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Gobena S, Admassu B, Kinde MZ, Gessese AT. Proteomics and Its Current Application in Biomedical Area: Concise Review. ScientificWorldJournal 2024; 2024:4454744. [PMID: 38404932 PMCID: PMC10894052 DOI: 10.1155/2024/4454744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024] Open
Abstract
Biomedical researchers tirelessly seek cutting-edge technologies to advance disease diagnosis, drug discovery, and therapeutic interventions, all aimed at enhancing human and animal well-being. Within this realm, proteomics stands out as a pivotal technology, focusing on extensive studies of protein composition, structure, function, and interactions. Proteomics, with its subdivisions of expression, structural, and functional proteomics, plays a crucial role in unraveling the complexities of biological systems. Various sophisticated techniques are employed in proteomics, including polyacrylamide gel electrophoresis, mass spectrometry analysis, NMR spectroscopy, protein microarray, X-ray crystallography, and Edman sequencing. These methods collectively contribute to the comprehensive understanding of proteins and their roles in health and disease. In the biomedical field, proteomics finds widespread application in cancer research and diagnosis, stem cell studies, and the diagnosis and research of both infectious and noninfectious diseases. In addition, it plays a pivotal role in drug discovery and the emerging frontier of personalized medicine. The versatility of proteomics allows researchers to delve into the intricacies of molecular mechanisms, paving the way for innovative therapeutic approaches. As infectious and noninfectious diseases continue to emerge and the field of biomedical research expands, the significance of proteomics becomes increasingly evident. Keeping abreast of the latest developments in proteomics applications becomes paramount for the development of therapeutics, translational research, and study of diverse diseases. This review aims to provide a comprehensive overview of proteomics, offering a concise outline of its current applications in the biomedical domain. By doing so, it seeks to contribute to the understanding and advancement of proteomics, emphasizing its pivotal role in shaping the future of biomedical research and therapeutic interventions.
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Affiliation(s)
- Semira Gobena
- College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Bemrew Admassu
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Mebrie Zemene Kinde
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
| | - Abebe Tesfaye Gessese
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia
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2
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Salazar IL, Lourenço AST, Manadas B, Baldeiras I, Ferreira C, Teixeira AC, Mendes VM, Novo AM, Machado R, Batista S, Macário MDC, Grãos M, Sousa L, Saraiva MJ, Pais AACC, Duarte CB. Posttranslational modifications of proteins are key features in the identification of CSF biomarkers of multiple sclerosis. J Neuroinflammation 2022; 19:44. [PMID: 35135578 PMCID: PMC8822857 DOI: 10.1186/s12974-022-02404-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/26/2022] [Indexed: 12/27/2022] Open
Abstract
Background Multiple sclerosis is an inflammatory and degenerative disease of the central nervous system (CNS) characterized by demyelination and concomitant axonal loss. The lack of a single specific test, and the similarity to other inflammatory diseases of the central nervous system, makes it difficult to have a clear diagnosis of multiple sclerosis. Therefore, laboratory tests that allows a clear and definite diagnosis, as well as to predict the different clinical courses of the disease are of utmost importance. Herein, we compared the cerebrospinal fluid (CSF) proteome of patients with multiple sclerosis (in the relapse–remitting phase of the disease) and other diseases of the CNS (inflammatory and non-inflammatory) aiming at identifying reliable biomarkers of multiple sclerosis. Methods CSF samples from the discovery group were resolved by 2D-gel electrophoresis followed by identification of the protein spots by mass spectrometry. The results were analyzed using univariate (Student’s t test) and multivariate (Hierarchical Cluster Analysis, Principal Component Analysis, Linear Discriminant Analysis) statistical and numerical techniques, to identify a set of protein spots that were differentially expressed in CSF samples from patients with multiple sclerosis when compared with other two groups. Validation of the results was performed in samples from a different set of patients using quantitative (e.g., ELISA) and semi-quantitative (e.g., Western Blot) experimental approaches. Results Analysis of the 2D-gels showed 13 protein spots that were differentially expressed in the three groups of patients: Alpha-1-antichymotrypsin, Prostaglandin-H2-isomerase, Retinol binding protein 4, Transthyretin (TTR), Apolipoprotein E, Gelsolin, Angiotensinogen, Agrin, Serum albumin, Myosin-15, Apolipoprotein B-100 and EF-hand calcium-binding domain—containing protein. ELISA experiments allowed validating part of the results obtained in the proteomics analysis and showed that some of the alterations in the CSF proteome are also mirrored in serum samples from multiple sclerosis patients. CSF of multiple sclerosis patients was characterized by TTR oligomerization, thus highlighting the importance of analyzing posttranslational modifications of the proteome in the identification of novel biomarkers of the disease. Conclusions The model built based on the results obtained upon analysis of the 2D-gels and in the validation phase attained an accuracy of about 80% in distinguishing multiple sclerosis patients and the other two groups. Supplementary Information The online version contains supplementary material available at 10.1186/s12974-022-02404-2.
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Affiliation(s)
- Ivan L Salazar
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Ana S T Lourenço
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Inês Baldeiras
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Cláudia Ferreira
- Coimbra Chemistry Centre, Department of Chemistry, University of Coimbra, Coimbra, Portugal
| | - Anabela Claro Teixeira
- Molecular Neurobiology Group, Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
| | - Vera M Mendes
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ana Margarida Novo
- Neurology Department, CHUC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Rita Machado
- Neurology Department, CHUC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Sónia Batista
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Neurology Department, CHUC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Maria do Carmo Macário
- Neurology Department, CHUC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Mário Grãos
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal.,Biocant-Associação de Transferência de Tecnologia, Cantanhede, Portugal
| | - Lívia Sousa
- Neurology Department, CHUC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Maria João Saraiva
- Molecular Neurobiology Group, Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
| | - Alberto A C C Pais
- Coimbra Chemistry Centre, Department of Chemistry, University of Coimbra, Coimbra, Portugal
| | - Carlos B Duarte
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal. .,Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
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3
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Tsypin M, Asmellash S, Meyer K, Touchet B, Roder H. Extending the information content of the MALDI analysis of biological fluids via multi-million shot analysis. PLoS One 2019; 14:e0226012. [PMID: 31815946 PMCID: PMC6901224 DOI: 10.1371/journal.pone.0226012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 11/18/2019] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION Reliable measurements of the protein content of biological fluids like serum or plasma can provide valuable input for the development of personalized medicine tests. Standard MALDI analysis typically only shows high abundance proteins, which limits its utility for test development. It also exhibits reproducibility issues with respect to quantitative measurements. In this paper we show how the sensitivity of MALDI profiling of intact proteins in unfractionated human serum can be substantially increased by exposing a sample to many more laser shots than are commonly used. Analytical reproducibility is also improved. METHODS To assess what is theoretically achievable we utilized spectra from the same samples obtained over many years and combined them to generate MALDI spectral averages of up to 100,000,000 shots for a single sample, and up to 8,000,000 shots for a set of 40 different serum samples. Spectral attributes, such as number of peaks and spectral noise of such averaged spectra were investigated together with analytical reproducibility as a function of the number of shots. We confirmed that results were similar on MALDI instruments from different manufacturers. RESULTS We observed an expected decrease of noise, roughly proportional to the square root of the number of shots, over the whole investigated range of the number of shots (5 orders of magnitude), resulting in an increase in the number of reliably detected peaks. The reproducibility of the amplitude of these peaks, measured by CV and concordance analysis also improves with very similar dependence on shot number, reaching median CVs below 2% for shot numbers > 4 million. Measures of analytical information content and association with biological processes increase with increasing number of shots. CONCLUSIONS We demonstrate that substantially increasing the number of laser shots in a MALDI-TOF analysis leads to more informative and reliable data on the protein content of unfractionated serum. This approach has already been used in the development of clinical tests in oncology.
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Affiliation(s)
- Maxim Tsypin
- Biodesix Inc., Boulder, Colorado, United States of America
| | | | - Krista Meyer
- Biodesix Inc., Boulder, Colorado, United States of America
| | | | - Heinrich Roder
- Biodesix Inc., Boulder, Colorado, United States of America
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4
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Singh V, Tripathi A, Dutta R. Proteomic Approaches to Decipher Mechanisms Underlying Pathogenesis in Multiple Sclerosis Patients. Proteomics 2019; 19:e1800335. [PMID: 31119864 PMCID: PMC6690771 DOI: 10.1002/pmic.201800335] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 05/15/2019] [Indexed: 12/13/2022]
Abstract
Multiple sclerosis (MS) is a chronic inflammatory demyelinating and neurodegenerative disease of the central nervous system (CNS). The cause of MS is unknown, with no effective therapies available to halt the progressive neurological disability. Development of new and improvement of existing therapeutic strategies therefore require a better understanding of MS pathogenesis, especially during the progressive phase of the disease. This can be achieved through development of biomarkers that can help to identify disease pathophysiology and monitor disease progression. Proteomics is a powerful and promising tool to accelerate biomarker detection and contribute to novel therapeutics. In this review, an overview of how proteomic technology using CNS tissues and biofluids from MS patients has provided important clues to the pathogenesis of MS is provided. Current publications, pitfalls, as well as directions of future research involving proteomic approaches to understand the pathogenesis of MS are discussed.
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Affiliation(s)
- Vaibhav Singh
- Department of Neurosciences, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Ajai Tripathi
- Department of Neurosciences, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Ranjan Dutta
- Department of Neurosciences, Cleveland Clinic, Cleveland, OH, 44195, USA
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5
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Valko PO, Roschitzki B, Faigle W, Grossmann J, Panse C, Biro P, Dambach M, Spahn DR, Weller M, Martin R, Baumann CR. In search of cerebrospinal fluid biomarkers of fatigue in multiple sclerosis: A proteomics study. J Sleep Res 2018; 28:e12721. [DOI: 10.1111/jsr.12721] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/19/2018] [Accepted: 05/25/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Philipp O. Valko
- Department of NeurologyUniversity Hospital ZurichUniversity of Zurich Zurich Switzerland
| | - Bernd Roschitzki
- Functional Genomics Center Zurich University of Zurich/ETH Zurich Zurich Switzerland
| | - Wolfgang Faigle
- Department of NeurologyUniversity Hospital ZurichUniversity of Zurich Zurich Switzerland
| | - Jonas Grossmann
- Functional Genomics Center Zurich University of Zurich/ETH Zurich Zurich Switzerland
| | - Christian Panse
- Functional Genomics Center Zurich University of Zurich/ETH Zurich Zurich Switzerland
| | - Peter Biro
- Department of AnesthesiologyUniversity Hospital ZurichUniversity of Zurich Zurich Switzerland
| | - Micha Dambach
- Department of AnesthesiologyUniversity Hospital ZurichUniversity of Zurich Zurich Switzerland
| | - Donat R. Spahn
- Department of AnesthesiologyUniversity Hospital ZurichUniversity of Zurich Zurich Switzerland
| | - Michael Weller
- Department of NeurologyUniversity Hospital ZurichUniversity of Zurich Zurich Switzerland
| | - Roland Martin
- Department of NeurologyUniversity Hospital ZurichUniversity of Zurich Zurich Switzerland
| | - Christian R. Baumann
- Department of NeurologyUniversity Hospital ZurichUniversity of Zurich Zurich Switzerland
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6
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Kernalléguen A, Steinhoff R, Bachler S, Dittrich PS, Saint-Marcoux F, El Bakhi S, Vorspan F, Léonetti G, Lafitte D, Pélissier-Alicot AL, Zenobi R. High-Throughput Monitoring of Cocaine and Its Metabolites in Hair Using Microarrays for Mass Spectrometry and Matrix-Assisted Laser Desorption/Ionization-Tandem Mass Spectrometry. Anal Chem 2018; 90:2302-2309. [DOI: 10.1021/acs.analchem.7b04693] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Angéline Kernalléguen
- Department
of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
- Aix Marseille University, INSERM, CRO2, UMR_S
911, PIT2, 13005 Marseille, France
- Aix Marseille University, CNRS, EFS, ADES UMR
7268, 13005 Marseille, France
| | - Robert Steinhoff
- Department
of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Simon Bachler
- Bioanalytics
Group, Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Petra S. Dittrich
- Bioanalytics
Group, Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | | | - Souleiman El Bakhi
- Laboratoire
de Pharmacologie et Toxicologie, CHU Limoges, 87000 Limoges, France
| | - Florence Vorspan
- Services
de Psychiatrie et de Médecine Addictologique, Hôpital Fernand Widal, APHP, 75475 Paris, France
- Universités Paris Descartes-Paris Diderot, INSERM UMR-S
1114, 75013 Paris France
| | - Georges Léonetti
- Aix Marseille University, CNRS, EFS, ADES UMR
7268, 13005 Marseille, France
- Aix Marseille University, APHM, CHU Timone, Service de
Médecine Légale, 13005 Marseille, France
| | - Daniel Lafitte
- Aix Marseille University, INSERM, CRO2, UMR_S
911, PIT2, 13005 Marseille, France
| | | | - Renato Zenobi
- Department
of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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7
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Stoop MP, Runia TF, Stingl C, van der Vuurst de Vries RM, Luider TM, Hintzen RQ. Decreased Neuro-Axonal Proteins in CSF at First Attack of Suspected Multiple Sclerosis. Proteomics Clin Appl 2017; 11. [PMID: 28941200 DOI: 10.1002/prca.201700005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 08/23/2017] [Indexed: 01/10/2023]
Abstract
The pathology of multiple sclerosis is located in the central nervous system, therefore cerebrospinal fluid (CSF) is an attractive biofluid for biomarker research for proteins related to the early stages of this disease. In this study, the CSF proteome of patients with a clinically isolated syndrome of demyelination (CIS, a first attack of multiple sclerosis) is compared to the CSF proteome of control patients to identify differentially abundant proteins. CSF samples of 47 CIS patients and 45 control subjects are enzymatically digested and subsequently measured by LC-MS/MS (LTQ-Orbitrap). Following mass spectrometry differential abundances of the identified proteins between groups are investigated. A total of 3159 peptides are identified, relating to 485 proteins. One protein is significantly more abundant in CSF of CIS patients than in controls: Ig kappa chain C region. In contrast, 35 proteins are significantly lower in CIS patients than controls, most of them with functions in nervous system development and function, such as amyloid-like protein 1 (validated by ELISA in an independent sample set (p < 0.01)), contactin 1, contactin 2 and neuronal cell adhesion molecule. A remarkably lower abundance of neuro-axonal proteins is observed in patients with a first demyelinating event compared to controls.
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Affiliation(s)
- Marcel P Stoop
- Departments of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | - Tessel F Runia
- Departments of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | - Christoph Stingl
- Departments of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | | | - Theo M Luider
- Departments of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | - Rogier Q Hintzen
- Departments of Neurology, Erasmus MC, Rotterdam, the Netherlands.,Departments of Immunology, Erasmus MC, Rotterdam, the Netherlands
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8
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Bastos P, Ferreira R, Manadas B, Moreira PI, Vitorino R. Insights into the human brain proteome: Disclosing the biological meaning of protein networks in cerebrospinal fluid. Crit Rev Clin Lab Sci 2017; 54:185-204. [PMID: 28393582 DOI: 10.1080/10408363.2017.1299682] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cerebrospinal fluid (CSF) is an excellent source of biological information regarding the nervous system, once it is in close contact and accurately reflects alterations in this system. Several studies have analyzed differential protein profiles of CSF samples between healthy and diseased human subjects. However, the pathophysiological mechanisms and how CSF proteins relate to diseases are still poorly known. By applying bioinformatics tools, we attempted to provide new insights on the biological and functional meaning of proteomics data envisioning the identification of putative disease biomarkers. Bioinformatics analysis of data retrieved from 99 mass spectrometry (MS)-based studies on CSF profiling highlighted 1985 differentially expressed proteins across 49 diseases. A large percentage of the modulated proteins originate from exosome vesicles, and the majority are involved in either neuronal cell growth, development, maturation, migration, or neurotransmitter-mediated cellular communication. Nevertheless, some diseases present a unique CSF proteome profile, which were critically analyzed in the present study. For instance, 48 proteins were found exclusively upregulated in the CSF of patients with Alzheimer's disease and are mainly involved in steroid esterification and protein activation cascade processes. A higher number of exclusively upregulated proteins were found in the CSF of patients with multiple sclerosis (76 proteins) and with bacterial meningitis (70 proteins). Whereas in multiple sclerosis, these proteins are mostly involved in the regulation of RNA metabolism and apoptosis, in bacterial meningitis the exclusively upregulated proteins participate in inflammation and antibacterial humoral response, reflecting disease pathogenesis. The exploration of the contribution of exclusively upregulated proteins to disease pathogenesis will certainly help to envision potential biomarkers in the CSF for the clinical management of nervous system diseases.
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Affiliation(s)
- Paulo Bastos
- a Department of Chemistry , University of Aveiro , Aveiro , Portugal.,b Department of Medical Sciences , Institute for Biomedicine - iBiMED, University of Aveiro , Aveiro , Portugal
| | - Rita Ferreira
- c QOPNA, Department of Chemistry , University of Aveiro , Aveiro , Portugal
| | - Bruno Manadas
- d CNC, Center for Neuroscience and Cell Biology, University of Coimbra , Coimbra , Portugal
| | - Paula I Moreira
- d CNC, Center for Neuroscience and Cell Biology, University of Coimbra , Coimbra , Portugal.,e Laboratory of Physiology, Faculty of Medicine , University of Coimbra , Coimbra , Portugal
| | - Rui Vitorino
- b Department of Medical Sciences , Institute for Biomedicine - iBiMED, University of Aveiro , Aveiro , Portugal.,f Departmento de Cirurgia e Fisiologia, Faculdade de Medicina , Unidade de Investigação Cardiovascular, Universidade do Porto , Porto , Portugal
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9
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van Luijn MM, van Meurs M, Stoop MP, Verbraak E, Wierenga-Wolf AF, Melief MJ, Kreft KL, Verdijk RM, 't Hart BA, Luider TM, Laman JD, Hintzen RQ. Elevated Expression of the Cerebrospinal Fluid Disease Markers Chromogranin A and Clusterin in Astrocytes of Multiple Sclerosis White Matter Lesions. J Neuropathol Exp Neurol 2016; 75:86-98. [PMID: 26683597 DOI: 10.1093/jnen/nlv004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Using proteomics, we previously identified chromogranin A (CgA) and clusterin (CLU) as disease-related proteins in the cerebrospinal fluid (CSF) of patients with multiple sclerosis (MS). CgA and CLU are involved in cell survival and are implicated in neurodegenerative disorders and may also have roles in MS pathophysiology. We investigated CgA and CLU expression in lesions and nonlesional regions in postmortem brains of MS patients and controls and in the brains of marmosets with experimental autoimmune encephalomyelitis. By quantitative PCR, mRNA levels of CgA and CLU were elevated in white matter but not in grey matter of MS patients. In situ analyses showed greater expression of CgA and CLU in white matter lesions than in normal-appearing regions in MS patients and in the marmosets, primarily in or adjacent to perivascular spaces and inflammatory infiltrates. Both proteins were expressed by glial fibrillary acidic protein-positive astrocytes. CgA was more localized in astrocytic processes and endfeet surrounding blood vessels and was abundant in the superficial glia limitans and ependyma, 2 CSF-brain borders. Increased expression of CgA and CLU in reactive astrocytes in MS white matter lesions supports a role for these molecules as neuro-inflammatory mediators and their potential as CSF markers of active pathological processes in MS patients.
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10
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Singh V, van Pelt ED, Stoop MP, Stingl C, Ketelslegers IA, Neuteboom RF, Catsman-Berrevoets CE, Luider TM, Hintzen RQ. Gray matter-related proteins are associated with childhood-onset multiple sclerosis. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2015; 2:e155. [PMID: 26445729 PMCID: PMC4582906 DOI: 10.1212/nxi.0000000000000155] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/25/2015] [Indexed: 11/25/2022]
Abstract
Objective: To identify CSF biomarkers for multiple sclerosis (MS) in children with an initial acquired CNS demyelinating syndrome (ADS). Methods: CSF was collected from a cohort of 39 children with initial ADS, 18 of whom were diagnosed with MS and 21 of whom had a monophasic disease course. Proteomic analysis of trypsinized CSF (20 μL) was performed by nano-liquid chromatography Orbitrap mass spectrometry. Univariate statistical analysis was used to identify differentially abundant proteins between childhood-onset MS and monophasic ADS. Results: A total of 2,260 peptides corresponding to 318 proteins were identified in the total set of samples. Of these 2,260 peptides, 88 were identified as being most distinctive between MS and ADS. Fifty-three peptides, corresponding to 14 proteins, had higher abundance in children with MS compared to children with monophasic ADS. Twelve of these 14 proteins were linked to neuronal functions and structures, such as synapses, axons, and CNS proteases (e.g., neurofascin, carboxypeptidase E, brevican core protein, and contactin-2). The other 2 were functionally related to immune function. The 35 peptides identified with decreased abundance in children with MS corresponded to 7 proteins. Six of them were linked to innate immune function (e.g., haptoglobin, haptoglobin-related protein, C4b-binding protein alpha chain, and monocyte differentiation antigen CD14) and 1 was linked to cellular adhesion (protein diaphanous homolog 1). Conclusion: At first onset of ADS, CSF of children diagnosed with MS showed increased abundance of CNS gray matter–related proteins, whereas CSF of children with a monophasic disease course showed increased abundance of innate immunity–related proteins.
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Affiliation(s)
- Vaibhav Singh
- MS Centre ErasMS, Department of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | - E Daniëlle van Pelt
- MS Centre ErasMS, Department of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | - Marcel P Stoop
- MS Centre ErasMS, Department of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | - Christoph Stingl
- MS Centre ErasMS, Department of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | - Immy A Ketelslegers
- MS Centre ErasMS, Department of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | - Rinze F Neuteboom
- MS Centre ErasMS, Department of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | | | - Theo M Luider
- MS Centre ErasMS, Department of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | - Rogier Q Hintzen
- MS Centre ErasMS, Department of Neurology, Erasmus MC, Rotterdam, the Netherlands
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11
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Hinsinger G, Galéotti N, Nabholz N, Urbach S, Rigau V, Demattei C, Lehmann S, Camu W, Labauge P, Castelnovo G, Brassat D, Loussouarn D, Salou M, Laplaud D, Casez O, Bockaert J, Marin P, Thouvenot E. Chitinase 3-like proteins as diagnostic and prognostic biomarkers of multiple sclerosis. Mult Scler 2015; 21:1251-61. [DOI: 10.1177/1352458514561906] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 11/05/2014] [Indexed: 01/15/2023]
Abstract
Background: Despite sensitivity of MRI to diagnose multiple sclerosis (MS), prognostic biomarkers are still needed for optimized treatment. Objective: The objective of this paper is to identify cerebrospinal fluid (CSF) diagnostic biomarkers of MS using quantitative proteomics and to analyze their expression at different disease stages. Methods: We conducted differential analysis of the CSF proteome from control and relapsing–remitting MS (RRMS) patients followed by verification by ELISA of candidate biomarkers in CSF and serum in control, clinically isolated syndrome (CIS), RRMS and progressive MS (PMS) patients. Results: Twenty-two of the 527 quantified proteins exhibited different abundances in control and RRMS CSF. These include chitinase 3-like protein 1 (CHI3L1) and 2 (CHI3L2), which showed a strong expression in brain of MS patients, especially in astrocytes and microglial cells from white matter plaques. CSF and serum CHI3L1 levels increased with the disease stage and CIS patients with high CSF (>189 ng/ml) and serum (>33 ng/ml) CHI3L1 converted more rapidly to RRMS (log rank test, p < 0.05 and p < 0.001, respectively). In contrast, CSF CHI3L2 levels were lower in PMS than in RRMS patients. Accordingly, CSF CHI3L1/CHI3L2 ratio accurately discriminated PMS from RRMS. Conclusions: CSF CHI3L1 and CHI3L2 and serum CHI3L1 might help to define MS disease stage and have a prognostic value in CIS.
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Affiliation(s)
- G Hinsinger
- Institut de Génomique Fonctionnelle, CNRS UMR 5203, INSERM U661, Université Montpellier 1, Université Montpellier 2, France
| | - N Galéotti
- Institut de Génomique Fonctionnelle, CNRS UMR 5203, INSERM U661, Université Montpellier 1, Université Montpellier 2, France
| | - N Nabholz
- Service d’Ophtalmologie, Hôpital Gui de Chauliac, CHU de Montpellier, France
| | - S Urbach
- Institut de Génomique Fonctionnelle, CNRS UMR 5203, INSERM U661, Université Montpellier 1, Université Montpellier 2, France
| | - V Rigau
- Service d’Anatomopathologie, Hôpital Gui de Chauliac, CHU de Montpellier, France
| | - C Demattei
- Département d’Information Médicale, CHU de Nîmes, France
| | - S Lehmann
- Service de Biochimie, Hôpital Gui de Chauliac, CHU de Montpellier, France
| | - W Camu
- Service de Neurologie, Hôpital Gui de Chauliac, CHU de Montpellier, France
| | - P Labauge
- Service de Neurologie, Hôpital Gui de Chauliac, CHU de Montpellier, France
| | - G Castelnovo
- Service de Neurologie, Hôpital Carémeau, CHU de Nîmes, France
| | - D Brassat
- Service de Neurologie, Hôpital Purpan, CHU de Toulouse, France
| | - D Loussouarn
- Service d’Anatomopathologie, CHU de Nantes, France
| | | | - D Laplaud
- INSERM 1064, France/Service de Neurologie, CHU de Nantes, France
| | - O Casez
- Service de Neurologie, CHU de Grenoble, France
| | - J Bockaert
- Institut de Génomique Fonctionnelle, CNRS UMR 5203, INSERM U661, Université Montpellier 1, Université Montpellier 2, France
| | - P Marin
- Institut de Génomique Fonctionnelle, CNRS UMR 5203, INSERM U661, Université Montpellier 1, Université Montpellier 2, France
| | - E Thouvenot
- Institut de Génomique Fonctionnelle, CNRS UMR 5203, INSERM U661, Université Montpellier 1, Université Montpellier 2, France/Service de Neurologie, Hôpital Carémeau, CHU de Nîmes, France
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12
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Shevchenko G, Konzer A, Musunuri S, Bergquist J. Neuroproteomics tools in clinical practice. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:705-17. [PMID: 25680928 DOI: 10.1016/j.bbapap.2015.01.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/30/2015] [Indexed: 12/13/2022]
Abstract
Neurodegenerative disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) are characterized by neuronal impairment that leads to disease-specific changes in the neuronal proteins. The early diagnosis of these disorders is difficult, thus, the need for identifying, developing and using valid clinically applicable biomarkers that meet the criteria of precision, specificity and repeatability is very vital. The application of rapidly emerging technology such as mass spectrometry (MS) in proteomics has opened new avenues to accelerate biomarker discovery, both for diagnostic as well as for prognostic purposes. This review summarizes the most recent advances in the mass spectrometry-based neuroproteomics and analyses the current and future directions in the biomarker discovery for the neurodegenerative diseases. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Affiliation(s)
- Ganna Shevchenko
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden
| | - Anne Konzer
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden
| | - Sravani Musunuri
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden
| | - Jonas Bergquist
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden.
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13
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Malekzadeh A, Teunissen C. Recent progress in omics-driven analysis of MS to unravel pathological mechanisms. Expert Rev Neurother 2014; 13:1001-16. [PMID: 24053344 DOI: 10.1586/14737175.2013.835602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
At present, the pathophysiology and specific biological markers reflecting pathology of multiple sclerosis (MS) remain undetermined. The risk of developing MS is considered to depend on genetic susceptibility and environmental factors. The interaction of environmental factors with epigenetic mechanisms could affect the transcriptional level and therefore also the translational level. In the last decade, growing amount of hypothesis-free 'omics' studies have shed light on the potential MS mechanisms and raised potential biomarker targets. To understand MS pathophysiology and discover a subset of biomarkers, it is becoming essential to take a step forward and integrate the findings of the different fields of 'omics' into a systems biology network. In this review, we will discuss the recent findings of the genomic, transcriptomic and proteomic fields for MS and aim to make a unifying model.
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Affiliation(s)
- Arjan Malekzadeh
- Department of Clinical Chemistry, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
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14
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Dagley LF, Emili A, Purcell AW. Application of quantitative proteomics technologies to the biomarker discovery pipeline for multiple sclerosis. Proteomics Clin Appl 2014; 7:91-108. [PMID: 23112123 DOI: 10.1002/prca.201200104] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/04/2012] [Accepted: 10/11/2012] [Indexed: 11/08/2022]
Abstract
Multiple sclerosis is an inflammatory-mediated demyelinating disorder most prevalent in young Caucasian adults. The various clinical manifestations of the disease present several challenges in the clinic in terms of diagnosis, monitoring disease progression and response to treatment. Advances in MS-based proteomic technologies have revolutionized the field of biomarker research and paved the way for the identification and validation of disease-specific markers. This review focuses on the novel candidates discovered by the application of quantitative proteomics to relevant disease-affected tissues in both the human context and within the animal model of the disease known as experimental autoimmune encephalomyelitis. The role of targeted MS approaches for biomarker validation studies, such as multiple reaction monitoring will also be discussed.
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Affiliation(s)
- Laura F Dagley
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
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15
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van Gool AJ, Hendrickson RC. The proteomic toolbox for studying cerebrospinal fluid. Expert Rev Proteomics 2014; 9:165-79. [DOI: 10.1586/epr.12.6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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16
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Dagley LF, Croft NP, Isserlin R, Olsen JB, Fong V, Emili A, Purcell AW. Discovery of novel disease-specific and membrane-associated candidate markers in a mouse model of multiple sclerosis. Mol Cell Proteomics 2013; 13:679-700. [PMID: 24361864 DOI: 10.1074/mcp.m113.033340] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Multiple sclerosis is a chronic demyelinating disorder characterized by the infiltration of auto-reactive immune cells from the periphery into the central nervous system resulting in axonal injury and neuronal cell death. Experimental autoimmune encephalomyelitis represents the best characterized animal model as common clinical, histological, and immunological features are recapitulated. A label-free mass spectrometric proteomics approach was used to detect differences in protein abundance within specific fractions of disease-affected tissues including the soluble lysate derived from the spinal cord and membrane protein-enriched peripheral blood mononuclear cells. Tissues were harvested from actively induced experimental autoimmune encephalomyelitis mice and sham-induced ("vehicle" control) counterparts at the disease peak followed by subsequent analysis by nanoflow liquid chromatography tandem mass spectrometry. Relative protein quantitation was performed using both intensity- and fragmentation-based approaches. After statistical evaluation of the data, over 500 and 250 differentially abundant proteins were identified in the spinal cord and peripheral blood mononuclear cell data sets, respectively. More than half of these observations have not previously been linked to the disease. The biological significance of all candidate disease markers has been elucidated through rigorous literature searches, pathway analysis, and validation studies. Results from comprehensive targeted mass spectrometry analyses have confirmed the differential abundance of ∼ 200 candidate markers (≥ twofold dysregulated expression) at a 70% success rate. This study is, to our knowledge, the first to examine the cell-surface proteome of peripheral blood mononuclear cells in experimental autoimmune encephalomyelitis. These data provide a unique mechanistic insight into the dynamics of peripheral immune cell infiltration into CNS-privileged sites at a molecular level and has identified several candidate markers, which represent promising targets for future multiple sclerosis therapies. The mass spectrometry proteomics data associated with this manuscript have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000255.
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Affiliation(s)
- Laura F Dagley
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
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17
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Pabst M, Fagerer SR, Köhling R, Küster SK, Steinhoff R, Badertscher M, Wahl F, Dittrich PS, Jefimovs K, Zenobi R. Self-Aliquoting Microarray Plates for Accurate Quantitative Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Anal Chem 2013; 85:9771-6. [DOI: 10.1021/ac4021775] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martin Pabst
- Department
of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang-Pauli-Strasse
10, 8093 Zürich, Switzerland
| | - Stephan R. Fagerer
- Department
of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang-Pauli-Strasse
10, 8093 Zürich, Switzerland
| | - Rudolf Köhling
- Sigma-Aldrich, Industriestrasse 25, 9471 Buchs, Switzerland
| | - Simon K. Küster
- Department
of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang-Pauli-Strasse
10, 8093 Zürich, Switzerland
| | - Robert Steinhoff
- Department
of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang-Pauli-Strasse
10, 8093 Zürich, Switzerland
| | - Martin Badertscher
- Department
of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang-Pauli-Strasse
10, 8093 Zürich, Switzerland
| | - Fabian Wahl
- Sigma-Aldrich, Industriestrasse 25, 9471 Buchs, Switzerland
| | - Petra S. Dittrich
- Department
of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang-Pauli-Strasse
10, 8093 Zürich, Switzerland
| | - Konstantins Jefimovs
- Swiss Federal Laboratories for Material Science and Technology EMPA, Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Renato Zenobi
- Department
of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang-Pauli-Strasse
10, 8093 Zürich, Switzerland
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18
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Stoop MP, Singh V, Stingl C, Martin R, Khademi M, Olsson T, Hintzen RQ, Luider TM. Effects of natalizumab treatment on the cerebrospinal fluid proteome of multiple sclerosis patients. J Proteome Res 2013; 12:1101-7. [PMID: 23339689 DOI: 10.1021/pr3012107] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Natalizumab is a very effective, relatively new drug for the treatment of relapsing remitting multiple sclerosis. Inflammatory and neurodegenerative processes in the central nervous system are presumed to cause adverse effects during the course of this disease. To monitor the effects of natalizumab treatment on the cerebrospinal fluid (CSF) proteome of patients, CSF samples were taken from patients before commencing treatment as well as after 1 year of treatment. Profiling proteomics experiments using electrospray Orbitrap mass spectrometry and pair wise comparison of patients before and after 1 year of natalizumab treatment revealed a number of candidate biomarkers that were significantly differentially abundant between the before and after treatment groups. Three proteins were subsequently validated using selected reaction monitoring (SRM) in a new, independent sample set. All three proteins, Ig mu chain C region and haptoglobin, both known inflammation-related proteins, as well as Chitinase-3-like protein 1, were confirmed by SRM to be significantly lower abundant in CSF of multiple sclerosis patients after 1 year of natalizumab treatment. The findings for Chitinase-3-like protein 1, a presumed biomarker for more rapid progression from a first clinically isolated syndrome to clinically definite multiple sclerosis, was further confirmed by ELISA measurements.
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Affiliation(s)
- Marcel P Stoop
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
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19
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Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM. J Proteomics 2012; 78:312-25. [PMID: 23059536 DOI: 10.1016/j.jprot.2012.09.037] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 09/14/2012] [Accepted: 09/30/2012] [Indexed: 12/25/2022]
Abstract
In the present study, we aimed to discover cerebrospinal fluid (CSF) proteins with significant abundance difference between early multiple sclerosis patients and controls, and do an initial verification of these proteins using selected reaction monitoring (SRM). iTRAQ and Orbitrap MS were used to compare the CSF proteome of patients with clinically isolated syndrome (CIS) (n=5), patients with relapsing-remitting multiple sclerosis that had CIS at the time of lumbar puncture (n=5), and controls with other inflammatory neurological disease (n=5). Of more than 1200 identified proteins, five proteins were identified with significant abundance difference between the patients and controls. In the initial verification using SRM we analyzed a larger patient and control cohort (n=132) and also included proteins reported as differentially abundant in multiple sclerosis in the literature. We found significant abundance difference for 11 proteins after verification, of which the five proteins alpha-1-antichymotrypsin, contactin-1, apolipoprotein D, clusterin, and kallikrein-6 were significantly differentially abundant in several of the group comparisons. This initial study form the basis for further biomarker verification studies in even larger sample cohorts, to determine if these proteins have relevance as diagnostic or prognostic biomarkers for multiple sclerosis.
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20
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Angel TE, Jacobs JM, Smith RP, Pasternack MS, Elias S, Gritsenko MA, Shukla A, Gilmore EC, McCarthy C, Camp DG, Smith RD, Warren HS. Cerebrospinal fluid proteome of patients with acute Lyme disease. J Proteome Res 2012; 11:4814-22. [PMID: 22900834 DOI: 10.1021/pr300577p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
During acute Lyme disease, bacteria can disseminate to the central nervous system (CNS), leading to the development of meningitis and other neurologic symptoms. Here we have analyzed pooled cerebrospinal fluid (CSF) allowing a deep view into the proteome for patients diagnosed with early disseminated Lyme disease and CSF inflammation. Additionally, we analyzed individual patient samples and quantified differences in protein abundance employing label-free quantitative mass spectrometry-based methods. We identified 108 proteins that differ significantly in abundance in patients with acute Lyme disease from controls. Comparison between infected patients and control subjects revealed differences in proteins in the CSF associated with cell death localized to brain synapses and others that likely originate from brain parenchyma.
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Affiliation(s)
- Thomas E Angel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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21
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Hölttä M, Zetterberg H, Mirgorodskaya E, Mattsson N, Blennow K, Gobom J. Peptidome analysis of cerebrospinal fluid by LC-MALDI MS. PLoS One 2012; 7:e42555. [PMID: 22880031 PMCID: PMC3412831 DOI: 10.1371/journal.pone.0042555] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 07/10/2012] [Indexed: 12/18/2022] Open
Abstract
We report on the analysis of endogenous peptides in cerebrospinal fluid (CSF) by mass spectrometry. A method was developed for preparation of peptide extracts from CSF. Analysis of the extracts by offline LC-MALDI MS resulted in the detection of 3,000–4,000 peptide-like features. Out of these, 730 peptides were identified by MS/MS. The majority of these peptides have not been previously reported in CSF. The identified peptides were found to originate from 104 proteins, of which several have been reported to be involved in different disorders of the central nervous system. These results support the notion that CSF peptidomics may be viable complement to proteomics in the search of biomarkers of CNS disorders.
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Affiliation(s)
- Mikko Hölttä
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Ekaterina Mirgorodskaya
- Department of Occupational and Environmental Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Niklas Mattsson
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Johan Gobom
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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22
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Stoop MP, Rosenling T, Attali A, Meesters RJW, Stingl C, Dekker LJ, van Aken H, Suidgeest E, Hintzen RQ, Tuinstra T, van Gool A, Luider TM, Bischoff R. Minocycline effects on the cerebrospinal fluid proteome of experimental autoimmune encephalomyelitis rats. J Proteome Res 2012; 11:4315-25. [PMID: 22768796 DOI: 10.1021/pr300428e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To identify response biomarkers for pharmaceutical treatment of multiple sclerosis, we induced experimental autoimmune encephalomyelitis (EAE) in rats and treated symptomatic animals with minocycline. Cerebrospinal fluid (CSF) samples were collected 14 days after EAE induction at the peak of neurological symptoms, and proteomics analysis was performed using nano-LC-Orbitrap mass spectrometry. Additionally, the minocycline concentration in CSF was determined using quantitative matrix-assisted laser desorption/ionization-triple-quadrupole tandem mass spectrometry (MALDI-MS/MS) in the selected reaction monitoring (SRM) mode. Fifty percent of the minocycline-treated EAE animals did not show neurological symptoms on day 14 ("responders"), while the other half displayed neurological symptoms ("nonresponders"), indicating that minocycline delayed disease onset and attenuated disease severity in some, but not all, animals. Neither CSF nor plasma minocycline concentrations correlated with the onset of symptoms or disease severity. Analysis of the proteomics data resulted in a list of 20 differentially abundant proteins between the untreated animals and the responder group of animals. Two of these proteins, complement C3 and carboxypeptidase B2, were validated by quantitative LC-MS/MS in the SRM mode. Differences in the CSF proteome between untreated EAE animals and minocycline-treated responders were similar to the differences between minocycline-treated responders and nonresponders (70% overlap). Six proteins that remained unchanged in the minocycline-treated animals but were elevated in untreated EAE animals may be related to the mechanism of action of minocycline.
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Affiliation(s)
- Marcel P Stoop
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
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23
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Komori M, Matsuyama Y, Nirasawa T, Thiele H, Becker M, Alexandrov T, Saida T, Tanaka M, Matsuo H, Tomimoto H, Takahashi R, Tashiro K, Ikegawa M, Kondo T. Proteomic pattern analysis discriminates among multiple sclerosis-related disorders. Ann Neurol 2012; 71:614-23. [PMID: 22522477 DOI: 10.1002/ana.22633] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVE To use a new, unbiased biomarker discovery strategy to obtain and assess proteomic data from cerebrospinal fluid (CSF) of patients with multiple sclerosis (MS)-related disorders. METHODS CSF protein profiles were analyzed from 107 patients with either MS-related disorders (including relapsing remitting MS [RRMS], primary progressive MS [PPMS], anti-aquaporin4 antibody seropositive-neuromyelitis optica spectrum disorder [SP-NMOSD], and seronegative-NMOSD with long cord lesions on spinal magnetic resonance imaging [SN-NMOSD]), amyotrophic lateral sclerosis (ALS), or other inflammatory neurological diseases (used as controls). CSF peptides/proteins were purified with magnetic beads, and directly measured by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The obtained spectra were analyzed with multivariate statistics and pattern matching algorithms. These analyses were replicated in an independent sample set of 84 patients composed of those with MS-related disorders or with other neurological diseases (the second cohort). RESULTS MS-related disorders differed considerably in terms of CSF protein profiles. SP-NMOSD and SN-NMOSD, both of which fit within the NMO spectrum, were distinguishable from RRMS with high cross-validation accuracy on a support vector machine classifier, especially in relapse phases. Some peaks derived from samples of relapsed SP-NMOSD can discriminate RRMS with high area under curve scores (>0.95) and this was reproduced on the second cohort. The similarity of proteomic patterns between selected neurological diseases were demonstrated by pattern matching analysis. To our surprise, the spectral differences between RRMS and PPMS were much larger than those of PPMS and ALS. INTERPRETATION Our findings suggest that CSF proteomic pattern analysis can increase the accuracy of disease diagnosis of MS-related disorders and will aid physicians in appropriate therapeutic decision-making.
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Affiliation(s)
- Mika Komori
- Department of Neurology, Graduate School of Medicine, Kyoto University, Japan
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24
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Aye TT, Low TY, Bjørlykke Y, Barsnes H, Heck AJR, Berven FS. Use of stable isotope dimethyl labeling coupled to selected reaction monitoring to enhance throughput by multiplexing relative quantitation of targeted proteins. Anal Chem 2012; 84:4999-5006. [PMID: 22548487 DOI: 10.1021/ac300596r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In this manuscript, we present a proof-of-concept study for targeted relative protein quantitation workflow using chemical labeling in the form of dimethylation, coupled with selected reaction monitoring (dimethyl-SRM). We first demonstrate close to complete isotope incorporation for all peptides tested. The accuracy, reproducibility, and linear dynamic range of quantitation are further assessed based on known ratios of nonhuman standard proteins spiked into human cerebrospinal fluid (CSF) as a model complex matrix. Quantitation reproducibility below 20% (CV < 20%) was obtained for analyte concentrations present at a dynamic range of 4 orders of magnitude lower than that of the background proteins. An error of less than 15% was observed when measuring the abundance of 44 out of 45 major human plasma proteins. Dimethyl-SRM was further examined by comparing the relative quantitation of eight proteins in human CSF with the relative quantitation obtained using synthetic heavy peptides coupled to stable isotope dilution-SRM (SID-SRM). Comparison between the two methods reveals that the correlation between dimethyl-SRM and SID-SRM is within 0.3-33% variation, demonstrating the accuracy of relative quantitation using dimethyl-SRM. Dimethyl labeling coupled with SRM provides a fast, convenient, and cost-effective alternative for relative quantitation of a large number of candidate proteins/peptides.
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Affiliation(s)
- Thin Thin Aye
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway.
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25
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Angel TE, Jacobs JM, Spudich SS, Gritsenko MA, Fuchs D, Liegler T, Zetterberg H, Camp DG, Price RW, Smith RD. The cerebrospinal fluid proteome in HIV infection: change associated with disease severity. Clin Proteomics 2012; 9:3. [PMID: 22433316 PMCID: PMC3353874 DOI: 10.1186/1559-0275-9-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 03/20/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Central nervous system (CNS) infection is a nearly universal feature of untreated systemic HIV infection with a clinical spectrum that ranges from chronic asymptomatic infection to severe cognitive and motor dysfunction. Analysis of cerebrospinal fluid (CSF) has played an important part in defining the character of this evolving infection and response to treatment. To further characterize CNS HIV infection and its effects, we applied advanced high-throughput proteomic methods to CSF to identify novel proteins and their changes with disease progression and treatment. RESULTS After establishing an accurate mass and time (AMT) tag database containing 23,141 AMT tags for CSF peptides, we analyzed 91 CSF samples by LC-MS from 12 HIV-uninfected and 14 HIV-infected subjects studied in the context of initiation of antiretroviral therapy and correlated abundances of identified proteins a) within and between subjects, b) with all other proteins across the entire sample set, and c) with "external" CSF biomarkers of infection (HIV RNA), immune activation (neopterin) and neural injury (neurofilament light chain protein, NFL). We identified a mean of 2,333 +/- 328 (SD) peptides covering 307 +/-16 proteins in the 91 CSF sample set. Protein abundances differed both between and within subjects sampled at different time points and readily separated those with and without HIV infection. Proteins also showed inter-correlations across the sample set that were associated with biologically relevant dynamic processes. One-hundred and fifty proteins showed correlations with the external biomarkers. For example, using a threshold of cross correlation coefficient (Pearson's) ≤ -0.3 and ≥0.3 for potentially meaningful relationships, a total of 99 proteins correlated with CSF neopterin (43 negative and 56 positive correlations) and related principally to neuronal plasticity and survival and to innate immunity. Pathway analysis defined several networks connecting the identified proteins, including one with amyloid precursor protein as a central node. CONCLUSIONS Advanced CSF proteomic analysis enabled the identification of an array of novel protein changes across the spectrum of CNS HIV infection and disease. This initial analysis clearly demonstrated the value of contemporary state-of-the-art proteomic CSF analysis as a discovery tool in HIV infection with likely similar application to other neurological inflammatory and degenerative diseases.
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Affiliation(s)
- Thomas E Angel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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26
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Rosenling T, Stoop MP, Attali A, Aken HV, Suidgeest E, Christin C, Stingl C, Suits F, Horvatovich P, Hintzen RQ, Tuinstra T, Bischoff R, Luider TM. Profiling and Identification of Cerebrospinal Fluid Proteins in a Rat EAE Model of Multiple Sclerosis. J Proteome Res 2012; 11:2048-60. [DOI: 10.1021/pr201244t] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Therese Rosenling
- Department
of Analytical Biochemistry,
Centre for Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Marcel P. Stoop
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Amos Attali
- Abbott Healthcare Products B.V., Weesp, The Netherlands
| | - Hans van Aken
- Abbott Healthcare Products B.V., Weesp, The Netherlands
| | | | - Christin Christin
- Department
of Analytical Biochemistry,
Centre for Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Christoph Stingl
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Frank Suits
- IBM TJ Watson Research Center, Yorktown Heights, New York, United States
| | - Peter Horvatovich
- Department
of Analytical Biochemistry,
Centre for Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Rogier Q. Hintzen
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Rainer Bischoff
- Department
of Analytical Biochemistry,
Centre for Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Theo M. Luider
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
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Rosenling T, Stoop MP, Smolinska A, Muilwijk B, Coulier L, Shi S, Dane A, Christin C, Suits F, Horvatovich PL, Wijmenga SS, Buydens LMC, Vreeken R, Hankemeier T, van Gool AJ, Luider TM, Bischoff R. The Impact of Delayed Storage on the Measured Proteome and Metabolome of Human Cerebrospinal Fluid. Clin Chem 2011; 57:1703-11. [DOI: 10.1373/clinchem.2011.167601] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND
Because cerebrospinal fluid (CSF) is in close contact with diseased areas in neurological disorders, it is an important source of material in the search for molecular biomarkers. However, sample handling for CSF collected from patients in a clinical setting might not always be adequate for use in proteomics and metabolomics studies.
METHODS
We left CSF for 0, 30, and 120 min at room temperature immediately after sample collection and centrifugation/removal of cells. At 2 laboratories CSF proteomes were subjected to tryptic digestion and analyzed by use of nano-liquid chromatography (LC) Orbitrap mass spectrometry (MS) and chipLC quadrupole TOF-MS. Metabolome analysis was performed at 3 laboratories by NMR, GC-MS, and LC-MS. Targeted analyses of cystatin C and albumin were performed by LC–tandem MS in the selected reaction monitoring mode.
RESULTS
We did not find significant changes in the measured proteome and metabolome of CSF stored at room temperature after centrifugation, except for 2 peptides and 1 metabolite, 2,3,4-trihydroxybutanoic (threonic) acid, of 5780 identified peptides and 93 identified metabolites. A sensitive protein stability marker, cystatin C, was not affected.
CONCLUSIONS
The measured proteome and metabolome of centrifuged human CSF is stable at room temperature for up to 2 hours. We cannot exclude, however, that changes undetectable with our current methodology, such as denaturation or proteolysis, might occur because of sample handling conditions. The stability we observed gives laboratory personnel at the collection site sufficient time to aliquot samples before freezing and storage at −80 °C.
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Affiliation(s)
- Therese Rosenling
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, the Netherlands
| | - Marcel P Stoop
- Department of Neurology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Agnieszka Smolinska
- Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, the Netherlands
| | | | | | - Shanna Shi
- Netherlands Metabolomics Centre, Leiden/Amsterdam Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Adrie Dane
- Netherlands Metabolomics Centre, Leiden/Amsterdam Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Christin Christin
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, the Netherlands
| | - Frank Suits
- IBM TJ Watson Research Centre, Yorktown Heights, NY
| | - Peter L Horvatovich
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, the Netherlands
| | - Sybren S Wijmenga
- Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Lutgarde MC Buydens
- Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Rob Vreeken
- Analytical BioSciences, Leiden/Amsterdam Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Thomas Hankemeier
- Netherlands Metabolomics Centre, Leiden/Amsterdam Centre for Drug Research, Leiden University, Leiden, the Netherlands
- Analytical BioSciences, Leiden/Amsterdam Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | | | - Theo M Luider
- Department of Neurology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Rainer Bischoff
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Groningen, the Netherlands
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Bartolomucci A, Possenti R, Mahata SK, Fischer-Colbrie R, Loh YP, Salton SRJ. The extended granin family: structure, function, and biomedical implications. Endocr Rev 2011; 32:755-97. [PMID: 21862681 PMCID: PMC3591675 DOI: 10.1210/er.2010-0027] [Citation(s) in RCA: 228] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The chromogranins (chromogranin A and chromogranin B), secretogranins (secretogranin II and secretogranin III), and additional related proteins (7B2, NESP55, proSAAS, and VGF) that together comprise the granin family subserve essential roles in the regulated secretory pathway that is responsible for controlled delivery of peptides, hormones, neurotransmitters, and growth factors. Here we review the structure and function of granins and granin-derived peptides and expansive new genetic evidence, including recent single-nucleotide polymorphism mapping, genomic sequence comparisons, and analysis of transgenic and knockout mice, which together support an important and evolutionarily conserved role for these proteins in large dense-core vesicle biogenesis and regulated secretion. Recent data further indicate that their processed peptides function prominently in metabolic and glucose homeostasis, emotional behavior, pain pathways, and blood pressure modulation, suggesting future utility of granins and granin-derived peptides as novel disease biomarkers.
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Affiliation(s)
- Alessandro Bartolomucci
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota 55455, USA
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29
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Singh V, Hintzen RQ, Luider TM, Stoop MP. Proteomics technologies for biomarker discovery in multiple sclerosis. J Neuroimmunol 2011; 248:40-7. [PMID: 22129845 DOI: 10.1016/j.jneuroim.2011.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 11/02/2011] [Indexed: 12/17/2022]
Abstract
Multiple sclerosis is a disabling inflammatory and neurodegenerative disorder that predominantly affects young adults. There is a great need for biomarkers, which could elucidate pathology as well as provide prognosis of disease progression and therapy response in multiple sclerosis. Rapidly evolving, technology driven applications such as mass spectrometry based proteomics are currently being developed for this purpose. In this review, we will outline the current status of the field and detail a number of the bottlenecks as well as future prospects of this type of biomarker research.
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Affiliation(s)
- Vaibhav Singh
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
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30
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Smolders J, Moen SM, Damoiseaux J, Huitinga I, Holmøy T. Vitamin D in the healthy and inflamed central nervous system: access and function. J Neurol Sci 2011; 311:37-43. [PMID: 21862439 DOI: 10.1016/j.jns.2011.07.033] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 06/25/2011] [Accepted: 07/18/2011] [Indexed: 11/16/2022]
Abstract
High exposure to vitamin D may protect against development and progression of multiple sclerosis (MS), possibly through the immunomodulatory properties of its biologically active metabolite 1,25-dihydroxyvitamin D. So far, most studies on the possible mechanisms for vitamin D involvement in MS have focused on immune modulation outside the central nervous system (CNS). However, vitamin D may also interfere with the pathophysiology of MS within the CNS. In this review, the potential presence and functions of vitamin D in the inflamed and healthy CNS are explored. We discuss that vitamin D, vitamin D binding protein (DBP), the vitamin D receptor (VDR) and enzymes needed for metabolism (CYP27B1) are present in the CNS. Both VDR and CYP27B1 are expressed on a variety of cells, including neurons, glial cells, and invading lymphocytes. Additionally, vitamin D has been postulated to play a modulating role in several key-processes in MS pathophysiology, including inflammation, demyelination, axonal damage, and remyelination. We conclude that a local role of vitamin D in the inflamed CNS is likely and potentially relevant to MS. Future studies should further characterize the impact of vitamin D on the local disease process of MS in the CNS.
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Affiliation(s)
- Joost Smolders
- Department of Internal Medicine, Division of Clinical and Experimental Immunology, and School for Mental Health and Neuroscience, Maastricht University Medical Center, Maastricht, The Netherlands
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31
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Teunissen CE, Koel-Simmelink MJA, Pham TV, Knol JC, Khalil M, Trentini A, Killestein J, Nielsen J, Vrenken H, Popescu V, Dijkstra CD, Jimenez CR. Identification of biomarkers for diagnosis and progression of MS by MALDI-TOF mass spectrometry. Mult Scler 2011; 17:838-50. [PMID: 21505015 DOI: 10.1177/1352458511399614] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
INTRODUCTION Body fluid biomarkers for clinical subtyping and monitoring of disease progression are of considerable interest in multiple sclerosis (MS). Proteomics tools are optimal for the unbiased simultaneous detection of large series of peptides and proteins. OBJECTIVES To identify novel candidate biomarkers discriminating patients with MS from patients with other neurological diseases (OND), and for subtyping of relapsing-remitting (RR), secondary progressive (SP) and primary progressive (PP) MS patients using a high-throughput MALDI-TOF-based mass spectrometry method. METHODS Paired cerebrospinal fluid (CSF) and serum samples of 41 RRMS, 30 SPMS, 13 PPMS patients and 25 patients with OND were analysed. RESULTS Out of a total of 100 detected peptides in CSF and 200 peptides in serum, 11 peptides were differentially regulated in serum and two in CSF between patients with MS and the OND control group. Eleven peptides were differentially regulated in both serum and CSF between relapse-onset MS and PPMS patients. Lastly, four peptides were differentially regulated in serum and two in CSF between RRMS and SPMS patients. Specific peaks regulated in MS were tentatively identified as fragments of secretogranin III and complement C3. The peak intensity of the CSF peptide ion with m/z value 8607.7 correlated to atrophy (r = -0.27, p < 0.005), black hole volumes (r = 0.31, p < 0.008) and total lesion load (r = 0.34, p < 0.003). A serum peptide with m/z value of 872.4 elevated in SPMS correlated to Expanded Disability Status Scale (r = 0.341, p < 0.005) and atrophy (r = -0.286, p < 0.028). CONCLUSIONS Using high-throughput body fluid profiling by MALDI-TOF mass spectrometry, small proteins and peptides were detected as promising candidate biomarkers for diagnosis and disease progression of MS.
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Affiliation(s)
- C E Teunissen
- NUBIN, Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands.
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32
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Kroksveen A, Opsahl J, Aye T, Ulvik R, Berven F. Proteomics of human cerebrospinal fluid: Discovery and verification of biomarker candidates in neurodegenerative diseases using quantitative proteomics. J Proteomics 2011; 74:371-88. [DOI: 10.1016/j.jprot.2010.11.010] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Revised: 11/16/2010] [Accepted: 11/16/2010] [Indexed: 01/01/2023]
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33
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34
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The experimental autoimmune encephalomyelitis model for proteomic biomarker studies: from rat to human. Clin Chim Acta 2011; 412:812-22. [PMID: 21333641 DOI: 10.1016/j.cca.2011.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 02/01/2011] [Accepted: 02/01/2011] [Indexed: 01/13/2023]
Abstract
Multiple sclerosis (MScl) is defined by central nervous system (CNS) inflammation, demyelination and axonal damage. Some of the disease mechanisms are known but the cause of this complex disorder stays an enigma. Experimental autoimmune encephalomyelitis (EAE) is an animal model mimicking many aspects of MScl. This review aims to provide an overview over proteomic biomarker studies in the EAE model emphasizing the translational aspects with respect to MScl in humans.
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35
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Stoop MP, Coulier L, Rosenling T, Shi S, Smolinska AM, Buydens L, Ampt K, Stingl C, Dane A, Muilwijk B, Luitwieler RL, Sillevis Smitt PAE, Hintzen RQ, Bischoff R, Wijmenga SS, Hankemeier T, van Gool AJ, Luider TM. Quantitative proteomics and metabolomics analysis of normal human cerebrospinal fluid samples. Mol Cell Proteomics 2011. [PMID: 20811074 DOI: 10.1074/mcp.m110.000877] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The analysis of cerebrospinal fluid (CSF) is used in biomarker discovery studies for various neurodegenerative central nervous system (CNS) disorders. However, little is known about variation of CSF proteins and metabolites between patients without neurological disorders. A baseline for a large number of CSF compounds appears to be lacking. To analyze the variation in CSF protein and metabolite abundances in a number of well-defined individual samples of patients undergoing routine, non-neurological surgical procedures, we determined the variation of various proteins and metabolites by multiple analytical platforms. A total of 126 common proteins were assessed for biological variations between individuals by ESI-Orbitrap. A large spread in inter-individual variation was observed (relative standard deviations [RSDs] ranged from 18 to 148%) for proteins with both high abundance and low abundance. Technical variation was between 15 and 30% for all 126 proteins. Metabolomics analysis was performed by means of GC-MS and nuclear magnetic resonance (NMR) imaging and amino acids were specifically analyzed by LC-MS/MS, resulting in the detection of more than 100 metabolites. The variation in the metabolome appears to be much more limited compared with the proteome: the observed RSDs ranged from 12 to 70%. Technical variation was less than 20% for almost all metabolites. Consequently, an understanding of the biological variation of proteins and metabolites in CSF of neurologically normal individuals appears to be essential for reliable interpretation of biomarker discovery studies for CNS disorders because such results may be influenced by natural inter-individual variations. Therefore, proteins and metabolites with high variation between individuals ought to be assessed with caution as candidate biomarkers because at least part of the difference observed between the diseased individuals and the controls will not be caused by the disease, but rather by the natural biological variation between individuals.
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Affiliation(s)
- Marcel P Stoop
- Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
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36
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Stoop MP, Coulier L, Rosenling T, Shi S, Smolinska AM, Buydens L, Ampt K, Stingl C, Dane A, Muilwijk B, Luitwieler RL, Sillevis Smitt PAE, Hintzen RQ, Bischoff R, Wijmenga SS, Hankemeier T, van Gool AJ, Luider TM. Quantitative proteomics and metabolomics analysis of normal human cerebrospinal fluid samples. Mol Cell Proteomics 2011; 9:2063-75. [PMID: 20811074 DOI: 10.1074/mcp.m900877-mcp200] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The analysis of cerebrospinal fluid (CSF) is used in biomarker discovery studies for various neurodegenerative central nervous system (CNS) disorders. However, little is known about variation of CSF proteins and metabolites between patients without neurological disorders. A baseline for a large number of CSF compounds appears to be lacking. To analyze the variation in CSF protein and metabolite abundances in a number of well-defined individual samples of patients undergoing routine, non-neurological surgical procedures, we determined the variation of various proteins and metabolites by multiple analytical platforms. A total of 126 common proteins were assessed for biological variations between individuals by ESI-Orbitrap. A large spread in inter-individual variation was observed (relative standard deviations [RSDs] ranged from 18 to 148%) for proteins with both high abundance and low abundance. Technical variation was between 15 and 30% for all 126 proteins. Metabolomics analysis was performed by means of GC-MS and nuclear magnetic resonance (NMR) imaging and amino acids were specifically analyzed by LC-MS/MS, resulting in the detection of more than 100 metabolites. The variation in the metabolome appears to be much more limited compared with the proteome: the observed RSDs ranged from 12 to 70%. Technical variation was less than 20% for almost all metabolites. Consequently, an understanding of the biological variation of proteins and metabolites in CSF of neurologically normal individuals appears to be essential for reliable interpretation of biomarker discovery studies for CNS disorders because such results may be influenced by natural inter-individual variations. Therefore, proteins and metabolites with high variation between individuals ought to be assessed with caution as candidate biomarkers because at least part of the difference observed between the diseased individuals and the controls will not be caused by the disease, but rather by the natural biological variation between individuals.
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Affiliation(s)
- Marcel P Stoop
- Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
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37
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Popp BV, Ball ZT. Proximity-driven metallopeptide catalysis: Remarkable side-chain scope enables modification of the Fos bZip domain. Chem Sci 2011. [DOI: 10.1039/c0sc00564a] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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38
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Teng PN, Bateman NW, Hood BL, Conrads TP. Advances in proximal fluid proteomics for disease biomarker discovery. J Proteome Res 2010; 9:6091-100. [PMID: 21028795 DOI: 10.1021/pr100904q] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although serum/plasma has been the preferred source for identification of disease biomarkers, these efforts have been met with little success, in large part due the relatively small number of highly abundant proteins that render the reliable detection of low abundant disease-related proteins challenging due to the expansive dynamic range of concentration of proteins in this sample. Proximal fluid, the fluid derived from the extracellular milieu of tissues, contains a large repertoire of shed and secreted proteins that are likely to be present at higher concentrations relative to plasma/serum. It is hypothesized that many, if not all, proximal fluid proteins exchange with peripheral circulation, which has provided significant motivation for utilizing proximal fluids as a primary sample source for protein biomarker discovery. The present review highlights recent advances in proximal fluid proteomics, including the various protocols utilized to harvest proximal fluids along with detailing the results from mass spectrometry- and antibody-based analyses.
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Affiliation(s)
- Pang-ning Teng
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
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39
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The emerging role of vitamin D binding protein in multiple sclerosis. J Neurol 2010; 258:353-8. [DOI: 10.1007/s00415-010-5797-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 09/20/2010] [Accepted: 10/07/2010] [Indexed: 01/22/2023]
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40
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Nicolardi S, Palmblad M, Dalebout H, Bladergroen M, Tollenaar RAEM, Deelder AM, van der Burgt YEM. Quality control based on isotopic distributions for high-throughput MALDI-TOF and MALDI-FTICR serum peptide profiling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1515-1525. [PMID: 20541438 DOI: 10.1016/j.jasms.2010.05.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 04/23/2010] [Accepted: 05/06/2010] [Indexed: 05/29/2023]
Abstract
In this study, we have implemented a new quality control (QC) parameter for peptide profiling based on isotopic distributions. This QC parameter is an objective measure and facilitates automatic sorting of large numbers of peptide spectra. Peptides in human serum samples were enriched using reversed-phase C(18)-functionalized magnetic beads using a high-throughput robotic platform. High-resolution MALDI-TOF and ultrahigh resolution MALDI-FTICR mass spectra were obtained and a workflow was developed for automated analysis and evaluation of these profiles. To this end, the isotopic distributions of multiple peptides were quantified from both MALDI-TOF and MALDI-FTICR spectra. Odd peptide isotope distributions in TOF spectra could be rationalized from ultrahigh resolution FTICR spectra that showed overlap of different peptides. The comparison of isotope patterns with estimated polyaveragine distributions was used to calculate a QC value for each single mass spectrum. Sorting these QC values enabled the best MALDI spectrum to be selected from replicate spots. Moreover, using this approach spectra containing high intensities of polymers or other contaminants and lacking peptides of interest can be efficiently removed from a clinical dataset. In general, this method simplifies the exclusion of low quality spectra from further statistical analysis.
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Affiliation(s)
- Simone Nicolardi
- Department of Parasitology, Biomolecular Mass Spectrometry Unit, Leiden University Medical Center, Leiden, The Netherlands
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41
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Stoop MP, Singh V, Dekker LJ, Titulaer MK, Stingl C, Burgers PC, Sillevis Smitt PAE, Hintzen RQ, Luider TM. Proteomics comparison of cerebrospinal fluid of relapsing remitting and primary progressive multiple sclerosis. PLoS One 2010; 5:e12442. [PMID: 20805994 PMCID: PMC2929207 DOI: 10.1371/journal.pone.0012442] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 08/03/2010] [Indexed: 01/16/2023] Open
Abstract
Background Based on clinical representation of disease symptoms multiple sclerosis (MScl) patients can be divided into two major subtypes; relapsing remitting (RR) MScl (85–90%) and primary progressive (PP) MScl (10–15%). Proteomics analysis of cerebrospinal fluid (CSF) has detected a number of proteins that were elevated in MScl patients. Here we specifically aimed to differentiate between the PP and RR subtypes of MScl by comparing CSF proteins. Methodology/Principal Findings CSF samples (n = 31) were handled according to the same protocol for quantitative mass spectrometry measurements we reported previously. In the comparison of PP MScl versus RR MScl we observed a number of differentially abundant proteins, such as protein jagged-1 and vitamin D-binding protein. Protein jagged-1 was over three times less abundant in PP MScl compared to RR MScl. Vitamin D-binding protein was only detected in the RR MScl samples. These two proteins were validated by independent techniques (western blot and ELISA) as differentially abundant in the comparison between both MScl types. Conclusions/Significance The main finding of this comparative study is the observation that the proteome profiles of CSF in PP and RR MScl patients overlap to a large extent. Still, a number of differences could be observed. Protein jagged-1 is a ligand for multiple Notch receptors and involved in the mediation of Notch signaling. It is suggested in literature that the Notch pathway is involved in the remyelination of MScl lesions. Aberration of normal homeostasis of Vitamin D, of which approximately 90% is bound to vitamin D-binding protein, has been widely implicated in MScl for some years now. Vitamin D directly and indirectly regulates the differentiation, activation of CD4+ T-lymphocytes and can prevent the development of autoimmune processes, and so it may be involved in neuroprotective elements in MScl.
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Affiliation(s)
- Marcel P. Stoop
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Vaibhav Singh
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Lennard J. Dekker
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Mark K. Titulaer
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Christoph Stingl
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Peter C. Burgers
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Peter A. E. Sillevis Smitt
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Rogier Q. Hintzen
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Theo M. Luider
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
- * E-mail:
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42
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Bartolomucci A, Pasinetti GM, Salton SRJ. Granins as disease-biomarkers: translational potential for psychiatric and neurological disorders. Neuroscience 2010; 170:289-97. [PMID: 20600637 DOI: 10.1016/j.neuroscience.2010.06.057] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 06/17/2010] [Accepted: 06/23/2010] [Indexed: 12/12/2022]
Abstract
The identification of biomarkers represents a fundamental medical advance that can lead to an improved understanding of disease pathogenesis, and holds the potential to define surrogate diagnostic and prognostic endpoints. Because of the inherent difficulties in assessing brain function in patients and objectively identifying neurological and cognitive/emotional symptoms, future application of biomarkers to neurological and psychiatric disorders is extremely desirable. This article discusses the biomarker potential of the granin family, a group of acidic proteins present in the secretory granules of a wide variety of endocrine, neuronal and neuroendocrine cells: chromogranin A (CgA), CgB, Secretogranin II (SgII), SgIII, HISL-19 antigen, 7B2, NESP55, VGF and ProSAAS. Their relative abundance, functional significance, and secretion into the cerebrospinal fluid (CSF), saliva, and the general circulation have made granins tractable targets as biomarkers for many diseases of neuronal and endocrine origin, recently impacting diagnosis of a number of neurological and psychiatric disorders including amyotrophic lateral sclerosis (ALS), Alzheimer's disease, frontotemporal dementia, and schizophrenia. Although research has not yet validated the clinical utility of granins as surrogate endpoints for the progression or treatment of neurological or psychiatric disease, a growing body of experimental evidence indicates that the use of granins as biomarkers might be of great potential clinical interest. Advances that further elucidate the mechanism(s) of action of granins, coupled with improvements in biomarker technology and direct clinical application, should increase the translational effectiveness of this family of proteins in disease diagnosis and drug discovery.
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Affiliation(s)
- A Bartolomucci
- Department of Evolutionary and Functional Biology, University of Parma, 43124 Parma, Italy.
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43
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Rajalahti T, Kroksveen AC, Arneberg R, Berven FS, Vedeler CA, Myhr KM, Kvalheim OM. A Multivariate Approach To Reveal Biomarker Signatures for Disease Classification: Application to Mass Spectral Profiles of Cerebrospinal Fluid from Patients with Multiple Sclerosis. J Proteome Res 2010; 9:3608-20. [DOI: 10.1021/pr100142m] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Tarja Rajalahti
- Department of Clinical Medicine, University of Bergen, Bergen, Norway, Department of Neurology, Haukeland University Hospital, Bergen, Norway, Institute of Medicine, University of Bergen, Bergen, Norway, Pattern Recognition Systems AS, Bergen, Norway, Proteomic Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway, The Norwegian Multiple Sclerosis National Competence Centre, Haukeland University Hospital, Bergen, Norway, and Department of Chemistry, University of Bergen, Bergen,
| | - Ann C. Kroksveen
- Department of Clinical Medicine, University of Bergen, Bergen, Norway, Department of Neurology, Haukeland University Hospital, Bergen, Norway, Institute of Medicine, University of Bergen, Bergen, Norway, Pattern Recognition Systems AS, Bergen, Norway, Proteomic Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway, The Norwegian Multiple Sclerosis National Competence Centre, Haukeland University Hospital, Bergen, Norway, and Department of Chemistry, University of Bergen, Bergen,
| | - Reidar Arneberg
- Department of Clinical Medicine, University of Bergen, Bergen, Norway, Department of Neurology, Haukeland University Hospital, Bergen, Norway, Institute of Medicine, University of Bergen, Bergen, Norway, Pattern Recognition Systems AS, Bergen, Norway, Proteomic Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway, The Norwegian Multiple Sclerosis National Competence Centre, Haukeland University Hospital, Bergen, Norway, and Department of Chemistry, University of Bergen, Bergen,
| | - Frode S. Berven
- Department of Clinical Medicine, University of Bergen, Bergen, Norway, Department of Neurology, Haukeland University Hospital, Bergen, Norway, Institute of Medicine, University of Bergen, Bergen, Norway, Pattern Recognition Systems AS, Bergen, Norway, Proteomic Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway, The Norwegian Multiple Sclerosis National Competence Centre, Haukeland University Hospital, Bergen, Norway, and Department of Chemistry, University of Bergen, Bergen,
| | - Christian A. Vedeler
- Department of Clinical Medicine, University of Bergen, Bergen, Norway, Department of Neurology, Haukeland University Hospital, Bergen, Norway, Institute of Medicine, University of Bergen, Bergen, Norway, Pattern Recognition Systems AS, Bergen, Norway, Proteomic Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway, The Norwegian Multiple Sclerosis National Competence Centre, Haukeland University Hospital, Bergen, Norway, and Department of Chemistry, University of Bergen, Bergen,
| | - Kjell-Morten Myhr
- Department of Clinical Medicine, University of Bergen, Bergen, Norway, Department of Neurology, Haukeland University Hospital, Bergen, Norway, Institute of Medicine, University of Bergen, Bergen, Norway, Pattern Recognition Systems AS, Bergen, Norway, Proteomic Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway, The Norwegian Multiple Sclerosis National Competence Centre, Haukeland University Hospital, Bergen, Norway, and Department of Chemistry, University of Bergen, Bergen,
| | - Olav M. Kvalheim
- Department of Clinical Medicine, University of Bergen, Bergen, Norway, Department of Neurology, Haukeland University Hospital, Bergen, Norway, Institute of Medicine, University of Bergen, Bergen, Norway, Pattern Recognition Systems AS, Bergen, Norway, Proteomic Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway, The Norwegian Multiple Sclerosis National Competence Centre, Haukeland University Hospital, Bergen, Norway, and Department of Chemistry, University of Bergen, Bergen,
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Popp BV, Ball ZT. Structure-Selective Modification of Aromatic Side Chains with Dirhodium Metallopeptide Catalysts. J Am Chem Soc 2010; 132:6660-2. [DOI: 10.1021/ja101456c] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Brian V. Popp
- Department of Chemistry, Rice University, MS 60, 6100 Main Street, Houston, Texas 77251
| | - Zachary T. Ball
- Department of Chemistry, Rice University, MS 60, 6100 Main Street, Houston, Texas 77251
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Ingram G, Hakobyan S, Hirst CL, Harris CL, Pickersgill TP, Cossburn MD, Loveless S, Robertson NP, Morgan BP. Complement regulator factor H as a serum biomarker of multiple sclerosis disease state. Brain 2010; 133:1602-11. [DOI: 10.1093/brain/awq085] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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