13/2016] [Indexed: 12/20/2022] Open
Abstract
Platelets play a crucial role in the pathogenesis of stroke and antiplatelet agents exist for its treatment and prevention. Through the use of LC-MS based protein expression profiling, platelets from stroke patients were analyzed and then correlated with the proteomic analyses results in the context of this disease. This study was based on patients who post ischemic stroke were admitted to hospital and had venous blood drawn within 24 hrs of the incidence. Label-free protein expression analyses of the platelets' tryptic digest was performed in triplicate on a UPLC-ESI-qTOF-MS/MS system and ProteinLynx Global Server (v2.5, Waters) was used for tandem mass data extraction. The peptide sequences were searched against the reviewed homo sapiens database (www.uniprot.org) and the quantitation of protein variation was achieved through Progenesis LC-MS software (V4.0, Nonlinear Dynamics). These Label-free differential proteomics analysis of platelets ensured that 500 proteins were identified and 83 of these proteins were found to be statistically significant. The differentially expressed proteins are involved in various processes such as inflammatory response, cellular movement, immune cell trafficking, cell-to-cell signaling and interaction, hematological system development and function and nucleic acid metabolism. The expressions of myeloperoxidase, arachidonate 12-Lipoxygenase and histidine-rich glycoprotein are involved in cellular metabolic processes, crk-like protein and ras homolog gene family member A involved in cell signaling with vitronectin, thrombospondin 1, Integrin alpha 2b, and integrin beta 3 involved in cell adhesion. Apolipoprotein H, immunoglobulin heavy constant gamma 1 and immunoglobulin heavy constant gamma 3 are involved in structural, apolipoprotein A-I, and alpha-1-microglobulin/bikunin precursor is involved in transport, complement component 3 and clusterin is involved in immunity proteins as has been discussed. Our data provides an insight into the proteins that are involved in the platelets' activation response during ischemic stroke. It could be argued that this study lays the foundation for future mechanistic studies.
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Affiliation(s)
- Ozge Cevik
- Cumhuriyet University, Faculty of Pharmacy, Department of Biochemistry, Sivas, Turkey
- Marmara University, Faculty of Pharmacy, Department of Biochemistry, Istanbul, Turkey
- * E-mail:
| | - Ahmet Tarik Baykal
- Acibadem University, School of Medicine, Department of Medical Biochemistry, Istanbul, Turkey
| | - Azize Sener
- Marmara University, Faculty of Pharmacy, Department of Biochemistry, Istanbul, Turkey
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Quantitative Proteomics of the Infectious and Replicative Forms of Chlamydia trachomatis. PLoS One 2016; 11:e0149011. [PMID: 26871455 PMCID: PMC4752267 DOI: 10.1371/journal.pone.0149011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/26/2016] [Indexed: 12/24/2022] Open
Abstract
The obligate intracellular developmental cycle of Chlamydia trachomatis presents significant challenges in defining its proteome. In this study we have applied quantitative proteomics to both the intracellular reticulate body (RB) and the extracellular elementary body (EB) from C. trachomatis. We used C. trachomatis L2 as a model chlamydial isolate for our study since it has a high infectivity:particle ratio and there is an excellent quality genome sequence. EBs and RBs (>99% pure) were quantified by chromosomal and plasmid copy number using PCR, from which the concentrations of chlamydial proteins per bacterial cell/genome were determined. RBs harvested at 15h post infection (PI) were purified by three successive rounds of gradient centrifugation. This is the earliest possible time to obtain purified RBs, free from host cell components in quantity, within the constraints of the technology. EBs were purified at 48h PI. We then used two-dimensional reverse phase UPLC to fractionate RB or EB peptides before mass spectroscopic analysis, providing absolute amount estimates of chlamydial proteins. The ability to express the data as molecules per cell gave ranking in both abundance and energy requirements for synthesis, allowing meaningful identification of rate-limiting components. The study assigned 562 proteins with high confidence and provided absolute estimates of protein concentration for 489 proteins. Interestingly, the data showed an increase in TTS capacity at 15h PI. Most of the enzymes involved in peptidoglycan biosynthesis were detected along with high levels of muramidase (in EBs) suggesting breakdown of peptidoglycan occurs in the non-dividing form of the microorganism. All the genome-encoded enzymes for glycolysis, pentose phosphate pathway and tricarboxylic acid cycle were identified and quantified; these data supported the observation that the EB is metabolically active. The availability of detailed, accurate quantitative proteomic data will be invaluable for investigations into gene regulation and function.
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Comparison of serum fractionation methods by data independent label-free proteomics. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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25
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Kramer G, Woolerton Y, van Straalen JP, Vissers JPC, Dekker N, Langridge JI, Beynon RJ, Speijer D, Sturk A, Aerts JMFG. Accuracy and Reproducibility in Quantification of Plasma Protein Concentrations by Mass Spectrometry without the Use of Isotopic Standards. PLoS One 2015; 10:e0140097. [PMID: 26474480 PMCID: PMC4608811 DOI: 10.1371/journal.pone.0140097] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/22/2015] [Indexed: 12/28/2022] Open
Abstract
Background Quantitative proteomic analysis with mass spectrometry holds great promise for simultaneously quantifying proteins in various biosamples, such as human plasma. Thus far, studies addressing the reproducible measurement of endogenous protein concentrations in human plasma have focussed on targeted analyses employing isotopically labelled standards. Non-targeted proteomics, on the other hand, has been less employed to this end, even though it has been instrumental in discovery proteomics, generating large datasets in multiple fields of research. Results Using a non-targeted mass spectrometric assay (LCMSE), we quantified abundant plasma proteins (43 mg/mL—40 ug/mL range) in human blood plasma specimens from 30 healthy volunteers and one blood serum sample (ProteomeXchange: PXD000347). Quantitative results were obtained by label-free mass spectrometry using a single internal standard to estimate protein concentrations. This approach resulted in quantitative results for 59 proteins (cut off ≥11 samples quantified) of which 41 proteins were quantified in all 31 samples and 23 of these with an inter-assay variability of ≤ 20%. Results for 7 apolipoproteins were compared with those obtained using isotope-labelled standards, while 12 proteins were compared to routine immunoassays. Comparison of quantitative data obtained by LCMSE and immunoassays showed good to excellent correlations in relative protein abundance (r = 0.72–0.96) and comparable median concentrations for 8 out of 12 proteins tested. Plasma concentrations of 56 proteins determined by LCMSE were of similar accuracy as those reported by targeted studies and 7 apolipoproteins quantified by isotope-labelled standards, when compared to reference concentrations from literature. Conclusions This study shows that LCMSE offers good quantification of relative abundance as well as reasonable estimations of concentrations of abundant plasma proteins.
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Affiliation(s)
- Gertjan Kramer
- Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
- * E-mail:
| | - Yvonne Woolerton
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jan P. van Straalen
- Department of Clinical Chemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Nick Dekker
- Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Robert J. Beynon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Dave Speijer
- Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Auguste Sturk
- Department of Clinical Chemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
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26
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Csősz É, Emri G, Kalló G, Tsaprailis G, Tőzsér J. Highly abundant defense proteins in human sweat as revealed by targeted proteomics and label-free quantification mass spectrometry. J Eur Acad Dermatol Venereol 2015; 29:2024-31. [PMID: 26307449 DOI: 10.1111/jdv.13221] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 05/12/2015] [Indexed: 12/29/2022]
Abstract
BACKGROUND The healthy human skin with its effective antimicrobial defense system forms an efficient barrier against invading pathogens. There is evidence suggesting that the composition of this chemical barrier varies between diseases, making the easily collected sweat an ideal candidate for biomarker discoveries. OBJECTIVE Our aim was to provide information about the normal composition of the sweat, and to study the chemical barrier found at the surface of skin. METHODS Sweat samples from healthy individuals were collected during sauna bathing, and the global protein panel was analysed by label-free mass spectrometry. SRM-based targeted proteomic methods were designed and stable isotope labelled reference peptides were used for method validation. RESULTS Ninety-five sweat proteins were identified, 20 of them were novel proteins. It was shown that dermcidin is the most abundant sweat protein, and along with apolipoprotein D, clusterin, prolactin-inducible protein and serum albumin, they make up 91% of secreted sweat proteins. The roles of these highly abundant proteins were reviewed; all of which have protective functions, highlighting the importance of sweat glands in composing the first line of innate immune defense system, and maintaining the epidermal barrier integrity. CONCLUSION Our findings with regard to the proteins forming the chemical barrier of the skin as determined by label-free quantification and targeted proteomics methods are in accordance with previous studies, and can be further used as a starting point for non-invasive sweat biomarker research.
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Affiliation(s)
- É Csősz
- Department of Biochemistry and Molecular Biology, Proteomics Core Facility, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - G Emri
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - G Kalló
- Department of Biochemistry and Molecular Biology, Proteomics Core Facility, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - G Tsaprailis
- Center for Toxicology, University of Arizona, Tucson, AZ, USA
| | - J Tőzsér
- Department of Biochemistry and Molecular Biology, Proteomics Core Facility, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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Piras C, Soggiu A, Greco V, Martino PA, Del Chierico F, Putignani L, Urbani A, Nally JE, Bonizzi L, Roncada P. Mechanisms of antibiotic resistance to enrofloxacin in uropathogenic Escherichia coli in dog. J Proteomics 2015; 127:365-76. [PMID: 26066767 DOI: 10.1016/j.jprot.2015.05.040] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 05/12/2015] [Accepted: 05/29/2015] [Indexed: 01/25/2023]
Abstract
Escherichia coli (E. coli) urinary tract infections (UTIs) are becoming a serious problem both for pets and humans (zoonosis) due to the close contact and to the increasing resistance to antibiotics. This study has been performed in order to unravel the mechanism of induced enrofloxacin resistance in canine E. coli isolates that represent a good tool to study this pathology. The isolated E. coli has been induced with enrofloxacin and studied through 2D DIGE and shotgun MS. Discovered differentially expressed proteins are principally involved in antibiotic resistance and linked to oxidative stress response, to DNA protection and to membrane permeability. Moreover, since enrofloxacin is an inhibitor of DNA gyrase, the overexpression of DNA starvation/stationary phase protection protein (Dsp) could be a central point to discover the mechanism of this clone to counteract the effects of enrofloxacin. In parallel, the dramatic decrease of the synthesis of the outer membrane protein W, which represents one of the main gates for enrofloxacin entrance, could explain additional mechanism of E. coli defense against this antibiotic. All 2D DIGE and MS data have been deposited into the ProteomeXchange Consortium with identifier PXD002000 and DOI http://dx.doi.org/10.6019/PXD002000. This article is part of a Special Issue entitled: HUPO 2014.
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Affiliation(s)
- Cristian Piras
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università degli studi di Milano, Milan, Italy
| | - Alessio Soggiu
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università degli studi di Milano, Milan, Italy
| | - Viviana Greco
- Fondazione Santa Lucia - IRCCS, Rome, Italy; Dipartimento di Medicina Sperimentale e Chirurgia, Università degli Studi di Roma "Tor Vergata", Italy
| | - Piera Anna Martino
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università degli studi di Milano, Milan, Italy
| | | | - Lorenza Putignani
- Parasitology and Metagenomics Units, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Urbani
- Fondazione Santa Lucia - IRCCS, Rome, Italy; Dipartimento di Medicina Sperimentale e Chirurgia, Università degli Studi di Roma "Tor Vergata", Italy
| | - Jarlath E Nally
- Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, United States
| | - Luigi Bonizzi
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università degli studi di Milano, Milan, Italy
| | - Paola Roncada
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università degli studi di Milano, Milan, Italy; Istituto Sperimentale Italiano L. Spallanzani, Milano, Italy.
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Al Feteisi H, Achour B, Barber J, Rostami-Hodjegan A. Choice of LC-MS methods for the absolute quantification of drug-metabolizing enzymes and transporters in human tissue: a comparative cost analysis. AAPS JOURNAL 2015; 17:438-46. [PMID: 25663651 DOI: 10.1208/s12248-014-9712-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/23/2014] [Indexed: 11/30/2022]
Abstract
The quantification of drug-metabolizing enzymes and transporters is important for in vitro-in vivo extrapolation (IVIVE) of xenobiotic clearance, which has become an integral part of drug development. There are different mass spectrometry-based techniques used for quantitative proteomics, and as more laboratories are opting for the use of these methods, selecting the most appropriate tool is becoming a concern. For the first time, we attempt to determine the significance of cost of different LC-MS methods of quantitative analysis of these proteins and to present a framework to objectively assess the choice of the techniques. Based on our analysis, quantification using labeled internal standards is more expensive per sample but provides higher quality data than label-free quantification. Quantification using absolute quantification synthetic peptides is the approach of choice for analyzing less than nine proteins, whereas when quantifying a defined set of proteins (10-50), such as enzymes, in a reasonably large number of samples (20-100), the quantification concatemer technique is more economical, followed by label-free quantification. When analyzing proteomes or sub-proteomes (≥500 proteins), label-free quantification is more cost-effective than the use of labeled internal standards. A cost-benefit approach is described to assess the choice of the most appropriate mass spectrometry-based approach for the quantification of proteins relevant to IVIVE.
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Affiliation(s)
- Hajar Al Feteisi
- Manchester Pharmacy School, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK
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Quero S, Párraga-Niño N, García-Núñez M, Sabrià M. [Proteomics in infectious diseases]. Enferm Infecc Microbiol Clin 2015; 34:253-60. [PMID: 25583331 DOI: 10.1016/j.eimc.2014.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 07/22/2014] [Accepted: 07/30/2014] [Indexed: 11/27/2022]
Abstract
Infectious diseases have a high incidence in the population, causing a major impact on global health. In vitro culture of microorganisms is the first technique applied for infection diagnosis which is laborious and time consuming. In recent decades, efforts have been focused on the applicability of "Omics" sciences, highlighting the progress provided by proteomic techniques in the field of infectious diseases. This review describes the management, processing and analysis of biological samples for proteomic research.
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Affiliation(s)
- Sara Quero
- Unitat de Malalties Infeccioses, Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Barcelona, España; Universitat Autònoma de Barcelona, Cerdanyola, Barcelona, España
| | - Noemí Párraga-Niño
- Unitat de Malalties Infeccioses, Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Barcelona, España.
| | - Marian García-Núñez
- Unitat de Malalties Infeccioses, Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Barcelona, España; CIBER de Enfermedades Respiratorias, Bunyola, Illes Balears, España
| | - Miquel Sabrià
- Universitat Autònoma de Barcelona, Cerdanyola, Barcelona, España; CIBER de Enfermedades Respiratorias, Bunyola, Illes Balears, España; Unitat de Malalties Infeccioses, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, España
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Yerlikaya A, Okur E, Baykal AT, Acılan C, Boyacı I, Ulukaya E. A proteomic analysis of p53-independent induction of apoptosis by bortezomib in 4T1 breast cancer cell line. J Proteomics 2014; 113:315-25. [PMID: 25305590 DOI: 10.1016/j.jprot.2014.09.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 09/05/2014] [Accepted: 09/15/2014] [Indexed: 11/16/2022]
Abstract
UNLABELLED The 26S proteasome is a proteolytic enzyme found in both cytoplasm and nucleus. In this study, we examined the differential expression of proteasome inhibitor bortezomib-induced proteins in p53-deficient 4T1 cells. It was found that GRP78 and TCEB2 were over-expressed in response to treatment with bortezomib for 24h. Next, we analyzed the expression of intracellular proteins in response to treatment with 100nM bortezomib for 24h by label-free LC-MS/MS. These analyses showed that Hsp70, the 26S proteasome non-ATPase regulatory subunit 14 and sequestosome 1 were increased at least 2 fold in p53-deficient 4T1 cells. The proteins identified by label-free LC-MS/MS were then analyzed by Ingenuity Pathway Analysis (IPA) Tool to determine biological networks affected by inhibition of the 26S proteasome. The analysis results showed that post-translational modifications, protein folding, DNA replication, energy production and nucleic acid metabolism were found to be among the top functions affected by the 26S proteasome inhibition. The biological network analysis indicated that ubiquitin may be the central regulator of the pathways modulated after bortezomib-treatment. Further investigation of the mechanism of the proteins modulated in response to the proteasomal inhibition may lead to the design of more effective and novel therapeutic strategies for cancer. BIOLOGICAL SIGNIFICANCE Although the proteasome inhibitor bortezomib is approved and used for the treatment of human cancer (multiple myeloma), the mechanism of action is not entirely understood. A number of studies showed that proteasome inhibitors induced apoptosis through upregulation of tumor suppressor protein p53. However, the role of tumor suppressor protein p53 in bortezomib-induced apoptosis is controversial and not well-understood. The tumor suppressor p53 is mutated in at least 50% of human cancers and is strongly induced by proteasomal inhibition. Some also reported that the proteasome inhibitor can induce apoptosis in a p53-independent manner. Also, it is reported that Noxa, a target of p53, is induced in response to proteasomal inhibition in a p53-independent manner. However, we have also previously reported that neither Puma nor Noxa are induced by proteasomal inhibition in p53-null 4T1 breast cancer cells, which is commonly used for in vivo breast cancer tumor models. The current results provided additional targets of proteasome inhibitor bortezomib and may therefore help in understanding the p53-independent mechanism of apoptosis induction by proteasome inhibitors. In addition, the results presented in this current study report for the first time that proteasomal subunit Psmd14, anti-apoptotic GRP78, anti apoptotic protein Card10, Dffb, Traf3 and Trp53bp2 are regulated and overexpressed in response to proteasome inhibitor bortezomib in p53-deficient 4T1 cells. Therefore, novel therapeutic strategies targeting these anti-apoptotic or pro-apoptotic proteins as well as inhibiting the proteasome simultaneously may be more effective against cancer cells. The proteins identified here present new avenues for the development of anti-cancer drugs.
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Affiliation(s)
- Azmi Yerlikaya
- Dumlupınar University, Faculty of Medicine, Department of Medical Biology, Kütahya, Turkey.
| | - Emrah Okur
- Dumlupınar University, Art and Science Faculty, Department of Biology, Kütahya, Turkey
| | - Ahmet Tarık Baykal
- İstanbul Medipol University, Medical School, Department of Medical Biochemistry, İstanbul, Turkey
| | - Ceyda Acılan
- TÜBİTAK, MAM, Genetic Engineering and Biotechnology Department, Gebze, Kocaeli, Turkey
| | - Ihsan Boyacı
- İstanbul Medipol University, Vatan Clinic, İstanbul, 34214, Turkey
| | - Engin Ulukaya
- Department of Medical Biochemistry, Uludağ University, Bursa, Turkey
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Label-free LC-MSe in tissue and serum reveals protein networks underlying differences between benign and malignant serous ovarian tumors. PLoS One 2014; 9:e108046. [PMID: 25265318 PMCID: PMC4180266 DOI: 10.1371/journal.pone.0108046] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 08/21/2014] [Indexed: 11/19/2022] Open
Abstract
Purpose To identify proteins and (molecular/biological) pathways associated with differences between benign and malignant epithelial ovarian tumors. Experimental Procedures Serum of six patients with a serous adenocarcinoma of the ovary was collected before treatment, with a control group consisting of six matched patients with a serous cystadenoma. In addition to the serum, homogeneous regions of cells exhibiting uniform histology were isolated from benign and cancerous tissue by laser microdissection. We subsequently employed label-free liquid chromatography tandem mass spectrometry (LC-MSe) to identify proteins in these serum and tissues samples. Analyses of differential expression between samples were performed using Bioconductor packages and in-house scripts in the statistical software package R. Hierarchical clustering and pathway enrichment analyses were performed, as well as network enrichment and interactome analysis using MetaCore. Results In total, we identified 20 and 71 proteins that were significantly differentially expressed between benign and malignant serum and tissue samples, respectively. The differentially expressed protein sets in serum and tissue largely differed with only 2 proteins in common. MetaCore network analysis, however inferred GCR-alpha and Sp1 as common transcriptional regulators. Interactome analysis highlighted 14-3-3 zeta/delta, 14-3-3 beta/alpha, Alpha-actinin 4, HSP60, and PCBP1 as critical proteins in the tumor proteome signature based on their relative overconnectivity. The data have been deposited to the ProteomeXchange with identifier PXD001084. Discussion Our analysis identified proteins with both novel and previously known associations to ovarian cancer biology. Despite the small overlap between differentially expressed protein sets in serum and tissue, APOA1 and Serotransferrin were significantly lower expressed in both serum and cancer tissue samples, suggesting a tissue-derived effect in serum. Pathway and subsequent interactome analysis also highlighted common regulators in serum and tissue samples, suggesting a yet unknown role for PCBP1 in ovarian cancer pathophysiology.
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Comparison of two FFPE preparation methods using label-free shotgun proteomics: Application to tissues of diverticulitis patients. J Proteomics 2014; 112:250-61. [PMID: 25218866 DOI: 10.1016/j.jprot.2014.08.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/12/2014] [Accepted: 08/28/2014] [Indexed: 12/15/2022]
Abstract
UNLABELLED Formalin-fixed paraffin-embedded (FFPE) specimens of patients are useful sources of materials for clinical research and have recently gained interest for use in the discovery of clinical proteomic biomarkers. However, the critical step in this field is the ability to obtain an efficient and repeatable extraction using the limited quantities of material available for research in hospital biobanks. This work describes the evaluation of the peptide/protein extraction using FFPE sections treated by the following two methods before shotgun proteomic analysis: a commercial solution (FFPE-FASP) (filter aided sample preparation) and an antigen retrieval-derived protocol (On Slice AR). Their efficiencies and repeatabilities are compared using data-independent differential quantitative label-free analysis. FFPE-FASP was shown to be globally better both qualitatively and quantitatively than On Slice AR. FFPE-FASP was tested on several samples, and differential analysis was used to compare the tissues of diverticulitis patients (healthy and inflammatory tissues). In this differential proteomic analysis using retrospective clinical FFPE material, FFPE-FASP was reproducible and provided a high number of confident protein identifications, highlighting potential protein biomarkers. BIOLOGICAL SIGNIFICANCE In clinical proteomics, FFPE is an important resource for retrospective analysis and for the discovery of biomarkers. The challenge for FFPE shotgun proteomic analysis is preparation by an efficient and reproducible protocol, which includes protein extraction and digestion. In this study, we analyzed two different methods and evaluated their repeatabilities and efficiencies. We illustrated the reproducibility of the most efficient method, FFPE-FASP, by a pilot study on diverticulitis tissue and on FFPE samples amount accessible in hospital biobanks. These data showed that FFPE is suitable for use in clinical proteomics, especially when the FFPE-FASP method is combined with label-free shotgun proteomics as described in the workflow presented in this work.
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Law KP, Lim YP. Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring. Expert Rev Proteomics 2014; 10:551-66. [PMID: 24206228 DOI: 10.1586/14789450.2013.858022] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
New mass spectrometry (MS) methods, collectively known as data independent analysis and hyper reaction monitoring, have recently emerged. These methods hold promises to address the shortcomings of data-dependent analysis and selected reaction monitoring (SRM) employed in shotgun and targeted proteomics, respectively. They allow MS analyses of all species in a complex sample indiscriminately, or permit SRM-like experiments conducted with full high-resolution product ion spectra, potentially leading to higher sequence coverage or analytical selectivity. These methods include MS(E), all-ion fragmentation, Fourier transform-all reaction monitoring, SWATH Acquisition, multiplexed MS/MS, pseudo-SRM (pSRM) and parallel reaction monitoring (PRM). In this review, the strengths and pitfalls of these methods are discussed and illustrated with examples. In essence, the suitability of the use of each method is contingent on the biological questions posed. Although these methods do not fundamentally change the shape of proteomics, they are useful additional tools that should expedite biological discoveries.
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Affiliation(s)
- Kai Pong Law
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD4, Level 1, 14 Medical Drive, 117599, Singapore
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Ferraz MJ, Kallemeijn WW, Mirzaian M, Herrera Moro D, Marques A, Wisse P, Boot RG, Willems LI, Overkleeft H, Aerts J. Gaucher disease and Fabry disease: New markers and insights in pathophysiology for two distinct glycosphingolipidoses. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:811-25. [DOI: 10.1016/j.bbalip.2013.11.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 10/25/2013] [Accepted: 11/05/2013] [Indexed: 10/26/2022]
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Dator RP, Gaston KW, Limbach PA. Multiple enzymatic digestions and ion mobility separation improve quantification of bacterial ribosomal proteins by data independent acquisition liquid chromatography-mass spectrometry. Anal Chem 2014; 86:4264-70. [PMID: 24738621 PMCID: PMC4014174 DOI: 10.1021/ac404020j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Mass spectrometry-based quantification
of ribosomal proteins (r-proteins)
associated with mature ribosomes and ribosome assembly complexes is
typically accomplished by relative quantification strategies. These
strategies provide information on the relative stoichiometry of proteins
within the complex compared to a wild-type strain. Here we have evaluated
the applicability of a label-free approach, enhanced liquid chromatography–mass
spectrometry (LC–MSE), for absolute “ribosome-centric”
quantification of r-proteins in Escherichia coli mature ribosomes. Because the information obtained in this experiment
is related to the number of peptides identified per protein, experimental
conditions that allow accurate and reproducible quantification of
r-proteins were found. Using an additional dimension of gas-phase
separation through ion mobility and the use of multiple endoproteinase
digestion significantly improved quantification of proteins associated
with mature ribosomes. The actively translating ribosomes (polysomes)
contain amounts of proteins consistent with their known stoichiometry
within the complex. These measurements exhibited technical and biological
reproducibilities at %CV less than 15% and 35%, respectively. The
improved LC–MSE approach described here can be used
to characterize in vivo ribosome assembly complexes captured during
ribosome biogenesis and assembly under different perturbations (e.g.,
antibiotics, deletion mutants of assembly factors, oxidative stress,
nutrient deprivation). Quantitative analysis of these captured complexes
will provide information relating to the interplay and dynamics of
how these perturbations interfere with the assembly process.
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Affiliation(s)
- Romel P Dator
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, P.O. Box 210172, University of Cincinnati , Cincinnati, Ohio 45221-0172, United States
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Alberio T, Bondi H, Colombo F, Alloggio I, Pieroni L, Urbani A, Fasano M. Mitochondrial proteomics investigation of a cellular model of impaired dopamine homeostasis, an early step in Parkinson's disease pathogenesis. MOLECULAR BIOSYSTEMS 2014; 10:1332-44. [PMID: 24675778 DOI: 10.1039/c3mb70611g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Impaired dopamine homeostasis is an early event in the pathogenesis of Parkinson's disease. Generation of intracellular reactive oxygen species consequent to dopamine oxidation leads to mitochondrial dysfunction and eventually cell death. Alterations in the mitochondrial proteome due to dopamine exposure were investigated in the SH-SY5Y human neuroblastoma cell line. The combination of two orthogonal proteomic approaches, two-dimensional electrophoresis and shotgun proteomics (proteomeXchange dataset PXD000838), was used to highlight the specific pathways perturbed by the increase of intracellular dopamine, in comparison with those perturbed by a specific mitochondrial toxin (4-methylphenylpyridinium, MPP(+)), a neurotoxin causing Parkinsonism-like symptoms in animal models. Proteins altered by MPP(+) did not completely overlap with those affected by dopamine treatment. In particular, the MPP(+) target complex I component NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 was not affected by dopamine together with 26 other proteins. The comparison of proteomics approaches highlighted the fragmentation of some mitochondrial proteins, suggesting an alteration of the mitochondrial protease activity. Pathway and disease association analysis of the proteins affected by dopamine revealed the overrepresentation of the Parkinson's disease and the parkin-ubiquitin proteasomal system pathways and of gene ontologies associated with generation of precursor metabolites and energy, response to topologically incorrect proteins and programmed cell death. These alterations may be globally interpreted in part as the result of a direct effect of dopamine on mitochondria (e.g. alteration of the mitochondrial protease activity) and in part as the effect on mitochondria of a general activation of cellular processes (e.g. regulation of programmed cell death).
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Affiliation(s)
- Tiziana Alberio
- Biomedical Research Division, Department of Theoretical and Applied Sciences, University of Insubria, Busto Arsizio, Italy.
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A mass spectrometry-based workflow for the proteomic analysis of in vitro cultured cell subsets isolated by means of laser capture microdissection. Anal Bioanal Chem 2014; 406:2817-25. [PMID: 24633565 DOI: 10.1007/s00216-014-7724-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 12/19/2013] [Accepted: 02/24/2014] [Indexed: 01/18/2023]
Abstract
This paper describes a microproteomic workflow that is useful for simultaneously identifying and quantifying proteins from a minimal number of morphotypically heterogeneous cultured adherent cells. The analytical strategy makes use of laser capture microdissection, an effective means of harvesting pure cell populations, and label-free mass spectrometry. We optimised the workflow with particular reference to cell fixation which is crucial for successful laser-based microdissection and also downstream molecular studies. In addition, we defined the minimum number of cells to be isolated and analysed for satisfactory proteome coverage. To set up this workflow, we choose human monocyte-derived macrophages spontaneously differentiated in vitro. These cells, under our culture conditions, show distinct morphotypes, reminiscent of the heterogeneity observed in tissues in various homeostatic and pathological states, e.g. atherosclerosis. This optimised workflow may provide new insights into biology and pathology of heterogeneous cell in culture, particularly when other cell selection approaches are not suitable.
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Quantification by LC–MSE of outer membrane vesicle proteins of the Bexsero® vaccine. Vaccine 2014; 32:1273-9. [DOI: 10.1016/j.vaccine.2014.01.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 12/09/2013] [Accepted: 01/02/2014] [Indexed: 01/24/2023]
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Muntel J, Fromion V, Goelzer A, Maaβ S, Mäder U, Büttner K, Hecker M, Becher D. Comprehensive absolute quantification of the cytosolic proteome of Bacillus subtilis by data independent, parallel fragmentation in liquid chromatography/mass spectrometry (LC/MS(E)). Mol Cell Proteomics 2014; 13:1008-19. [PMID: 24696501 DOI: 10.1074/mcp.m113.032631] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In the growing field of systems biology, the knowledge of protein concentrations is highly required to truly understand metabolic and adaptational networks within the cells. Therefore we established a workflow relying on long chromatographic separation and mass spectrometric analysis by data independent, parallel fragmentation of all precursor ions at the same time (LC/MS(E)). By prevention of discrimination of co-eluting low and high abundant peptides a high average sequence coverage of 40% could be achieved, resulting in identification of almost half of the predicted cytosolic proteome of the Gram-positive model organism Bacillus subtilis (>1,050 proteins). Absolute quantification was achieved by correlation of average MS signal intensities of the three most intense peptides of a protein to the signal intensity of a spiked standard protein digest. Comparative analysis with heavily labeled peptides (AQUA approach) showed the use of only one standard digest is sufficient for global quantification. The quantification results covered almost four orders of magnitude, ranging roughly from 10 to 150,000 copies per cell. To prove this method for its biological relevance selected physiological aspects of B. subtilis cells grown under conditions requiring either amino acid synthesis or alternatively amino acid degradation were analyzed. This allowed both in particular the validation of the adjustment of protein levels by known regulatory events and in general a perspective of new insights into bacterial physiology. Within new findings the analysis of "protein costs" of cellular processes is extremely important. Such a comprehensive and detailed characterization of cellular protein concentrations based on data independent, parallel fragmentation in liquid chromatography/mass spectrometry (LC/MS(E)) data has been performed for the first time and should pave the way for future comprehensive quantitative characterization of microorganisms as physiological entities.
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Affiliation(s)
- Jan Muntel
- Institute for Microbiology, Ernst Moritz Arndt University Greifswald, D-17487 Greifswald, Germany
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Boot RG, van Breemen MJ, Wegdam W, Sprenger RR, de Jong S, Speijer D, Hollak CEM, Van Dussen L, Hoefsloot HCJ, Smilde AK, De Koster CG, Vissers JPC, Aerts JMFG. Gaucher disease: a model disorder for biomarker discovery. Expert Rev Proteomics 2014; 6:411-9. [DOI: 10.1586/epr.09.54] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Li C, Qiu Q, Wang Y, Li P, Xiao C, Wang H, Lin Y, Wang W. Time course label-free quantitative analysis of cardiac muscles of rats after myocardial infarction. MOLECULAR BIOSYSTEMS 2014; 10:505-13. [PMID: 24382414 DOI: 10.1039/c3mb70422j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Heart failure is a worldwide cause of mortality and morbidity and is the ultimate ending of a variety of complex diseases. This reflects our incomplete understanding of its underlying molecular mechanisms and furthermore increases the complexity of the disease. To better understand the molecular mechanisms of heart failure, we investigated dynamic proteomic differences between the heart tissue of myocardial infarction rats and the rats in the sham group at days 4, 14, 28, 45 after operation. Using a label-free quantitative proteomic approach based on nanoscale ultra-performance liquid chromatography-ESI-MS(E), 133 proteins were identified at the four time points in 8 groups. 13 non-redundant proteins changed dynamically after acute myocardial infarction (AMI) in rat left ventricular (LV) tissue, including cytoskeletal proteins, metabolic enzymes, oxidative stress related proteins and ion channel proteins. The network analysis showed that the differential protein might play an important role in lipid metabolism and hypertrophic cardiomyopathy. The dynamic changes in the expression of beta-actin, alpha B-crystallin (CryAB), heat shock protein 8(HSP8), desmin and l-lactate dehydrogenase B (LDHB) were tested by the western-blot assay, and the results were consistent with the label-free quantitative proteomic results. Correlative analysis indicates that the CryAB and desmin have a better linear relation with heart function (ejection fraction) than cardiac troponin T (cTNT). Our results provide the first experimental evidence of the proteins that are differentially expressed following myocardial infarction, using time-course label-free quantitative proteomics in vivo without ischemia-reperfusion injury or myocardial ischemia. These differential functional proteins (especially CryAB and desmin) have different patterns during the myocardial infarction, which may partially account for the underlying mechanisms involved in cardiac rehabilitation.
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Affiliation(s)
- Chun Li
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
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Tu WJ, Liu XY, Dong H, Yu Y, Wang Y, Chen H. Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatase 1: A Meaningful and Independent Marker to Predict Stroke in the Chinese Population. J Mol Neurosci 2013; 52:507-14. [PMID: 24352714 DOI: 10.1007/s12031-013-0206-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 12/05/2013] [Indexed: 02/07/2023]
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Benjamin AM, Thompson JW, Soderblom EJ, Geromanos SJ, Henao R, Kraus VB, Moseley MA, Lucas JE. A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information. BMC Bioinformatics 2013; 14:364. [PMID: 24341404 PMCID: PMC3878627 DOI: 10.1186/1471-2105-14-364] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 12/06/2013] [Indexed: 11/30/2022] Open
Abstract
Background The goal of many proteomics experiments is to determine the abundance of proteins in biological samples, and the variation thereof in various physiological conditions. High-throughput quantitative proteomics, specifically label-free LC-MS/MS, allows rapid measurement of thousands of proteins, enabling large-scale studies of various biological systems. Prior to analyzing these information-rich datasets, raw data must undergo several computational processing steps. We present a method to address one of the essential steps in proteomics data processing - the matching of peptide measurements across samples. Results We describe a novel method for label-free proteomics data alignment with the ability to incorporate previously unused aspects of the data, particularly ion mobility drift times and product ion information. We compare the results of our alignment method to PEPPeR and OpenMS, and compare alignment accuracy achieved by different versions of our method utilizing various data characteristics. Our method results in increased match recall rates and similar or improved mismatch rates compared to PEPPeR and OpenMS feature-based alignment. We also show that the inclusion of drift time and product ion information results in higher recall rates and more confident matches, without increases in error rates. Conclusions Based on the results presented here, we argue that the incorporation of ion mobility drift time and product ion information are worthy pursuits. Alignment methods should be flexible enough to utilize all available data, particularly with recent advancements in experimental separation methods.
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Affiliation(s)
- Ashlee M Benjamin
- Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, North Carolina, USA.
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Kaga E, Karademir B, Baykal AT, Ozer NK. Identification of differentially expressed proteins in atherosclerotic aorta and effect of vitamin E. J Proteomics 2013; 92:260-73. [DOI: 10.1016/j.jprot.2013.06.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 06/06/2013] [Accepted: 06/09/2013] [Indexed: 10/26/2022]
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Parviainen VI, Joenväärä S, Tohmola N, Renkonen R. Label-free mass spectrometry proteome quantification of human embryonic kidney cells following 24 hours of sialic acid overproduction. Proteome Sci 2013; 11:38. [PMID: 23915316 PMCID: PMC3750590 DOI: 10.1186/1477-5956-11-38] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/25/2013] [Indexed: 01/15/2023] Open
Abstract
Background Cell surface glycoprotein sialylation is one of the most ubiquitous glycan modifications found on higher eukaryotes. The surface sialylation pattern of cells is influenced by the cellular environment but also by the Golgi sialyltransferase activity and flux of metabolites through sialic acid producing pathways. Altered cell surface sialic acid patterns have been observed in several cancers and other pathological conditions. In this experiment we examined the cellular proteomic changes that occur in human embryonic kidney cells after 24 hours of sialic acid overproduction using N-Acetylmannosamine. We utilized high resolution mass spectrometry and label free protein quantification to characterize the relative changes in protein abundance as well as multiple reaction monitoring to quantify the cellular sialic acid levels. Results Using N-Acetylmannosamine we were able to induce sialic acid production to almost 70-fold compared to non-induced control cells. Mass spectrometric analysis of cellular proteome of control and induced cells identified 1802 proteins of which 105 displayed significant changes in abundance. Functional analysis of the resulting relative changes in protein abundance revealed regulation of several cellular pathways including protein transport, metabolic and signaling pathways and remodeling of epithelial adherens junctions. We also identified several physically interacting co-regulated proteins in the set of changed proteins. Conclusions In this experiment we show that increased metabolic flux through sialic acid producing pathway affects the abundance of several protein transport, epithelial adherens junction, signaling and metabolic pathway related proteins.
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Affiliation(s)
- Ville I Parviainen
- Transplantation Laboratory, Haartman Institute, University of Helsinki & HUSLAB, Helsinki University Central Hospital, Helsinki, Finland.
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Wang J, Lam H. Graph-based peak alignment algorithms for multiple liquid chromatography-mass spectrometry datasets. ACTA ACUST UNITED AC 2013; 29:2469-76. [PMID: 23904508 DOI: 10.1093/bioinformatics/btt435] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
UNLABELLED Liquid chromatography coupled to mass spectrometry (LC-MS) is the dominant technological platform for proteomics. An LC-MS analysis of a complex biological sample can be visualized as a 'map' of which the positional coordinates are the mass-to-charge ratio (m/z) and chromatographic retention time (RT) of the chemical species profiled. Label-free quantitative proteomics requires the alignment and comparison of multiple LC-MS maps to ascertain the reproducibility of experiments or reveal proteome changes under different conditions. The main challenge in this task lies in correcting inevitable RT shifts. Similar, but not identical, LC instruments and settings can cause peptides to elute at very different times and sometimes in a different order, violating the assumptions of many state-of-the-art alignment tools. To meet this challenge, we developed LWBMatch, a new algorithm based on weighted bipartite matching. Unlike existing tools, which search for accurate warping functions to correct RT shifts, we directly seek a peak-to-peak mapping by maximizing a global similarity function between two LC-MS maps. For alignment tasks with large RT shifts (>500 s), an approximate warping function is determined by locally weighted scatterplot smoothing of potential matched features, detected using a novel voting scheme based on co-elution. For validation, we defined the ground truth for alignment success based on tandem mass spectrometry identifications from sequence searching. We showed that our method outperforms several existing tools in terms of precision and recall, and is capable of aligning maps from different instruments and settings. AVAILABILITY Available at https://sourceforge.net/projects/rt-alignment/.
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Affiliation(s)
- Jijie Wang
- Division of Biomedical Engineering and Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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Moon PG, Kwack MH, Lee JE, Cho YE, Park JH, Hwang D, Kim MK, Kim JC, Sung YK, Baek MC. Proteomic analysis of balding and non-balding mesenchyme-derived dermal papilla cells from androgenetic alopecia patients using on-line two-dimensional reversed phase-reversed phase LC–MS/MS. J Proteomics 2013; 85:174-91. [DOI: 10.1016/j.jprot.2013.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/15/2013] [Accepted: 04/04/2013] [Indexed: 01/20/2023]
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Ning DL, Liu CC, Liu JW, Shen Z, Chen S, Liu F, Wang BC, Yang CP. Label-free quantitative proteomics analysis of dormant terminal buds of poplar. Mol Biol Rep 2013; 40:4529-42. [PMID: 23677710 DOI: 10.1007/s11033-013-2548-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 04/29/2013] [Indexed: 01/02/2023]
Abstract
Induction and break of bud dormancy are important features for perennial plants surviving extreme seasonal variations in climate. However, the molecular mechanism of the dormancy regulation, still remain poorly understood. To better understand the molecular basis of poplar bud dormancy, we used a label-free quantitative proteomics method based on nanoscale ultra performance liquid chromatography-ESI-MS(E) for investigation of differential protein expression during dormancy induction, dormancy, and dormancy break in apical buds of poplar (Populus simonii × P. nigra). Among these identified over 300 proteins during poplar bud dormancy, there are 74 significantly altered proteins, most of which involved in carbohydrate metabolism (22 %), redox regulation (19 %), amino acid transport and metabolism (10 %), and stress response (8 %). Thirty-one of these proteins were up-regulated, five were down-regulated during three phase, and thirty-eight were expressed specifically under different conditions. Pathway analysis suggests that there are still the presence of various physiological activities and a particular influence on photosynthesis and energy metabolism during poplar bud dormancy. Differential expression patterns were identified for key enzymes involved in major metabolic pathways such as glycolysis and the pentose phosphate pathway, thus manifesting the interplay of intricate molecular events in energy generation for new protein synthesis in the dormant buds. Furthermore, there are significant changes present in redox regulation and defense response proteins, for instance in peroxidase and ascorbate peroxidase. Overall, this study provides a better understanding of the possible regulation mechanisms during poplar bud dormancy.
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Affiliation(s)
- De-Li Ning
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
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Di Girolamo F, Del Chierico F, Caenaro G, Lante I, Muraca M, Putignani L. Human serum proteome analysis: new source of markers in metabolic disorders. Biomark Med 2013; 6:759-73. [PMID: 23227840 DOI: 10.2217/bmm.12.92] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The prevalence of metabolic disorders (MDs), especially diabetes, is rapidly increasing worldwide, leading to an increasing risk of cardiovascular and other socially relevant complications. To boost MD biomarker discovery, advanced proteomics can harmonize metabolomics. Indeed, the rapid development of mass spectrometry (MS) has designated proteomics as an emerging platform to interrogate the plasma/serum proteome for the discovery of next-generation biomarkers exploitable for risk assessment, early detection and prognosis of MDs. Preanalytical plasma/serum treatment, such as combinatorial peptide ligand libraries with nano-liquid chromatography coupled with tandem MS or selected reaction monitoring coupled to triple-quadrupole time-of-flight instruments, are proven clinical laboratory techniques for quantitative analyses. New strategies, such as SWATH™ MS, which allows us to systematically characterize and quantify query sample sets of 'any protein of interest' in complex biological samples, may dramatically improve next-generation MD biomarkers, especially considering the plethora of candidates coming from the 'bioreactor' gut microbiota affecting MD onset and progression.
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Affiliation(s)
- Francesco Di Girolamo
- Parasitology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
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Pieragostino D, Agnifili L, Fasanella V, D'Aguanno S, Mastropasqua R, Di Ilio C, Sacchetta P, Urbani A, Del Boccio P. Shotgun proteomics reveals specific modulated protein patterns in tears of patients with primary open angle glaucoma naïve to therapy. MOLECULAR BIOSYSTEMS 2013; 9:1108-16. [PMID: 23580065 DOI: 10.1039/c3mb25463a] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Primary open angle glaucoma (POAG) is one of the main causes of irreversible blindness worldwide. The pathogenesis of POAG is still unclear. Alteration and sclerosis of trabecular meshwork with changes in aqueous humor molecular composition seem to play the key role. Increased intraocular pressure is widely known to be the main risk factor for the onset and progression of the disease. Unfortunately, the early diagnosis of POAG still remains the main challenge. In order to provide insight into the patho-physiology of glaucoma, here we report a shotgun proteomics approach to tears of patients with POAG naïve to therapy. Our proteomics results showed 27 differential tear proteins in POAG vs. CTRL comparison (25 up regulated proteins in the POAG group and two unique proteins in the CTRL group), 16 of which were associated with inflammatory response, free radical scavenging, cell-to-cell signaling and interaction. Overall the protein modulation shown in POAG tears proves the involvement of biochemical networks linked to inflammation. Among all regulated proteins, a sub-group of 12 up-regulated proteins in naïve POAG patients were found to be down-regulated in medically controlled POAG patients treated with prostanoid analogues (PGA), as reported in our previous work (i.e., lipocalin-1, lysozyme C, lactotransferrin, proline-rich-protein 4, prolactin-inducible protein, zinc-alpha-2-glycoprotein, polymeric immunoglobulin receptor, cystatin S, Ig kappa chain C region, Ig alpha-2 chain C region, immunoglobulin J chain, Ig alpha-1 chain C region). In summary, our findings indicate that the POAG tears protein expression is a mixture of increased inflammatory proteins that could be potential biomarkers of the disease, and their regulation may be involved in the mechanism by which PGA are able to decrease the intraocular pressure in glaucoma patients.
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Affiliation(s)
- Damiana Pieragostino
- Department of Experimental and Clinical Sciences, University G. d'Annunzio of Chieti-Pescara, Via dei Vestini, 66100 Chieti, Italy.
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