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Lereim RR, Nytrova P, Guldbrandsen A, Havrdova EK, Myhr KM, Barsnes H, Berven FS. Natalizumab promotes anti-inflammatory and repair effects in multiple sclerosis. PLoS One 2024; 19:e0300914. [PMID: 38527011 PMCID: PMC10962820 DOI: 10.1371/journal.pone.0300914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Multiple sclerosis is an inflammatory and degenerative disease of the central nervous system leading to demyelination and axonal loss. Relapsing-remitting multiple sclerosis (RRMS) is commonly treated by anti-inflammatory drugs, where one of the most effective drugs to date is the monoclonal antibody natalizumab. METHODS The cerebrospinal fluid (CSF) proteome was analyzed in 56 patients with RRMS before and after natalizumab treatment, using label-free mass spectrometry and a subset of the changed proteins were verified by parallel reaction monitoring in a new cohort of 20 patients, confirming the majority of observed changes. RESULTS A total of 287 differentially abundant proteins were detected including (i) the decrease of proteins with roles in immunity, such as immunoglobulin heavy constant mu, chitinase-3-like protein 1 and chitotriosidase, (ii) an increase of proteins involved in metabolism, such as lactate dehydrogenase A and B and malate-dehydrogenase cytoplasmic, and (iii) an increase of proteins associated with the central nervous system, including lactadherin and amyloid precursor protein. Comparison with the CSF-PR database provided evidence that natalizumab counters protein changes commonly observed in RRMS. Furthermore, vitamin-D binding protein and apolipoprotein 1 and 2 were unchanged during treatment with natalizumab, implying that these may be involved in disease activity unaffected by natalizumab. CONCLUSIONS Our study revealed that some of the previously suggested biomarkers for MS were affected by the natalizumab treatment while others were not. Proteins not previously suggested as biomarkers were also found affected by the treatment. In sum, the results provide new information on how the natalizumab treatment impacts the CSF proteome of MS patients, and points towards processes affected by the treatment. These findings ought to be explored further to disclose potential novel disease mechanisms and predict treatment responses.
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Affiliation(s)
- Ragnhild Reehorst Lereim
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Bergen, Norway
| | - Petra Nytrova
- Department of Neurology and Center for Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Astrid Guldbrandsen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Bergen, Norway
| | - Eva Kubala Havrdova
- Department of Neurology and Center for Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Kjell-Morten Myhr
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Bergen, Norway
| | - Frode S. Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
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2
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Gomes Moreira D, Jan A. A beginner's guide into curated analyses of open access datasets for biomarker discovery in neurodegeneration. Sci Data 2023; 10:432. [PMID: 37414779 PMCID: PMC10325954 DOI: 10.1038/s41597-023-02338-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
The discovery of surrogate biomarkers reflecting neuronal dysfunction in neurodegenerative diseases (NDDs) remains an active area of research. To boost these efforts, we demonstrate the utility of publicly available datasets for probing the pathogenic relevance of candidate markers in NDDs. As a starting point, we introduce the readers to several open access resources, which contain gene expression profiles and proteomics datasets from patient studies in common NDDs, including proteomics analyses of cerebrospinal fluid (CSF). Then, we illustrate the method for curated gene expression analyses across select brain regions from four cohorts of Parkinson disease patients (and from one study in common NDDs), probing glutathione biogenesis, calcium signaling and autophagy. These data are complemented by findings of select markers in CSF-based studies in NDDs. Additionally, we enclose several annotated microarray studies, and summarize reports on CSF proteomics across the NDDs, which the readers can utilize for translational purposes. We anticipate that this "beginner's guide" will benefit the research community in NDDs, and would serve as a useful educational tool.
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Affiliation(s)
- Diana Gomes Moreira
- Department of Clinical Medicine, Palle Juul-Jensens Boulevard 165, DK-8200, Aarhus N, Denmark
| | - Asad Jan
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, DK-8000, Aarhus C, Denmark.
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3
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Bruijstens AL, Stingl C, Güzel C, Stoop MP, Wong YYM, van Pelt ED, Banwell BL, Bar-Or A, Luider TM, Neuteboom RF. Neurodegeneration and humoral response proteins in cerebrospinal fluid associate with pediatric-onset multiple sclerosis and not monophasic demyelinating syndromes in childhood. Mult Scler 2023; 29:52-62. [PMID: 36154753 PMCID: PMC9896265 DOI: 10.1177/13524585221125369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Pediatric-onset multiple sclerosis (POMS) represents the earliest stage of disease pathogenesis. Investigating the cerebrospinal fluid (CSF) proteome in POMS may provide novel insights into early MS processes. OBJECTIVE To analyze CSF obtained from children at time of initial central nervous system (CNS) acquired demyelinating syndrome (ADS), to compare CSF proteome of those subsequently ascertained as having POMS versus monophasic acquired demyelinating syndrome (mADS). METHODS Patients were selected from two prospective pediatric ADS studies. Liquid chromatography-mass spectrometry (LC-MS) was performed in a Dutch discovery cohort (POMS n = 28; mADS n = 39). Parallel reaction monitoring-mass spectrometry (PRM-MS) was performed on selected proteins more abundant in POMS in a combined Dutch and Canadian validation cohort (POMS n = 48; mADS n = 106). RESULTS Discovery identified 5580 peptides belonging to 576 proteins; 58 proteins were differentially abundant with ⩾2 peptides between POMS and mADS, of which 28 more abundant in POMS. Fourteen had increased abundance in POMS with ⩾8 unique peptides. Five selected proteins were all confirmed within validation. Adjusted for age, 2 out of 5 proteins remained more abundant in POMS, that is, Carboxypeptidase E (CPE) and Semaphorin-7A (SEMA7A). CONCLUSION This exploratory study identified several CSF proteins associated with POMS and not mADS, potentially reflecting neurodegeneration, compensatory neuroprotection, and humoral response in POMS. The proteins associated with POMS highly correlated with age at CSF sampling.
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Affiliation(s)
- Arlette L Bruijstens
- AL Bruijstens Department of Neurology, Erasmus University Medical Center, Room Ee-2230, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
| | - Christoph Stingl
- Laboratory of Neuro-Oncology, Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Coşkun Güzel
- Laboratory of Neuro-Oncology, Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel P Stoop
- Laboratory of Neuro-Oncology, Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yu Yi M Wong
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - E Daniëlle van Pelt
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
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4
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Floro S, Carandini T, Pietroboni AM, De Riz MA, Scarpini E, Galimberti D. Role of Chitinase 3-like 1 as a Biomarker in Multiple Sclerosis: A Systematic Review and Meta-analysis. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2022; 9:9/4/e1164. [PMID: 35534236 PMCID: PMC9128043 DOI: 10.1212/nxi.0000000000001164] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/17/2022] [Indexed: 04/12/2023]
Abstract
BACKGROUND AND OBJECTIVES Multiple sclerosis (MS) is an autoimmune disease confined in the CNS, and its course is frequently subtle and variable. Therefore, predictive biomarkers are needed. In this scenario, we conducted a systematic review and meta-analysis to evaluate the reliability of chitinase 3-like 1 as a biomarker of MS. METHODS Research through the main scientific databases (PubMed, Scopus, Web of Science, and Cochrane Library) published from January 2010 to December 2020 was performed using the following keywords: "chitinase 3-like 1 and multiple sclerosis" and "YKL40 and multiple sclerosis." Articles were selected according to the 2020 updated Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines by 2 authors independently, and data were extracted; 20 of the 90 studies screened were included in the meta-analysis. The main efficacy measure was represented by the standardized mean difference of CSF and blood CHI3L1 levels; Review Manager version 5.4 and R software applications were used for analysis. RESULTS Higher levels of CHI3L1 were found in CSF of 673 patients with MS compared with 336 healthy controls (size-weighted mean difference [SMD] 50.88; 95% CI = 44.98-56.79; p < 0.00001) and in 461 patients with MS than 283 patients with clinically isolated syndrome (CIS) (SMD 28.18; 95% CI = 23.59-32.76; p < 0.00001). Mean CSF CHI3L1 levels were significantly higher in 561 converting than 445 nonconverting CIS (SMD 30.6; 95% CI = 28.31-32.93; p < 0.00001). CSF CHI3L1 levels were significantly higher in patients with primary progressive MS (PPMS) than in patients with relapsing-remitting MS (RRMS) (SMD 43.15; 95% CI = 24.41-61.90; p < 0.00001) and in patients with secondary progressive MS (SMD 41.86 with 95% CI = 32.39-51.33; p < 0.00001). CSF CHI3L1 levels in 407 patients with MS during remission phase of disease were significantly higher than those in 395 patients with MS with acute relapse (SMD 10.48; 95% CI = 08.51-12.44; p < 0.00001). The performances of CHI3L1 in blood for differentiating patients with MS from healthy controls were not significant (SMD 0.48; 95% CI = -1.18 to 2.14; p: 0.57). DISCUSSION CSF levels of CHI3L1 have a strong correlation with the MS pathologic course, in particular with the mechanism of progression of the disease; it helps to distinguish the PPMS from the RRMS. The potential role of CHI3L1 in serum needs to be further studied in the future.
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Affiliation(s)
- Stefano Floro
- From the Fondazione IRCCS Ca' Granda (S.F., T.C., A.M.P., M.A.D.R., E.S., D.G.), Ospedale Policlinico; and University of Milan (S.F., E.S., D.G.), Milan, Italy
| | - Tiziana Carandini
- From the Fondazione IRCCS Ca' Granda (S.F., T.C., A.M.P., M.A.D.R., E.S., D.G.), Ospedale Policlinico; and University of Milan (S.F., E.S., D.G.), Milan, Italy
| | - Anna Margherita Pietroboni
- From the Fondazione IRCCS Ca' Granda (S.F., T.C., A.M.P., M.A.D.R., E.S., D.G.), Ospedale Policlinico; and University of Milan (S.F., E.S., D.G.), Milan, Italy
| | - Milena Alessandra De Riz
- From the Fondazione IRCCS Ca' Granda (S.F., T.C., A.M.P., M.A.D.R., E.S., D.G.), Ospedale Policlinico; and University of Milan (S.F., E.S., D.G.), Milan, Italy
| | - Elio Scarpini
- From the Fondazione IRCCS Ca' Granda (S.F., T.C., A.M.P., M.A.D.R., E.S., D.G.), Ospedale Policlinico; and University of Milan (S.F., E.S., D.G.), Milan, Italy
| | - Daniela Galimberti
- From the Fondazione IRCCS Ca' Granda (S.F., T.C., A.M.P., M.A.D.R., E.S., D.G.), Ospedale Policlinico; and University of Milan (S.F., E.S., D.G.), Milan, Italy
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5
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Rzagalinski I, Bogdanova A, Raghuraman BK, Geertsma ER, Hersemann L, Ziemssen T, Shevchenko A. FastCAT Accelerates Absolute Quantification of Proteins Using Multiple Short Nonpurified Chimeric Standards. J Proteome Res 2022; 21:1408-1417. [PMID: 35561006 PMCID: PMC9171895 DOI: 10.1021/acs.jproteome.2c00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Absolute (molar)
quantification of clinically relevant proteins
determines their reference values in liquid and solid biopsies. The
FastCAT (for Fast-track QconCAT) method employs multiple short (<50
kDa), stable-isotope labeled chimeric proteins (CPs) composed of concatenated
quantotypic (Q)-peptides representing the quantified proteins. Each
CP also comprises scrambled sequences of reference (R)-peptides that
relate its abundance to a single protein standard (bovine serum albumin,
BSA). FastCAT not only alleviates the need to purify CP or use sodium
dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) but
also improves the accuracy, precision, and dynamic range of the absolute
quantification by grouping Q-peptides according to the expected abundance
of the target proteins. We benchmarked FastCAT against the reference
method of MS Western and tested it in the direct molar quantification
of neurological markers in human cerebrospinal fluid at the low ng/mL
level.
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Affiliation(s)
- Ignacy Rzagalinski
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Aliona Bogdanova
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | | | - Eric R Geertsma
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Lena Hersemann
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Tjalf Ziemssen
- Center of Clinical Neuroscience, Department of Neurology, University Hospital Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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6
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Proteomics in Multiple Sclerosis: The Perspective of the Clinician. Int J Mol Sci 2022; 23:ijms23095162. [PMID: 35563559 PMCID: PMC9100097 DOI: 10.3390/ijms23095162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 02/08/2023] Open
Abstract
Multiple sclerosis (MS) is the inflammatory demyelinating and neurodegenerative disease of the central nervous system (CNS) that affects approximately 2.8 million people worldwide. In the last decade, a new era was heralded in by a new phenotypic classification, a new diagnostic protocol and the first ever therapeutic guideline, making personalized medicine the aim of MS management. However, despite this great evolution, there are still many aspects of the disease that are unknown and need to be further researched. A hallmark of these research are molecular biomarkers that could help in the diagnosis, differential diagnosis, therapy and prognosis of the disease. Proteomics, a rapidly evolving discipline of molecular biology may fulfill this dire need for the discovery of molecular biomarkers. In this review, we aimed to give a comprehensive summary on the utility of proteomics in the field of MS research. We reviewed the published results of the method in case of the pathogenesis of the disease and for biomarkers of diagnosis, differential diagnosis, conversion of disease courses, disease activity, progression and immunological therapy. We found proteomics to be a highly effective emerging tool that has been providing important findings in the research of MS.
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7
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Update on Multiple Sclerosis Molecular Biomarkers to Monitor Treatment Effects. J Pers Med 2022; 12:jpm12040549. [PMID: 35455665 PMCID: PMC9024668 DOI: 10.3390/jpm12040549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 12/04/2022] Open
Abstract
Multiple sclerosis (MS) is an inflammatory and neurodegenerative disease of the central nervous system characterized by broad inter- and intraindividual heterogeneity. The relapse rate, disability progression, and lesion load assessed through MRI are used to detect disease activity and response to treatment. Although it is possible to standardize these characteristics in larger patient groups, so far, this has been difficult to achieve in individual patients. Easily detectable molecular biomarkers can be powerful tools, permitting a tailored therapy approach for MS patients. However, only a few molecular biomarkers have been routinely used in clinical practice as the validation process, and their transfer into clinical practice takes a long time. This review describes the characteristics of an ideal MS biomarker, the challenges of establishing new biomarkers, and promising molecular biomarkers from blood or CSF samples used to monitor MS treatment effects in clinical practice.
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8
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Proteomics of Multiple Sclerosis: Inherent Issues in Defining the Pathoetiology and Identifying (Early) Biomarkers. Int J Mol Sci 2021; 22:ijms22147377. [PMID: 34298997 PMCID: PMC8306353 DOI: 10.3390/ijms22147377] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple Sclerosis (MS) is a demyelinating disease of the human central nervous system having an unconfirmed pathoetiology. Although animal models are used to mimic the pathology and clinical symptoms, no single model successfully replicates the full complexity of MS from its initial clinical identification through disease progression. Most importantly, a lack of preclinical biomarkers is hampering the earliest possible diagnosis and treatment. Notably, the development of rationally targeted therapeutics enabling pre-emptive treatment to halt the disease is also delayed without such biomarkers. Using literature mining and bioinformatic analyses, this review assessed the available proteomic studies of MS patients and animal models to discern (1) whether the models effectively mimic MS; and (2) whether reasonable biomarker candidates have been identified. The implication and necessity of assessing proteoforms and the critical importance of this to identifying rational biomarkers are discussed. Moreover, the challenges of using different proteomic analytical approaches and biological samples are also addressed.
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9
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Guldbrandsen A, Lereim RR, Jacobsen M, Garberg H, Kroksveen AC, Barsnes H, Berven FS. Development of robust targeted proteomics assays for cerebrospinal fluid biomarkers in multiple sclerosis. Clin Proteomics 2020; 17:33. [PMID: 32963504 PMCID: PMC7499868 DOI: 10.1186/s12014-020-09296-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/08/2020] [Indexed: 12/25/2022] Open
Abstract
Background Verification of cerebrospinal fluid (CSF) biomarkers for multiple sclerosis and other neurological diseases is a major challenge due to a large number of candidates, limited sample material availability, disease and biological heterogeneity, and the lack of standardized assays. Furthermore, verification studies are often based on a low number of proteins from a single discovery experiment in medium-sized cohorts, where antibodies and surrogate peptides may differ, thus only providing an indication of proteins affected by the disease and not revealing the bigger picture or concluding on the validity of the markers. We here present a standard approach for locating promising biomarker candidates based on existing knowledge, resulting in high-quality assays covering the main biological processes affected by multiple sclerosis for comparable measurements over time. Methods Biomarker candidates were located in CSF-PR (proteomics.uib.no/csf-pr), and further filtered based on estimated concentration in CSF and biological function. Peptide surrogates for internal standards were selected according to relevant criteria, parallel reaction monitoring (PRM) assays created, and extensive assay quality testing performed, i.e. intra- and inter-day variation, trypsin digestion status over time, and whether the peptides were able to separate multiple sclerosis patients and controls. Results Assays were developed for 25 proteins, represented by 72 peptides selected according to relevant guidelines and available literature and tested for assay peptide suitability. Stability testing revealed 64 peptides with low intra- and inter-day variations, with 44 also being stably digested after 16 h of trypsin digestion, and 37 furthermore showing a significant difference between multiple sclerosis and controls, thereby confirming literature findings. Calibration curves and the linear area of measurement have, so far, been determined for 17 of these peptides. Conclusions We present 37 high-quality PRM assays across 21 CSF-proteins found to be affected by multiple sclerosis, along with a recommended workflow for future development of new assays. The assays can directly be used by others, thus enabling better comparison between studies. Finally, the assays can robustly and stably monitor biological processes in multiple sclerosis patients over time, thus potentially aiding in diagnosis and prognosis, and ultimately in treatment decisions.
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Affiliation(s)
- Astrid Guldbrandsen
- Proteomics Unit, PROBE, Department of Biomedicine, University of Bergen, Bergen, Norway.,Computational Biology Unit, CBU, Department of Informatics, University of Bergen, Bergen, Norway
| | - Ragnhild Reehorst Lereim
- Proteomics Unit, PROBE, Department of Biomedicine, University of Bergen, Bergen, Norway.,Computational Biology Unit, CBU, Department of Informatics, University of Bergen, Bergen, Norway
| | - Mari Jacobsen
- Proteomics Unit, PROBE, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Hilde Garberg
- Biobank Haukeland, Haukeland University Hospital, Bergen, Norway
| | | | - Harald Barsnes
- Proteomics Unit, PROBE, Department of Biomedicine, University of Bergen, Bergen, Norway.,Computational Biology Unit, CBU, Department of Informatics, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit, PROBE, Department of Biomedicine, University of Bergen, Bergen, Norway
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10
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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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11
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Deisenhammer F, Zetterberg H, Fitzner B, Zettl UK. The Cerebrospinal Fluid in Multiple Sclerosis. Front Immunol 2019; 10:726. [PMID: 31031747 PMCID: PMC6473053 DOI: 10.3389/fimmu.2019.00726] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/18/2019] [Indexed: 12/27/2022] Open
Abstract
Investigation of cerebrospinal fluid (CSF) in the diagnostic work-up in suspected multiple sclerosis (MS) patients has regained attention in the latest version of the diagnostic criteria due to its good diagnostic accuracy and increasing issues with misdiagnosis of MS based on over interpretation of neuroimaging results. The hallmark of MS-specific changes in CSF is the detection of oligoclonal bands (OCB) which occur in the vast majority of MS patients. Lack of OCB has a very high negative predictive value indicating a red flag during the diagnostic work-up, and alternative diagnoses should be considered in such patients. Additional molecules of CSF can help to support the diagnosis of MS, improve the differential diagnosis of MS subtypes and predict the course of the disease, thus selecting the optimal therapy for each patient.
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Affiliation(s)
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, London, United Kingdom.,The Fluid Biomarker Laboratory, UK Dementia Research Institute at UCL, London, United Kingdom
| | - Brit Fitzner
- Division of Neuroimmunology, Department of Neurology, University Medicine Rostock, Rostock, Germany
| | - Uwe K Zettl
- Division of Neuroimmunology, Department of Neurology, University Medicine Rostock, Rostock, Germany
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12
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van der Ende EL, Meeter LH, Stingl C, van Rooij JGJ, Stoop MP, Nijholt DAT, Sanchez-Valle R, Graff C, Öijerstedt L, Grossman M, McMillan C, Pijnenburg YAL, Laforce R, Binetti G, Benussi L, Ghidoni R, Luider TM, Seelaar H, van Swieten JC. Novel CSF biomarkers in genetic frontotemporal dementia identified by proteomics. Ann Clin Transl Neurol 2019; 6:698-707. [PMID: 31019994 PMCID: PMC6469343 DOI: 10.1002/acn3.745] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 12/11/2022] Open
Abstract
Objective To identify novel CSF biomarkers in GRN‐associated frontotemporal dementia (FTD) by proteomics using mass spectrometry (MS). Methods Unbiased MS was applied to CSF samples from 19 presymptomatic and 9 symptomatic GRN mutation carriers and 24 noncarriers. Protein abundances were compared between these groups. Proteins were then selected for validation if identified by ≥4 peptides and if fold change was ≤0.5 or ≥2.0. Validation and absolute quantification by parallel reaction monitoring (PRM), a high‐resolution targeted MS method, was performed on an international cohort (n = 210) of presymptomatic and symptomatic GRN, C9orf72 and MAPT mutation carriers. Results Unbiased MS revealed 20 differentially abundant proteins between symptomatic mutation carriers and noncarriers and nine between symptomatic and presymptomatic carriers. Seven of these proteins fulfilled our criteria for validation. PRM analyses revealed that symptomatic GRN mutation carriers had significantly lower levels of neuronal pentraxin receptor (NPTXR), receptor‐type tyrosine‐protein phosphatase N2 (PTPRN2), neurosecretory protein VGF, chromogranin‐A (CHGA), and V‐set and transmembrane domain‐containing protein 2B (VSTM2B) than presymptomatic carriers and noncarriers. Symptomatic C9orf72 mutation carriers had lower levels of NPTXR, PTPRN2, CHGA, and VSTM2B than noncarriers, while symptomatic MAPT mutation carriers had lower levels of NPTXR and CHGA than noncarriers. Interpretation We identified and validated five novel CSF biomarkers in GRN‐associated FTD. Our results show that synaptic, secretory vesicle, and inflammatory proteins are dysregulated in the symptomatic stage and may provide new insights into the pathophysiology of genetic FTD. Further validation is needed to investigate their clinical applicability as diagnostic or monitoring biomarkers.
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Affiliation(s)
- Emma L van der Ende
- Department of Neurology Erasmus Medical Center PO Box 2040 3015 GD Rotterdam The Netherlands
| | - Lieke H Meeter
- Department of Neurology Erasmus Medical Center PO Box 2040 3015 GD Rotterdam The Netherlands
| | - Christoph Stingl
- Laboratory of Neuro-oncology Clinical and Cancer Proteomics Department of Neurology Erasmus Medical Center PO Box 2040 3000 CA Rotterdam The Netherlands
| | - Jeroen G J van Rooij
- Department of Neurology Erasmus Medical Center PO Box 2040 3015 GD Rotterdam The Netherlands.,Department of Internal Medicine Erasmus Medical Center PO Box 2040 3015 GD Rotterdam The Netherlands
| | - Marcel P Stoop
- Laboratory of Neuro-oncology Clinical and Cancer Proteomics Department of Neurology Erasmus Medical Center PO Box 2040 3000 CA Rotterdam The Netherlands
| | - Diana A T Nijholt
- Laboratory of Neuro-oncology Clinical and Cancer Proteomics Department of Neurology Erasmus Medical Center PO Box 2040 3000 CA Rotterdam The Netherlands
| | - Raquel Sanchez-Valle
- Alzheimer's Disease and Other Cognitive Disorders Unit Department of Neurology Hospital Clínic Institut d'Investigació Biomèdica August Pi i Sunyer Villarroel, 170 08036 Barcelona Spain
| | - Caroline Graff
- Division of Neurogeriatrics Department NVS Karolinska Institutet Center for Alzheimer Research Visionsgatan 4 171 64 Solna Stockholm Sweden.,Unit for Hereditary Dementias Theme Aging Karolinska University Hospital-Solna 171 64 Stockholm Sweden
| | - Linn Öijerstedt
- Division of Neurogeriatrics Department NVS Karolinska Institutet Center for Alzheimer Research Visionsgatan 4 171 64 Solna Stockholm Sweden.,Unit for Hereditary Dementias Theme Aging Karolinska University Hospital-Solna 171 64 Stockholm Sweden
| | - Murray Grossman
- Department of Neurology Penn Frontotemporal Degeneration Center University of Pennsylvania Perelman School of Medicine Philadelphia Pennsylvania
| | - Corey McMillan
- Department of Neurology Penn Frontotemporal Degeneration Center University of Pennsylvania Perelman School of Medicine Philadelphia Pennsylvania
| | - Yolande A L Pijnenburg
- Alzheimer Center and Department of Neurology Neuroscience Campus Amsterdam VU University Medical Center PO Box 7057 1007 MB Amsterdam The Netherlands
| | - Robert Laforce
- Clinique Interdisciplinaire de Mémoire (CIME) CHU de Québec Département des Sciences Neurologiques Université Laval Québec Québec Canada
| | - Giuliano Binetti
- Molecular Markers Laboratory IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli via Pilastroni 4 Brescia 25125 Italy.,MAC Memory Clinic IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli via Pilastroni 4 Brescia 25125 Italy
| | - Luisa Benussi
- Molecular Markers Laboratory IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli via Pilastroni 4 Brescia 25125 Italy
| | - Roberta Ghidoni
- Molecular Markers Laboratory IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli via Pilastroni 4 Brescia 25125 Italy
| | - Theo M Luider
- Laboratory of Neuro-oncology Clinical and Cancer Proteomics Department of Neurology Erasmus Medical Center PO Box 2040 3000 CA Rotterdam The Netherlands
| | - Harro Seelaar
- Department of Neurology Erasmus Medical Center PO Box 2040 3015 GD Rotterdam The Netherlands
| | - John C van Swieten
- Department of Neurology Erasmus Medical Center PO Box 2040 3015 GD Rotterdam The Netherlands
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13
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Shedko ED, Tyumentseva MA. Cerebrospinal fluid molecular biomarkers of multiple sclerosis. Zh Nevrol Psikhiatr Im S S Korsakova 2019; 119:95-102. [DOI: 10.17116/jnevro201911907195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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14
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Zhang F, Wei J, Li X, Ma C, Gao Y. Early Candidate Urine Biomarkers for Detecting Alzheimer’s Disease Before Amyloid-β Plaque Deposition in an APP (swe)/PSEN1dE9 Transgenic Mouse Model. J Alzheimers Dis 2018; 66:613-637. [DOI: 10.3233/jad-180412] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fanshuang Zhang
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Wei
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
| | - Xundou Li
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Chao Ma
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Neuroscience Center; Joint Laboratory of Anesthesia and Pain, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
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15
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Barkovits K, Linden A, Galozzi S, Schilde L, Pacharra S, Mollenhauer B, Stoepel N, Steinbach S, May C, Uszkoreit J, Eisenacher M, Marcus K. Characterization of Cerebrospinal Fluid via Data-Independent Acquisition Mass Spectrometry. J Proteome Res 2018; 17:3418-3430. [PMID: 30207155 DOI: 10.1021/acs.jproteome.8b00308] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cerebrospinal fluid (CSF) is in direct contact with the brain and serves as a valuable specimen to examine diseases of the central nervous system through analyzing its components. These include the analysis of metabolites, cells as well as proteins. For identifying new suitable diagnostic protein biomarkers bottom-up data-dependent acquisition (DDA) mass spectrometry-based approaches are most popular. Drawbacks of this method are stochastic and irreproducible precursor ion selection. Recently, data-independent acquisition (DIA) emerged as an alternative method. It overcomes several limitations of DDA, since it combines the benefits of DDA and targeted methods like selected reaction monitoring (SRM). We established a DIA method for in-depth proteome analysis of CSF. For this, four spectral libraries were generated with samples from native CSF ( n = 5), CSF fractionation (15 in total) and substantia nigra fractionation (54 in total) and applied to three CSF DIA replicates. The DDA and DIA methods for CSF were conducted with the same nanoLC parameters using a 180 min gradient. Compared to a conventional DDA method, our DIA approach increased the number of identified protein groups from 648 identifications in DDA to 1574 in DIA using a comprehensive spectral library generated with DDA measurements from five native CSF and 54 substantia nigra fractions. We also could show that a sample specific spectral library generated from native CSF only increased the identification reproducibility from three DIA replicates to 90% (77% with a DDA method). Moreover, by utilizing a substantia nigra specific spectral library for CSF DIA, over 60 brain-originated proteins could be identified compared to only 11 with DDA. In conclusion, the here presented optimized DIA method substantially outperforms DDA and could develop into a powerful tool for biomarker discovery in CSF. Data are available via ProteomeXchange with the identifiers PXD010698, PXD010708, PXD010690, PXD010705, and PXD009624.
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Affiliation(s)
- Katalin Barkovits
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Andreas Linden
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Sara Galozzi
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Lukas Schilde
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Sandra Pacharra
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik , Klinikstraße 16 , D-34128 Kassel , Germany
| | - Nadine Stoepel
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Simone Steinbach
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Caroline May
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Julian Uszkoreit
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Martin Eisenacher
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Katrin Marcus
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
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16
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Shifting paradigms in multiple sclerosis: from disease-specific, through population-specific toward patient-specific. Curr Opin Neurol 2018; 29:354-61. [PMID: 27070218 DOI: 10.1097/wco.0000000000000324] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE OF REVIEW In recent years we notice paradigm shifts in the understanding of multiple sclerosis (MS), leading to important transition in the patients' management. This review discusses some of the recent findings and developments underlying the conceptual changes being translated from 'treating the disease' to 'treating the patient' with MS (PwMS). RECENT FINDINGS Applying advanced technologies combined with cross-disciplinary efforts in the fields of neuropathology, neuroimmunology, neurobiology, and neuroimaging, together with clinical neurology provided support for the notion that MS is not a single disease but rather a spectrum. Predictive markers of disease subtypes, disease activity and response to therapy are being developed; some already applied to practice, allowing informed management. In parallel, population-specific issues, some genetic-driven, others caused by environmental (sun-exposure, life-style, etc.), gender-related (hormones) and epigenetic factors, are being elucidated. Additionally, patient empowerment-based approaches, including integration of patient-reported outcome measures (PRO) as well as tools to enhance patients' adherence to medications, are being developed, some already provided as part of emerging mobile-health technologies. SUMMARY Developments in the MS field, elucidating disease subtypes and interpopulation diversities, together with integration of patient-centered approaches, allow transition toward precision medicine in MS clinical trials and patient care.
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17
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Lycke J, Zetterberg H. The role of blood and CSF biomarkers in the evaluation of new treatments against multiple sclerosis. Expert Rev Clin Immunol 2017; 13:1143-1153. [PMID: 29090607 DOI: 10.1080/1744666x.2017.1400380] [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: 01/30/2023]
Abstract
INTRODUCTION Multiple sclerosis (MS) is an immune-mediated chronic neurodegenerative disease of the central nervous system (CNS). Therapeutic interventions with immunomodulatory agents reduce disease activity and disability development, which are monitored clinically and by magnetic resonance imaging (MRI). However, these measures largely lack information on the impact from these therapies on inflammation, demyelination and axonal injury, the essential pathophysiological features of MS. Several biomarkers for inflammation and neurodegeneration have been detected in cerebrospinal fluid (CSF). In MS, some of these biomarkers seem to reflect disease activity, disability progression, and therapeutic response. Areas covered: In this review, we describe the most promising CSF biomarkers of inflammation and degeneration for monitoring therapeutic interventions in MS. We also describe the evolution of highly sensitive immunoassays that enable determination of neuron-specific biomarkers in blood. Expert commentary: Together with clinical and MRI measures, CSF biomarkers may improve the assessment of therapeutic efficacy and make personalized treatment possible. One disadvantage has been the need of repetitive lumbar punctures to obtain CSF. However, the technical development of highly sensitive immunoassays allows determination of extremely low quantities of neuron-specific proteins in blood. This will potentially open a new era for monitoring disease activity and treatment response in MS.
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Affiliation(s)
- Jan Lycke
- a Department of Clinical Neuroscience, Institute of Neuroscience and Physiology , The Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Henrik Zetterberg
- b Department of Psychiatry and Neurochemistry; Institute of Neuroscience and Physiology at Sahlgrenska Academy , University of Gothenburg , Gothenburg , Sweden.,c Clinical Neurochemistry Laboratory , Sahlgrenska University Hospital , Mölndal , Sweden.,d Department of Molecular Neuroscience , UCL Institute of Neurology , London , UK.,e UK Dementia Research Institute , London , UK
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18
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Dubuisson N, Puentes F, Giovannoni G, Gnanapavan S. Science is 1% inspiration and 99% biomarkers. Mult Scler 2017; 23:1442-1452. [PMID: 28537780 DOI: 10.1177/1352458517709362] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neurodegeneration plays a key role in multiple sclerosis (MS) contributing to long-term disability in patients. The prognosis is, however, unpredictable coloured by complex disease mechanisms which can only be clearly appreciated using biomarkers specific to pathobiology of the underlying process. Here, we describe six promising neurodegenerative biomarkers in MS (neurofilament proteins, neurofilament antibodies, tau, N-acetylaspartate, chitinase and chitinase-like proteins and osteopontin), critically evaluating the evidence using a modified Bradford Hill criteria.
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Affiliation(s)
- Nicolas Dubuisson
- Department of Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London, UK
| | - Fabiola Puentes
- Department of Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London, UK
| | - Gavin Giovannoni
- Department of Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London, UK
| | - Sharmilee Gnanapavan
- Department of Neuroscience and Trauma, Blizard Institute, Queen Mary University of London, London, UK
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19
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Harris VK, Tuddenham JF, Sadiq SA. Biomarkers of multiple sclerosis: current findings. Degener Neurol Neuromuscul Dis 2017; 7:19-29. [PMID: 30050375 PMCID: PMC6053099 DOI: 10.2147/dnnd.s98936] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune disease affecting the brain and spinal cord that is associated with chronic inflammation leading to demyelination and neurodegeneration. With the recent increase in the number of available therapies for MS, optimal treatment will be based on a personalized approach determined by an individual patient's prognosis and treatment risks. An integral part of such therapeutic decisions will be the use of molecular biomarkers to predict disability progression, monitor ongoing disease activity, and assess treatment response. This review describes current published findings within the past 3 years in biomarker research in MS, specifically highlighting recent advances in the validation of cerebrospinal fluid biomarkers such as neurofilaments (light and heavy chains), chitinases and chitinase 3-like proteins, soluble surface markers of innate immunity, and oligoclonal immunoglobulin M antibodies. Current research in circulating miRNAs as biomarkers of MS is also discussed. Continued validation and testing will be required before MS biomarkers are routinely applied in a clinical setting.
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Affiliation(s)
- Violaine K Harris
- Tisch Multiple Sclerosis Research Center of New York, New York, NY, USA,
| | - John F Tuddenham
- Tisch Multiple Sclerosis Research Center of New York, New York, NY, USA,
| | - Saud A Sadiq
- Tisch Multiple Sclerosis Research Center of New York, New York, NY, USA,
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20
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Opsahl JA, Vaudel M, Guldbrandsen A, Aasebø E, Van Pesch V, Franciotta D, Myhr KM, Barsnes H, Berle M, Torkildsen Ø, Kroksveen AC, Berven FS. Label-free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis. Proteomics 2016; 16:1154-65. [PMID: 26841090 DOI: 10.1002/pmic.201500284] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 12/08/2015] [Accepted: 01/28/2016] [Indexed: 11/05/2022]
Abstract
The aims of the study were to: (i) identify differentially regulated proteins in cerebrospinal fluid (CSF) between multiple sclerosis (MS) patients and non-MS controls; (ii) examine the effect of matching the CSF samples on either total protein amount or volume, and compare four protein normalization strategies for CSF protein quantification. CSF from MS patients (n = 37) and controls (n = 64), consisting of other noninflammatory neurological diseases (n = 50) and non neurological spinal anesthetic subjects (n = 14), were analyzed using label-free proteomics, quantifying almost 800 proteins. In total, 122 proteins were significantly regulated (p < 0.05), where 77 proteins had p-value <0.01 or AUC value >0.75. Hierarchical clustering indicated that there were two main groups of MS patients, those with increased levels of inflammatory response proteins and decreased levels of proteins involved in neuronal tissue development (n = 30), and those with normal protein levels for both of these protein groups (n = 7). The main subgroup of controls clustering with the MS patients showing increased inflammation and decreased neuronal tissue development were patients suffering from chronic fatigue. Our data indicate that the preferable way to quantify proteins in CSF is to first match the samples on total protein amount and then normalize the data based on the median intensities, preferably from the CNS-enriched proteins.
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Affiliation(s)
- Jill A Opsahl
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Astrid Guldbrandsen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Elise Aasebø
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Vincent Van Pesch
- Neurology Department, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Diego Franciotta
- Laboratory of Neuroimmunology, IRCCS, "C. Mondino" National Neurological Institute, Pavia, Italy
| | - Kjell-Morten Myhr
- The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Magnus Berle
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,Surgical Clinic, Haukeland University Hospital, Bergen, Norway
| | - Øivind Torkildsen
- The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway.,The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Ann C Kroksveen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.,The KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
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21
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Guldbrandsen A, Farag Y, Kroksveen AC, Oveland E, Lereim RR, Opsahl JA, Myhr KM, Berven FS, Barsnes H. CSF-PR 2.0: An Interactive Literature Guide to Quantitative Cerebrospinal Fluid Mass Spectrometry Data from Neurodegenerative Disorders. Mol Cell Proteomics 2016; 16:300-309. [PMID: 27890865 DOI: 10.1074/mcp.o116.064477] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/18/2016] [Indexed: 01/23/2023] Open
Abstract
The rapidly growing number of biomedical studies supported by mass spectrometry based quantitative proteomics data has made it increasingly difficult to obtain an overview of the current status of the research field. A better way of organizing the biomedical proteomics information from these studies and making it available to the research community is therefore called for. In the presented work, we have investigated scientific publications describing the analysis of the cerebrospinal fluid proteome in relation to multiple sclerosis, Parkinson's disease and Alzheimer's disease. Based on a detailed set of filtering criteria we extracted 85 data sets containing quantitative information for close to 2000 proteins. This information was made available in CSF-PR 2.0 (http://probe.uib.no/csf-pr-2.0), which includes novel approaches for filtering, visualizing and comparing quantitative proteomics information in an interactive and user-friendly environment. CSF-PR 2.0 will be an invaluable resource for anyone interested in quantitative proteomics on cerebrospinal fluid.
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Affiliation(s)
- Astrid Guldbrandsen
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Yehia Farag
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Ann Cathrine Kroksveen
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Eystein Oveland
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Ragnhild R Lereim
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Jill A Opsahl
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Kjell-Morten Myhr
- §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway.,¶Norwegian Multiple Sclerosis Registry and Biobank, Haukeland University Hospital, 5021 Bergen, Norway
| | - Frode S Berven
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway; .,§KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway.,‖Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Harald Barsnes
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,**Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.,‡‡Computational Biology Unit, Department of Informatics, University of Bergen, 5020 Bergen, Norway
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22
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Kroksveen AC, Guldbrandsen A, Vaudel M, Lereim RR, Barsnes H, Myhr KM, Torkildsen Ø, Berven FS. In-Depth Cerebrospinal Fluid Quantitative Proteome and Deglycoproteome Analysis: Presenting a Comprehensive Picture of Pathways and Processes Affected by Multiple Sclerosis. J Proteome Res 2016; 16:179-194. [PMID: 27728768 DOI: 10.1021/acs.jproteome.6b00659] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In the current study, we conducted a quantitative in-depth proteome and deglycoproteome analysis of cerebrospinal fluid (CSF) from relapsing-remitting multiple sclerosis (RRMS) and neurological controls using mass spectrometry and pathway analysis. More than 2000 proteins and 1700 deglycopeptides were quantified, with 484 proteins and 180 deglycopeptides significantly changed between pools of RRMS and pools of controls. Approximately 300 of the significantly changed proteins were assigned to various biological processes including inflammation, extracellular matrix organization, cell adhesion, immune response, and neuron development. Ninety-six significantly changed deglycopeptides mapped to proteins that were not found changed in the global protein study. In addition, four mapped to the proteins oligo-myelin glycoprotein and noelin, which were found oppositely changed in the global study. Both are ligands to the nogo receptor, and the glycosylation of these proteins appears to be affected by RRMS. Our study gives the most extensive overview of the RRMS affected processes observed from the CSF proteome to date, and the list of differential proteins will have great value for selection of biomarker candidates for further verification.
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Affiliation(s)
- Ann Cathrine Kroksveen
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Astrid Guldbrandsen
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Marc Vaudel
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Ragnhild Reehorst Lereim
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Harald Barsnes
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Kjell-Morten Myhr
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Øivind Torkildsen
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, ‡The KG Jebsen Centre for MS Research, Department of Clinical Medicine, §KG Jebsen Center for Diabetes Research, Department of Clinical Science, and ⊥Computational Biology Unit, Department of Informatics, University of Bergen , Bergen N-5009, Norway.,Center for Medical Genetics and Molecular Medicine and ∥The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Bergen N-5021, Norway
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van den Berg CB, Duvekot JJ, Güzel C, Hansson SR, de Leeuw TG, Steegers EAP, Versendaal J, Luider TM, Stoop MP. Elevated levels of protein AMBP in cerebrospinal fluid of women with preeclampsia compared to normotensive pregnant women. Proteomics Clin Appl 2016; 11. [PMID: 27615121 DOI: 10.1002/prca.201600082] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/03/2016] [Accepted: 09/08/2016] [Indexed: 11/09/2022]
Abstract
PURPOSE To investigate the cerebrospinal fluid (CSF) proteome of patients with preeclampsia (PE) and normotensive pregnant women, in order to provide a better understanding of brain involvement in PE. EXPERIMENTAL DESIGN Ninety-eight CSF samples (43 women with PE and 55 normotensive controls) were analyzed by LC-MS/MS proteome profiling. CSF was obtained during the spinal puncture before caesarean delivery. RESULTS Eight proteins were higher abundant and 17 proteins were lower abundant in patients with PE. The most significantly differentially abundant protein was protein AMBP (alpha-1-microglobulin/bikunin precursor). This finding was validated by performing an ELISA experiment (p = 0.002). CONCLUSIONS AND CLINICAL RELEVANCE The current study showed a clear difference between the protein profiles of CSF from patients with PE and normotensive pregnant women. Protein AMBP is a precursor of a heme-binding protein that counteracts the damaging effects of free hemoglobin, which may be related to the presence of free hemoglobin in CSF. Protein levels showed correlations with clinical symptoms during pregnancy and postpartum. To our knowledge, this is the first LC-MS/MS proteome profiling study on a unique set of CSF samples from (severe) preeclamptic patients and normotensive pregnant women.
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Affiliation(s)
- Caroline B van den Berg
- Department of Obstetrics and Gynecology, Division of Obstetrics and Prenatal Medicine, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Johannes J Duvekot
- Department of Obstetrics and Gynecology, Division of Obstetrics and Prenatal Medicine, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Coşkun Güzel
- Department of Neurology, Neuro-Oncology, Clinical and Cancer Proteomics Laboratory, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Stefan R Hansson
- Department of Obstetrics and Gynecology, Clinical Sciences, Lund University, Lund, Sweden
| | - Thomas G de Leeuw
- Department of Anaesthesiology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Eric A P Steegers
- Department of Obstetrics and Gynecology, Division of Obstetrics and Prenatal Medicine, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Johannes Versendaal
- Department of Obstetrics and Gynecology, Division of Obstetrics and Prenatal Medicine, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Theo M Luider
- Department of Neurology, Neuro-Oncology, Clinical and Cancer Proteomics Laboratory, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Marcel P Stoop
- Department of Neurology, Neuro-Oncology, Clinical and Cancer Proteomics Laboratory, Erasmus University Medical Centre, Rotterdam, The Netherlands
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24
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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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25
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Li X, Gao Y. Potential urinary aging markers of 20-month-old rats. PeerJ 2016; 4:e2058. [PMID: 27330854 PMCID: PMC4906655 DOI: 10.7717/peerj.2058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/29/2016] [Indexed: 01/08/2023] Open
Abstract
Urine is a very good source for biomarker discovery because it accumulates changes in the body. However, a major challenge in urinary biomarker discovery is the fact that the urinary proteome is influenced by various elements. To circumvent these problems, simpler systems, such as animal models, can be used to establish associations between physiological or pathological conditions and alterations in the urinary proteome. In this study, the urinary proteomes of young (two months old) and old rats (20 months old; nine in each group) were analyzed using LC-MS/MS and quantified using the Progenesis LC-MS software. A total of 371 proteins were identified, 194 of which were shared between the young and old rats. Based on criteria of a fold change ≥2, P < 0.05 and identification in each rat of the high-abundance group, 33 proteins were found to be changed (15 increased and 18 decreased in old rats). By adding a more stringent standard (protein spectral counts from every rat in the higher group greater than those in the lower group), eight proteins showed consistent changes in all rats of the groups; two of these proteins are also altered in the urinary proteome of aging humans. However, no shared proteins between our results and the previous aging plasma proteome were identified. Twenty of the 33 (60%) altered proteins have been reported to be disease biomarkers, suggesting that aging may share similar urinary changes with some diseases. The 33 proteins corresponded to 28 human orthologs which, according to the Human Protein Atlas, are strongly expressed in the kidney, intestine, cerebellum and lung. Therefore, the urinary proteome may reflect aging conditions in these organs.
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Affiliation(s)
- Xundou Li
- Department of Pathophysiology, Institute of Basic Medical Sciences , Beijing , China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering and Biotechnology Beijing Key Laboratory , Beijing , China
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26
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Del Boccio P, Rossi C, di Ioia M, Cicalini I, Sacchetta P, Pieragostino D. Integration of metabolomics and proteomics in multiple sclerosis: From biomarkers discovery to personalized medicine. Proteomics Clin Appl 2016; 10:470-84. [DOI: 10.1002/prca.201500083] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/17/2015] [Accepted: 12/30/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Piero Del Boccio
- Department of Medical Oral and Biotechnological Sciences; University “G. d'Annunzio” of Chieti- Pescara; Chieti Italy
- Analytical Biochemistry and Proteomics Unit, Research Centre on Aging (Ce.S.I); University “G. d'Annunzio” of Chieti-Pescara; Chieti Italy
| | - Claudia Rossi
- Department of Medical Oral and Biotechnological Sciences; University “G. d'Annunzio” of Chieti- Pescara; Chieti Italy
- Analytical Biochemistry and Proteomics Unit, Research Centre on Aging (Ce.S.I); University “G. d'Annunzio” of Chieti-Pescara; Chieti Italy
| | - Maria di Ioia
- Analytical Biochemistry and Proteomics Unit, Research Centre on Aging (Ce.S.I); University “G. d'Annunzio” of Chieti-Pescara; Chieti Italy
- Department of Neurosciences and Imaging; University “G. d'Annunzio” of Chieti-Pescara; Chieti Italy
| | - Ilaria Cicalini
- Department of Medical Oral and Biotechnological Sciences; University “G. d'Annunzio” of Chieti- Pescara; Chieti Italy
- Analytical Biochemistry and Proteomics Unit, Research Centre on Aging (Ce.S.I); University “G. d'Annunzio” of Chieti-Pescara; Chieti Italy
| | - Paolo Sacchetta
- Department of Medical Oral and Biotechnological Sciences; University “G. d'Annunzio” of Chieti- Pescara; Chieti Italy
- Analytical Biochemistry and Proteomics Unit, Research Centre on Aging (Ce.S.I); University “G. d'Annunzio” of Chieti-Pescara; Chieti Italy
| | - Damiana Pieragostino
- Department of Medical Oral and Biotechnological Sciences; University “G. d'Annunzio” of Chieti- Pescara; Chieti Italy
- Analytical Biochemistry and Proteomics Unit, Research Centre on Aging (Ce.S.I); University “G. d'Annunzio” of Chieti-Pescara; Chieti Italy
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27
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Borràs E, Cantó E, Choi M, Maria Villar L, Álvarez-Cermeño JC, Chiva C, Montalban X, Vitek O, Comabella M, Sabidó E. Protein-Based Classifier to Predict Conversion from Clinically Isolated Syndrome to Multiple Sclerosis. Mol Cell Proteomics 2016; 15:318-28. [PMID: 26552840 PMCID: PMC4762525 DOI: 10.1074/mcp.m115.053256] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/25/2015] [Indexed: 11/06/2022] Open
Abstract
Multiple sclerosis is an inflammatory, demyelinating, and neurodegenerative disease of the central nervous system. In most patients, the disease initiates with an episode of neurological disturbance referred to as clinically isolated syndrome, but not all patients with this syndrome develop multiple sclerosis over time, and currently, there is no clinical test that can conclusively establish whether a patient with a clinically isolated syndrome will eventually develop clinically defined multiple sclerosis. Here, we took advantage of the capabilities of targeted mass spectrometry to establish a diagnostic molecular classifier with high sensitivity and specificity able to differentiate between clinically isolated syndrome patients with a high and a low risk of developing multiple sclerosis. Based on the combination of abundances of proteins chitinase 3-like 1 and ala-β-his-dipeptidase in cerebrospinal fluid, we built a statistical model able to assign to each patient a precise probability of conversion to clinically defined multiple sclerosis. Our results are of special relevance for patients affected by multiple sclerosis as early treatment can prevent brain damage and slow down the disease progression.
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Affiliation(s)
- Eva Borràs
- From the ‡Proteomics Unit, Centre de Regulació Genòmica (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; §Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Ester Cantó
- ¶Servei de Neurologia-Neuroimmunologia. Centre d'Esclerosi Múltiple de Catalunya (Cemcat). Institut de Receca Vall d'Hebron (VHIR). Hospital Universitari Vall d'Hebron. Universitat Autònoma de Barcelona. Barcelona, Spain
| | - Meena Choi
- ‖Department of Statistics, Purdue University, West Lafayette, IN, USA
| | - Luisa Maria Villar
- **Department of Neurology and Immunology, Hospital Ramón y Cajal, Ctra. de Colmenar Viejo, km. 9,100, Madrid, 28034, Spain
| | - José Carlos Álvarez-Cermeño
- **Department of Neurology and Immunology, Hospital Ramón y Cajal, Ctra. de Colmenar Viejo, km. 9,100, Madrid, 28034, Spain
| | - Cristina Chiva
- From the ‡Proteomics Unit, Centre de Regulació Genòmica (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; §Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Xavier Montalban
- ¶Servei de Neurologia-Neuroimmunologia. Centre d'Esclerosi Múltiple de Catalunya (Cemcat). Institut de Receca Vall d'Hebron (VHIR). Hospital Universitari Vall d'Hebron. Universitat Autònoma de Barcelona. Barcelona, Spain
| | - Olga Vitek
- ‖Department of Statistics, Purdue University, West Lafayette, IN, USA
| | - Manuel Comabella
- ¶Servei de Neurologia-Neuroimmunologia. Centre d'Esclerosi Múltiple de Catalunya (Cemcat). Institut de Receca Vall d'Hebron (VHIR). Hospital Universitari Vall d'Hebron. Universitat Autònoma de Barcelona. Barcelona, Spain;
| | - Eduard Sabidó
- From the ‡Proteomics Unit, Centre de Regulació Genòmica (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; §Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain;
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28
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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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29
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Obry A, Hardouin J, Lequerré T, Jarnier F, Boyer O, Fardellone P, Philippe P, Marcelli C, Loët XL, Vittecoq O, Cosette P. Identification of 7 Proteins in Sera of RA Patients with Potential to Predict ETA/MTX Treatment Response. Am J Cancer Res 2015; 5:1214-24. [PMID: 26379787 PMCID: PMC4568449 DOI: 10.7150/thno.12403] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 07/08/2015] [Indexed: 01/07/2023] Open
Abstract
Objective: The recent growth of innovating biologics has opened fascinating avenues for the management of patients. In rheumatoid arthritis, many biologics are currently available, the choice of which being mostly determined empirically. Importantly, a given biologic may not be active in a fraction of patients and may even provoke side effects. Here, we conducted a comparative proteomics study in attempt to identify a predictive theranostic signature of non-response in patients with rheumatoid arthritis treated by etanercept/methotrexate combination. Methods: A serum sample was collected prior to treatment exposure from a cohort of 22 patients with active RA. A proteomic “label free” approach was then designed to quantitate protein biomarkers using mass spectrometry. To verify these results, a relative quantification followed by an absolute quantification of interesting protein candidates were performed on a second cohort. The criterion of judgment was the response to etanercept/methotrexate combination according to the EULAR criteria assessed at 6 months of treatment. Results: These investigations led to the identification of a set of 12 biomarkers with capacity to predict treatment response. A targeted quantitative analysis allowed to confirm the potential of 7 proteins from the latter combination on a new cohort of 16 patients. Two highly discriminating proteins, PROS and CO7, were further evaluated by ELISA on this second cohort. By combining the concentration threshold of each protein associated to a right classification (responders vs non-responders), the sensitivity and specificity reached 88.9 % and 100 %, respectively. Conclusion: Prior to methotrexate/etanercept treatment, abundance of several sera proteins, notably PROS and CO7, were associated to response status of RA patients 6 month after treatment initiation.
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30
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Fitzner B, Hecker M, Zettl UK. Molecular biomarkers in cerebrospinal fluid of multiple sclerosis patients. Autoimmun Rev 2015; 14:903-13. [PMID: 26071103 DOI: 10.1016/j.autrev.2015.06.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 06/03/2015] [Indexed: 12/15/2022]
Abstract
Multiple sclerosis (MS) is a chronic immune-mediated disease of the central nervous system, usually occurring in young adults and leading to disability. Despite the progress in technology and intensive research work of the last years, diagnosing MS can still be challenging. A heterogenic and complex pathophysiology with various types of disease courses makes MS unique for each patient. There is an urgent need to identify markers facilitating rapid and accurate diagnosis and prognostic assessments with regard to optimal therapy for each MS patient. Cerebrospinal fluid (CSF) is an outstanding source of specific markers related to MS pathology. Molecules reflecting specific pathological processes, such as inflammation, cellular damage, and loss of blood-brain-barrier integrity, are detectable in CSF. Clinically used biomarkers of CSF are oligoclonal bands, IgG-index, measles-rubella-zoster-reaction, anti-aquaporin 4 antibodies, and antibodies against John Cunningham virus. Many other potential biomarkers have been proposed in recent years. In this review we examine the current scientific knowledge on CSF molecular markers that could guide diagnosis and discrimination of different MS forms, support treatment decisions, or be helpful in monitoring and predicting disease progression, therapy response, and complications such as opportunistic infections.
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Affiliation(s)
- Brit Fitzner
- University Medicine Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany; STZ for Proteome Analysis, Schillingallee 69, 18057 Rostock, Germany.
| | - Michael Hecker
- University Medicine Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany; STZ for Proteome Analysis, Schillingallee 69, 18057 Rostock, Germany.
| | - Uwe Klaus Zettl
- STZ for Proteome Analysis, Schillingallee 69, 18057 Rostock, Germany.
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31
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Singh V, Stingl C, Stoop MP, Zeneyedpour L, Neuteboom RF, Smitt PS, Hintzen RQ, Luider TM. Proteomics urine analysis of pregnant women suffering from multiple sclerosis. J Proteome Res 2015; 14:2065-73. [PMID: 25793971 DOI: 10.1021/pr501162w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multiple sclerosis (MScl) frequently is remitted during the third trimester of pregnancy but exacerbated in the first postpartum period. In this context, we investigated protein identification, its abundance, and its change in urine related to these two periods. Using mass spectrometry (LTQ Orbitrap), we identified 1699 tryptic peptides (related to 402 proteins) in urine from 31 MScl and 8 control at these two periods. Pregnancy-related peptides were significantly elevated (p < 0.01) in MScl patients compared with controls (Analysis 1: 531 peptides in MScl and 36 peptides in controls higher abundant in the third trimester compared to postpartum). When comparing the longitudinal differences (Analysis 2), we identified 43 (related to 35 proteins) MScl disease-associated peptides (p < 0.01) with increased or decreased difference ratio in MScl compared with controls. The most discriminating peptides identified were trefoil factor 3 and lysosomal-associated membrane protein 2. Both proteins have a role in the innate immune system. Three proteins with a significant decreased ratio were plasma glutamate carboxypeptidase, Ig mu chain C region, and osteoclast associated immune like receptor. Our results indicate that the protein expression pattern in urine of MScl patients contains information about remote CNS and brain disease processes.
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Affiliation(s)
- Vaibhav Singh
- Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 50, Rotterdam 3015 GE, The Netherlands
| | - Christoph Stingl
- Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 50, Rotterdam 3015 GE, The Netherlands
| | - Marcel P Stoop
- Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 50, Rotterdam 3015 GE, The Netherlands
| | - Lona Zeneyedpour
- Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 50, Rotterdam 3015 GE, The Netherlands
| | - Rinze F Neuteboom
- Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 50, Rotterdam 3015 GE, The Netherlands
| | - Peter Sillevis Smitt
- Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 50, Rotterdam 3015 GE, The Netherlands
| | - Rogier Q Hintzen
- Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 50, Rotterdam 3015 GE, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus University Medical Center, Dr. Molewaterplein 50, Rotterdam 3015 GE, The Netherlands
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32
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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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Alfonso Romero-Sandoval E, Sweitzer S. Nonneuronal central mechanisms of pain: glia and immune response. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 131:325-58. [PMID: 25744678 DOI: 10.1016/bs.pmbts.2014.11.007] [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] [Indexed: 12/21/2022]
Abstract
The role of central glial cells in the mechanisms underlying pain has been intensively studied in the last two decades. Most studies on glia and pain focused on the potential detrimental role of glial cells following noxious stimulus/insults manifested as an "activation" or a "reactive" state (increase in glial marker expression and production of proinflammatory/nociceptive molecules). Therefore, "activated" or "reactive" glial cells became a target for the future generation of drugs to treat chronic pain. Several glial modulators that reduce the activation of glial cells have shown great efficacy in multiple animal (rodents mostly) models of pain (acute, subacute, chronic, inflammatory, neuropathic, surgical, etc.). These encouraging findings inspired clinical trials that have been completed in the last 5 years. Unfortunately, all clinical trials with these glial modulators have failed to demonstrate efficacy for the treatment of pain. New lines of investigation and elegant experimental designs are shedding light on alternative glial functions, which demonstrate that "glial reactivity" is not necessarily deleterious in some pathological conditions. New strategies to validate findings through our current animal models are necessary to enhance the translational value of our preclinical studies. Also, more studies using human subjects would enhance our understanding of glial cells in the context of pain. This chapter explores the available literature to objectively ponder the potential role of glial cells in human pain conditions.
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Affiliation(s)
- E Alfonso Romero-Sandoval
- Department of Pharmaceutical and Administrative Sciences, Presbyterian College School of Pharmacy, Clinton, South Carolina, USA.
| | - Sarah Sweitzer
- Department of Pharmaceutical and Administrative Sciences, Presbyterian College School of Pharmacy, Clinton, South Carolina, USA
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Kroksveen AC, Opsahl JA, Guldbrandsen A, Myhr KM, Oveland E, Torkildsen Ø, Berven FS. Cerebrospinal fluid proteomics in multiple sclerosis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:746-56. [PMID: 25526888 DOI: 10.1016/j.bbapap.2014.12.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/27/2014] [Accepted: 12/11/2014] [Indexed: 12/31/2022]
Abstract
Multiple sclerosis (MS) is an immune mediated chronic inflammatory disease of the central nervous system usually initiated during young adulthood, affecting approximately 2.5 million people worldwide. There is currently no cure for MS, but disease modifying treatment has become increasingly more effective, especially when started in the first phase of the disease. The disease course and prognosis are often unpredictable and it can be challenging to determine an early diagnosis. The detection of novel biomarkers to understand more of the disease mechanism, facilitate early diagnosis, predict disease progression, and find treatment targets would be very attractive. Over the last decade there has been an increasing effort toward finding such biomarker candidates. One promising strategy has been to use state-of-the-art quantitative proteomics approaches to compare the cerebrospinal fluid (CSF) proteome between MS and control patients or between different subgroups of MS. In this review we summarize and discuss the status of CSF proteomics in MS, including the latest findings with a focus on the last five years. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Affiliation(s)
- Ann C Kroksveen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway
| | - Jill A Opsahl
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway
| | - Astrid Guldbrandsen
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway
| | - Kjell-Morten Myhr
- The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway; Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway; The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway
| | - Eystein Oveland
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway
| | - Øivind Torkildsen
- The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway; Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway; The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postbox 7804, N-5009 Bergen, Norway; The KG Jebsen Centre for MS-Research, Department of Clinical Medicine, University of Bergen, Postbox 7804, N-5021 Bergen, Norway; The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Postbox 1400, 5021 Bergen, Norway.
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Abstract
Multiple sclerosis (MS) is an autoimmune disease of unknown cause, in which chronic inflammation drives multifocal demyelination of axons in both white and gray matter in the CNS. The pathological course of the disease is heterogeneous and involves an early, predominantly inflammatory demyelinating disease phase of relapsing-remitting MS (RRMS), which, over a variable period of time, evolves into a progressively degenerative stage associated with axonal loss and scar formation, causing physical and cognitive disability. For patients with RRMS, there is a growing arsenal of disease-modifying agents (DMAs), with varying degrees of efficacy, as defined by reduced relapse rates, improved magnetic resonance imaging outcomes, and preservation of neurological function. Establishment of personalized treatment plans remains one of the biggest challenges in therapeutic decision-making in MS because the disease prognosis and individual therapeutic outcomes are extremely difficult to predict. Current research is aimed at discovery and validation of biomarkers that reliably measure disease progression and effective therapeutic intervention. Individual biomarker candidates with evident clinical utility are highlighted in this review and include neutralizing autoantibodies against DMAs, fetuin-A, osteopontin, isoprostanes, chemokine (C-X-C motif) ligand 13 (CXCL13), neurofilament light and heavy, and chitinase 3-like protein. In addition, application of more advanced screening technologies has opened up new categories of biomarkers that move beyond detection of individual soluble proteins, including gene expression and autoantibody arrays, microRNAs, and circulating microvesicles/exosomes. Development of clinically useful biomarkers in MS will not only shape the practice of personalized medicine but will also serve as surrogate markers to enable investigation of innovative treatments within clinical trials that are less costly, are of shorter duration, and have more certainty of outcomes.
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Affiliation(s)
- Violaine K. Harris
- Tisch Multiple Sclerosis Research Center of New York, 521 West 57th Street, New York, NY 10019 USA
| | - Saud A. Sadiq
- Tisch Multiple Sclerosis Research Center of New York, 521 West 57th Street, New York, NY 10019 USA
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Abstract
New technologies in mass spectrometry are beginning to mature and show unique advantages for the identification and quantitation of proteins. In recent years, one of the significant goals of clinical proteomics has been to identify biomarkers that can be used for clinical diagnosis. As technology has progressed, the list of potential biomarkers has grown. However, the verification and validation of these potential biomarkers is increasingly challenging and require high-throughput quantitative assays, targeting specific candidates. Targeted proteomics bridges the gap between biomarker discovery and the development of clinically applicable biomarker assays.
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Affiliation(s)
- Robert Harlan
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
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CSF levels of YKL-40 are increased in MS and decrease with immunosuppressive treatment. J Neuroimmunol 2014; 269:87-9. [DOI: 10.1016/j.jneuroim.2014.02.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/21/2014] [Accepted: 02/03/2014] [Indexed: 11/19/2022]
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Li X, Zhao M, Li M, Jia L, Gao Y. Effects of three commonly-used diuretics on the urinary proteome. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:120-6. [PMID: 24508280 PMCID: PMC4411397 DOI: 10.1016/j.gpb.2013.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/08/2013] [Accepted: 12/12/2013] [Indexed: 12/22/2022]
Abstract
Biomarker is the measurable change associated with a physiological or pathophysiological process. Unlike blood which has mechanisms to keep the internal environment homeostatic, urine is more likely to reflect changes of the body. As a result, urine is likely to be a better biomarker source than blood. However, since the urinary proteome is affected by many factors, including diuretics, careful evaluation of those effects is necessary if urinary proteomics is used for biomarker discovery. Here, we evaluated the effects of three commonly-used diuretics (furosemide, F; hydrochlorothiazide, H; and spirolactone, S) on the urinary proteome in rats. Urine samples were collected before and after intragastric administration of diuretics at therapeutic doses and the proteomes were analyzed using label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS). Based on the criteria of P≤0.05, a fold change ≥2, a spectral count ≥5, and false positive rate (FDR) ≤1%, 14 proteins (seven for F, five for H, and two for S) were identified by Progenesis LC-MS. The human orthologs of most of these 14 proteins are stable in the healthy human urinary proteome, and ten of them are reported as disease biomarkers. Thus, our results suggest that the effects of diuretics deserve more attention in future urinary protein biomarker studies. Moreover, the distinct effects of diuretics on the urinary proteome may provide clues to the mechanisms of diuretics.
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Affiliation(s)
- Xundou Li
- National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Mindi Zhao
- National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Menglin Li
- National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Lulu Jia
- National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Youhe Gao
- National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China.
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Craft GE, Chen A, Nairn AC. Recent advances in quantitative neuroproteomics. Methods 2013; 61:186-218. [PMID: 23623823 PMCID: PMC3891841 DOI: 10.1016/j.ymeth.2013.04.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 03/29/2013] [Accepted: 04/13/2013] [Indexed: 01/07/2023] Open
Abstract
The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson's disease and Alzheimer's disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed light on a number of aspects of neuroscience that relates to normal brain function as well as of the changes in protein expression and regulation that occurs in neuropsychiatric and neurodegenerative disorders.
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Affiliation(s)
- George E Craft
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
| | - Anshu Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
| | - Angus C Nairn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06508
- Yale/NIDA Neuroproteomics Center, Yale University School of Medicine, New Haven, CT, 06508
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