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Berek K, Bauer A, Rudzki D, Auer M, Barket R, Zinganell A, Lerch M, Hofer L, Grams A, Poskaite P, Wurth S, Berger T, Di Pauli F, Deisenhammer F, Hegen H, Reindl M. Immune profiling in multiple sclerosis: a single-center study of 65 cytokines, chemokines, and related molecules in cerebrospinal fluid and serum. Front Immunol 2023; 14:1200146. [PMID: 37383229 PMCID: PMC10294231 DOI: 10.3389/fimmu.2023.1200146] [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] [Received: 04/04/2023] [Accepted: 05/22/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction The understanding of the pathophysiology of multiple sclerosis (MS) has evolved alongside the characterization of cytokines and chemokines in cerebrospinal fluid (CSF) and serum. However, the complex interplay of pro- and anti-inflammatory cytokines and chemokines in different body fluids in people with MS (pwMS) and their association with disease progression is still not well understood and needs further investigation. Therefore, the aim of this study was to profile a total of 65 cytokines, chemokines, and related molecules in paired serum and CSF samples of pwMS at disease onset. Methods Multiplex bead-based assays were performed and baseline routine laboratory diagnostics, magnetic resonance imaging (MRI), and clinical characteristics were assessed. Of 44 participants included, 40 had a relapsing-remitting disease course and four a primary progressive MS. Results There were 29 cytokines and chemokines that were significantly higher in CSF and 15 in serum. Statistically significant associations with moderate effect sizes were found for 34 of 65 analytes with sex, age, CSF, and MRI parameters and disease progression. Discussion In conclusion, this study provides data on the distribution of 65 different cytokines, chemokines, and related molecules in CSF and serum in newly diagnosed pwMS.
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Affiliation(s)
- Klaus Berek
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Angelika Bauer
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
- VASCage Research Centre on Vascular Ageing and Stroke, Innsbruck, Austria
| | - Dagmar Rudzki
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
- VASCage Research Centre on Vascular Ageing and Stroke, Innsbruck, Austria
| | - Michael Auer
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Robert Barket
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Anne Zinganell
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Magdalena Lerch
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Livia Hofer
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Astrid Grams
- Department of Neuroradiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Paulina Poskaite
- Department of Neuroradiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Wurth
- Department of Neurology, Medical University of Graz, Graz, Austria
| | - Thomas Berger
- Department of Neurology, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Franziska Di Pauli
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Harald Hegen
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Markus Reindl
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
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2
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Li J, Wang L, Ding J, Cheng Y, Diao L, Li L, Zhang Y, Yin T. Multiomics Studies Investigating Recurrent Pregnancy Loss: An Effective Tool for Mechanism Exploration. Front Immunol 2022; 13:826198. [PMID: 35572542 PMCID: PMC9094436 DOI: 10.3389/fimmu.2022.826198] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/31/2022] [Indexed: 12/18/2022] Open
Abstract
Patients with recurrent pregnancy loss (RPL) account for approximately 1%-5% of women aiming to achieve childbirth. Although studies have shown that RPL is associated with failure of endometrial decidualization, placental dysfunction, and immune microenvironment disorder at the maternal-fetal interface, the exact pathogenesis remains unknown. With the development of high-throughput technology, more studies have focused on the genomics, transcriptomics, proteomics and metabolomics of RPL, and new gene mutations and new biomarkers of RPL have been discovered, providing an opportunity to explore the pathogenesis of RPL from different biological processes. Bioinformatics analyses of these differentially expressed genes, proteins and metabolites also reflect the biological pathways involved in RPL, laying a foundation for further research. In this review, we summarize the findings of omics studies investigating decidual tissue, villous tissue and blood from patients with RPL and identify some possible limitations of current studies.
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Affiliation(s)
- Jianan Li
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Linlin Wang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China.,Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, China
| | - Jinli Ding
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yanxiang Cheng
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lianghui Diao
- Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, China
| | - Longfei Li
- Shenzhen Key Laboratory of Reproductive Immunology for Peri-implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Shenzhen Zhongshan Urology Hospital, Shenzhen, China
| | - Yan Zhang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Tailang Yin
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, China
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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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4
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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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Salazar IL, Lourenço AST, Manadas B, Baldeiras I, Ferreira C, Teixeira AC, Mendes VM, Novo AM, Machado R, Batista S, Macário MDC, Grãos M, Sousa L, Saraiva MJ, Pais AACC, Duarte CB. Posttranslational modifications of proteins are key features in the identification of CSF biomarkers of multiple sclerosis. J Neuroinflammation 2022; 19:44. [PMID: 35135578 PMCID: PMC8822857 DOI: 10.1186/s12974-022-02404-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/26/2022] [Indexed: 12/27/2022] Open
Abstract
Background Multiple sclerosis is an inflammatory and degenerative disease of the central nervous system (CNS) characterized by demyelination and concomitant axonal loss. The lack of a single specific test, and the similarity to other inflammatory diseases of the central nervous system, makes it difficult to have a clear diagnosis of multiple sclerosis. Therefore, laboratory tests that allows a clear and definite diagnosis, as well as to predict the different clinical courses of the disease are of utmost importance. Herein, we compared the cerebrospinal fluid (CSF) proteome of patients with multiple sclerosis (in the relapse–remitting phase of the disease) and other diseases of the CNS (inflammatory and non-inflammatory) aiming at identifying reliable biomarkers of multiple sclerosis. Methods CSF samples from the discovery group were resolved by 2D-gel electrophoresis followed by identification of the protein spots by mass spectrometry. The results were analyzed using univariate (Student’s t test) and multivariate (Hierarchical Cluster Analysis, Principal Component Analysis, Linear Discriminant Analysis) statistical and numerical techniques, to identify a set of protein spots that were differentially expressed in CSF samples from patients with multiple sclerosis when compared with other two groups. Validation of the results was performed in samples from a different set of patients using quantitative (e.g., ELISA) and semi-quantitative (e.g., Western Blot) experimental approaches. Results Analysis of the 2D-gels showed 13 protein spots that were differentially expressed in the three groups of patients: Alpha-1-antichymotrypsin, Prostaglandin-H2-isomerase, Retinol binding protein 4, Transthyretin (TTR), Apolipoprotein E, Gelsolin, Angiotensinogen, Agrin, Serum albumin, Myosin-15, Apolipoprotein B-100 and EF-hand calcium-binding domain—containing protein. ELISA experiments allowed validating part of the results obtained in the proteomics analysis and showed that some of the alterations in the CSF proteome are also mirrored in serum samples from multiple sclerosis patients. CSF of multiple sclerosis patients was characterized by TTR oligomerization, thus highlighting the importance of analyzing posttranslational modifications of the proteome in the identification of novel biomarkers of the disease. Conclusions The model built based on the results obtained upon analysis of the 2D-gels and in the validation phase attained an accuracy of about 80% in distinguishing multiple sclerosis patients and the other two groups. Supplementary Information The online version contains supplementary material available at 10.1186/s12974-022-02404-2.
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Affiliation(s)
- Ivan L Salazar
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Ana S T Lourenço
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Bruno Manadas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Inês Baldeiras
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Cláudia Ferreira
- Coimbra Chemistry Centre, Department of Chemistry, University of Coimbra, Coimbra, Portugal
| | - Anabela Claro Teixeira
- Molecular Neurobiology Group, Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
| | - Vera M Mendes
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ana Margarida Novo
- Neurology Department, CHUC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Rita Machado
- Neurology Department, CHUC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Sónia Batista
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Neurology Department, CHUC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Maria do Carmo Macário
- Neurology Department, CHUC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Mário Grãos
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal.,Biocant-Associação de Transferência de Tecnologia, Cantanhede, Portugal
| | - Lívia Sousa
- Neurology Department, CHUC-Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Maria João Saraiva
- Molecular Neurobiology Group, Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
| | - Alberto A C C Pais
- Coimbra Chemistry Centre, Department of Chemistry, University of Coimbra, Coimbra, Portugal
| | - Carlos B Duarte
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal. .,Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
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Auler N, Tonner H, Pfeiffer N, Grus FH. Antibody and Protein Profiles in Glaucoma: Screening of Biomarkers and Identification of Signaling Pathways. BIOLOGY 2021; 10:biology10121296. [PMID: 34943212 PMCID: PMC8698915 DOI: 10.3390/biology10121296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/24/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022]
Abstract
Simple Summary Glaucoma is a chronic eye disease that is one of the leading causes of blindness worldwide. Currently, the only therapeutic option is to lower intraocular pressure. The onset of the disease is often delayed because patients do not notice visual impairment until very late, which is why glaucoma is also known as “the silent thief of sight”. Therefore, early detection and definition of specific markers, the so-called biomarkers, are immensely important. For the methodical implementation, high-throughput methods and omic-based methods came more and more into focus. Thus, interesting targets for possible biomarkers were already suggested by clinical research and basic research, respectively. This review article aims to join the findings of the two disciplines by collecting overlaps as well as differences in various clinical studies and to shed light on promising candidates concerning findings from basic research, facilitating conclusions on possible therapy options. Abstract Glaucoma represents a group of chronic neurodegenerative diseases, constituting the second leading cause of blindness worldwide. To date, chronically elevated intraocular pressure has been identified as the main risk factor and the only treatable symptom. However, there is increasing evidence in the recent literature that IOP-independent molecular mechanisms also play an important role in the progression of the disease. In recent years, it has become increasingly clear that glaucoma has an autoimmune component. The main focus nowadays is elucidating glaucoma pathogenesis, finding early diagnostic options and new therapeutic approaches. This review article summarizes the impact of different antibodies and proteins associated with glaucoma that can be detected for example by microarray and mass spectrometric analyzes, which (i) provide information about expression profiles and associated molecular signaling pathways, (ii) can possibly be used as a diagnostic tool in future and, (iii) can identify possible targets for therapeutic approaches.
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7
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Jafari A, Babajani A, Rezaei-Tavirani M. Multiple Sclerosis Biomarker Discoveries by Proteomics and Metabolomics Approaches. Biomark Insights 2021; 16:11772719211013352. [PMID: 34017167 PMCID: PMC8114757 DOI: 10.1177/11772719211013352] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 04/05/2021] [Indexed: 12/22/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune inflammatory disorder of the central nervous system (CNS) resulting in demyelination and axonal loss in the brain and spinal cord. The precise pathogenesis and etiology of this complex disease are still a mystery. Despite many studies that have been aimed to identify biomarkers, no protein marker has yet been approved for MS. There is urgently needed for biomarkers, which could clarify pathology, monitor disease progression, response to treatment, and prognosis in MS. Proteomics and metabolomics analysis are powerful tools to identify putative and novel candidate biomarkers. Different human compartments analysis using proteomics, metabolomics, and bioinformatics approaches has generated new information for further clarification of MS pathology, elucidating the mechanisms of the disease, finding new targets, and monitoring treatment response. Overall, omics approaches can develop different therapeutic and diagnostic aspects of complex disorders such as multiple sclerosis, from biomarker discovery to personalized medicine.
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Affiliation(s)
- Ameneh Jafari
- Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amirhesam Babajani
- Department of Pharmacology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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8
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Bansal R, Khan MM, Dasari S, Verma I, Goodlett DR, Manes NP, Nita-Lazar A, Sharma SP, Kumar A, Singh N, Chakraborti A, Gupta V, Dogra MR, Ram J, Gupta A. Proteomic profile of vitreous in patients with tubercular uveitis. Tuberculosis (Edinb) 2021; 126:102036. [PMID: 33359883 PMCID: PMC11005023 DOI: 10.1016/j.tube.2020.102036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/31/2020] [Accepted: 11/29/2020] [Indexed: 12/27/2022]
Abstract
OBJECTIVE To elucidate disease-specific host protein profile in vitreous fluid of patients with intraocular inflammation due to tubercular uveitis (TBU). METHODS Vitreous samples from 13 patients with TBU (group A), 7 with non-TBU (group B) and 9 with no uveitis (group C) were analysed by shotgun proteomics using Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS). Differentially expressed proteins (DEPs) were subjected to pathway analysis using WEB-based Gene SeT Analysis Toolkit software. RESULTS Compared to control groups (B + C combined), group A (TBU) displayed 32 (11 upregulated, 21 downregulated) DEPs, which revealed an upregulation of coagulation cascades, complement and classic pathways, and downregulation of metabolism of carbohydrates, gluconeogenesis, glucose metabolism and glycolysis/gluconeogenesis pathways. When compared to group B (non-TBU) alone, TBU displayed 58 DEPs (21 upregulated, 37 downregulated), with an upregulation of apoptosis, KRAS signaling, diabetes pathways, classic pathways, and downregulation of MTORC1 signaling, glycolysis/gluconeogenesis, and glucose metabolism. CONCLUSION This differential protein profile provides novel insights into the molecular mechanisms of TBU and a baseline to explore vitreous biomarkers to differentiate TBU from non-TBU, warranting future studies to identify and validate them as a diagnostic tool in TBU. The enriched pathways generate interesting hypotheses and drive further research.
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Affiliation(s)
- Reema Bansal
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
| | - Mohd M Khan
- University of Maryland, School of Medicine, Baltimore, MD, USA; Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Surendra Dasari
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
| | - Indu Verma
- Department of Biochemistry, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
| | | | - Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Surya P Sharma
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
| | - Aman Kumar
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
| | - Nirbhai Singh
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
| | - Anuradha Chakraborti
- Department of Experimental Medicine & Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
| | - Vishali Gupta
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
| | - M R Dogra
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
| | - Jagat Ram
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
| | - Amod Gupta
- Advanced Eye Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
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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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Protein profiling of cerebrospinal fluid from patients undergoing vestibular schwannoma surgery and clinical significance. Biomed Pharmacother 2019; 116:108985. [PMID: 31146115 DOI: 10.1016/j.biopha.2019.108985] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/24/2019] [Accepted: 05/13/2019] [Indexed: 12/12/2022] Open
Abstract
Vestibular schwannoma (VS) is a common disease in the region of the cerebellopontine angle in the posterior cranial fossa. Large VS and its surgical management usually lead to severe cranial nerve dysfunction and affect the patient's quality of life. We aimed to find some possible progression markers of VS. Here, we sought to characterize the cerebrospinal fluid (CSF) proteome of patients with different VS grades and recurrence to identify biomarkers predictive of VS growth or recurrence. CSF was collected intraoperatively prior to removal of untreated VS, including grade I-V and recurrence. Isobaric tags for relative and absolute quantitation-based proteomic analysis of CSF from 43 VS patients and 3 control patients was used to identify candidate proteins. Ninety-three overlapping proteins were found to display differential expression in grade I, II, III, IV, and V VS patients compared with the control group. Nine proteins were chosen for validation with enzyme-linked immunosorbent assay. VS was distinguished from control patients based on the expression patterns of six proteins (ATP-binding cassette subfamily A member 3 [ABCA3], secretogranin-1 [SCG1], Krueppel-like factor 11 [KLF11], voltage-dependent calcium channel subunit alpha-2/delta-1 [CA2D1], brain acid soluble protein 1 [BASP1], and peroxiredoxin-2 [PRDX2]. ABCA3 and KLF11 were positively correlated with the size of early-phase of VS, while BASP1 and PRDX2 showed a negative correlation. ABCA3, CA2D1, and KLF11 were upregulated, while BASP1 and PRDX2 were downregulated in the CSF from VS recurrence. But SCG1 was increased only at early-phase. These data suggest that increased ABCA3 and KLF11 and decreased BASP1 and PRDX2 in CSF are associated with VS growth at the early phase or recurrence.
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Larssen E, Brede C, Hjelle A, Tjensvoll AB, Norheim KB, Bårdsen K, Jonsdottir K, Ruoff P, Omdal R, Nilsen MM. Fatigue in primary Sjögren's syndrome: A proteomic pilot study of cerebrospinal fluid. SAGE Open Med 2019; 7:2050312119850390. [PMID: 31205695 PMCID: PMC6537061 DOI: 10.1177/2050312119850390] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/22/2019] [Indexed: 12/16/2022] Open
Abstract
Objectives: Fatigue is a frequent and often disabling phenomenon that occurs in patients
with chronic inflammatory and immunological diseases, and the underlying
biological mechanisms are largely unknown. Because fatigue is generated in
the brain, we aimed to investigate cerebrospinal fluid and search for
molecules that participate in the pathophysiology of fatigue processes. Methods: A label-free shotgun proteomics approach was applied to analyze the
cerebrospinal fluid proteome of 20 patients with primary Sjögren’s syndrome.
Fatigue was measured with the fatigue visual analog scale. Results: A total of 828 proteins were identified and the 15 top discriminatory
proteins between patients with high and low fatigue were selected. Among
these were apolipoprotein A4, hemopexin, pigment epithelium-derived factor,
secretogranin-1, secretogranin-3, selenium-binding protein 1, and complement
factor B. Conclusion: Most of the discriminatory proteins have important roles in regulation of
innate immunity, cellular stress defense, and/or functions in the central
nervous system. These proteins and their interacting protein networks may
therefore have central roles in the generation and regulation of fatigue,
and the findings contribute with evidence to the concept of fatigue as a
biological phenomenon signaled through specific molecular pathways.
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Affiliation(s)
- Eivind Larssen
- Research Department, Stavanger University Hospital, Stavanger, Norway.,Norwegian Research Centre AS (NORCE), Stavanger, Norway
| | - Cato Brede
- Department of Medical Biochemistry, Stavanger University Hospital, Stavanger, Norway
| | - Anne Hjelle
- Research Department, Stavanger University Hospital, Stavanger, Norway
| | | | - Katrine Brække Norheim
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Kjetil Bårdsen
- Research Department, Stavanger University Hospital, Stavanger, Norway
| | - Kristin Jonsdottir
- Department of Pathology, Stavanger University Hospital, Stavanger, Norway
| | - Peter Ruoff
- Centre for Organelle Research (CORE), University of Stavanger, Stavanger, Norway
| | - Roald Omdal
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway.,Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Mari Mæland Nilsen
- Research Department, Stavanger University Hospital, Stavanger, Norway.,Norwegian Research Centre AS (NORCE), Stavanger, Norway
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13
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Bisht D, Sharma D, Sharma D, Singh R, Gupta VK. Recent insights intoMycobacterium tuberculosisthrough proteomics and implications for the clinic. Expert Rev Proteomics 2019; 16:443-456. [DOI: 10.1080/14789450.2019.1608185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - Devesh Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - Divakar Sharma
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Rananjay Singh
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
| | - Vivek Kumar Gupta
- Department of Biochemistry, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (ICMR), Agra, India
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14
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Timirci-Kahraman O, Karaaslan Z, Tuzun E, Kurtuncu M, Baykal AT, Gunduz T, Tuzuner MB, Akgun E, Gurel B, Eraksoy M, Kucukali CI. Identification of candidate biomarkers in converting and non-converting clinically isolated syndrome by proteomics analysis of cerebrospinal fluid. Acta Neurol Belg 2019; 119:101-111. [PMID: 29873030 DOI: 10.1007/s13760-018-0954-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/24/2018] [Indexed: 01/28/2023]
Abstract
Multiple sclerosis (MS) often starts in the form of clinically isolated syndrome (CIS) and only some of the CIS patients progress to relapsing-remitting MS (RRMS). Biomarkers to predict conversion from CIS to MS are thus greatly needed for making correct treatment decisions. To identify a predictive cerebrospinal fluid (CSF) protein, we analyzed the first-attack CSF samples of CIS patients who converted (CIS-MS) (n = 23) and did not convert (CIS-CIS) (n = 19) to RRMS in a follow-up period of 5 years using proteomics analysis by liquid chromatography tandem-mass spectrometry (LC-MS/MS) and verified by ELISA. Label-free differential proteomics analysis of CSF ensured that 637 proteins were identified and 132 of these proteins were found to be statistically significant. Further investigation with the ingenuity pathway analysis (IPA) software led to identification of three pathway networks mostly comprised proteins involved in inflammatory response, cellular growth and tissue proliferation. CSF levels of four of the most differentially expressed proteins belonging to the cellular proliferation network function, chitinase-3-like protein 1 (CHI3L1), tumor necrosis factor receptor superfamily member 21 (TNFRSF21), homeobox protein Hox-B3 (HOXB3) and iduronate 2-sulfatase (IDS), were measured by ELISA. CSF levels of HOXB3 were significantly increased in CIS-MS patients. Our results indicate that cell and tissue proliferation functions are dysregulated in MS as early as the first clinical episode. HOXB3 has emerged as a potential novel biomarker which might be used for prediction of CIS-MS conversion.
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15
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Masvekar R, Wu T, Kosa P, Barbour C, Fossati V, Bielekova B. Cerebrospinal fluid biomarkers link toxic astrogliosis and microglial activation to multiple sclerosis severity. Mult Scler Relat Disord 2019; 28:34-43. [PMID: 30553167 PMCID: PMC6411304 DOI: 10.1016/j.msard.2018.11.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/20/2018] [Accepted: 11/29/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND Once multiple sclerosis (MS) reaches the progressive stage, immunomodulatory treatments have limited efficacy. This suggests that processes other than activation of innate immunity may at least partially underlie disability progression during late stages of MS. Pathology identified these alternative processes as aberrant activation of astrocytes and microglia, and subsequent degeneration of oligodendrocytes and neurons. However, we mostly lack biomarkers that could measure central nervous system (CNS) cell-specific intrathecal processes in living subjects. This prevents differentiating pathogenic processes from an epiphenomenon. Therefore, we sought to develop biomarkers of CNS cell-specific processes and link them to disability progression in MS. METHODS In a blinded manner, we measured over 1000 proteins in the cerebrospinal fluid (CSF) of 431 patients with neuroimmunological diseases and healthy volunteers using modified DNA-aptamers (SOMAscan®). We defined CNS cell type-enriched clusters using variable cluster analysis, combined with in vitro modeling. Differences between diagnostic categories were identified in the training cohort (n = 217) and their correlation to disability measures were assessed; results were validated in an independent validation cohort (n = 214). RESULTS Astrocyte cluster 8 (MMP7, SERPINA3, GZMA and CLIC1) and microglial cluster 2 (DSG2 and TNFRSF25) were reproducibly elevated in MS and had a significant and reproducible correlation with MS severity suggesting their pathogenic role. In vitro studies demonstrated that proteins of astrocyte cluster 8 are noticeably released upon stimulation with proinflammatory stimuli and overlap with the phenotype of recently described neuro-toxic (A1) astrocytes. CONCLUSION Microglial activation and toxic astrogliosis are associated with MS disease process and may partake in CNS tissue destruction. This hypothesis should be tested in new clinical trials.
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Affiliation(s)
- Ruturaj Masvekar
- Neuroimmunological Diseases Section (NDS), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Room 5N248, 10 Center Drive, MSC1444, Bethesda, MD 20892, United States
| | - Tianxia Wu
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Peter Kosa
- Neuroimmunological Diseases Section (NDS), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Room 5N248, 10 Center Drive, MSC1444, Bethesda, MD 20892, United States
| | - Christopher Barbour
- Neuroimmunological Diseases Section (NDS), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Room 5N248, 10 Center Drive, MSC1444, Bethesda, MD 20892, United States; Department of Mathematical Sciences, Montana State University, Bozeman, MT, United States
| | - Valentina Fossati
- The New York Stem Cell Foundation Research Institute, New York, NY, United States
| | - Bibiana Bielekova
- Neuroimmunological Diseases Section (NDS), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 10, Room 5N248, 10 Center Drive, MSC1444, Bethesda, MD 20892, United States.
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16
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Rana A, Thakur S, Kumar G, Akhter Y. Recent Trends in System-Scale Integrative Approaches for Discovering Protective Antigens Against Mycobacterial Pathogens. Front Genet 2018; 9:572. [PMID: 30538722 PMCID: PMC6277634 DOI: 10.3389/fgene.2018.00572] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/06/2018] [Indexed: 11/21/2022] Open
Abstract
Mycobacterial infections are one of the deadliest infectious diseases still posing a major health burden worldwide. The battle against these pathogens needs to focus on novel approaches and key interventions. In recent times, availability of genome scale data has revolutionized the fields of computational biology and immunoproteomics. Here, we summarize the cutting-edge ‘omics’ technologies and innovative system scale strategies exploited to mine the available data. These may be targeted using high-throughput technologies to expedite the identification of novel antigenic candidates for the rational next generation vaccines and serodiagnostic development against mycobacterial pathogens for which traditional methods have been failing.
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Affiliation(s)
- Aarti Rana
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Shweta Thakur
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Girish Kumar
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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17
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Fukui K, Okihiro S, Ohfuchi Y, Hashimoto M, Kato Y, Yoshida N, Mochizuki K, Tsumoto H, Miura Y. Proteomic study on neurite responses to oxidative stress: search for differentially expressed proteins in isolated neurites of N1E-115 cells. J Clin Biochem Nutr 2018; 64:36-44. [PMID: 30705510 PMCID: PMC6348415 DOI: 10.3164/jcbn.18-31] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/14/2018] [Indexed: 01/09/2023] Open
Abstract
Reactive oxygen species attack several living organs and induce cell death. Previously, we found axonal/dendrite degeneration before the induction of cell death in hydrogen peroxide-treated neuroblastoma: N1E-115 cells and primary neurons. This phenomenon may be connected with membrane oxidation, microtubule destabilization and disruption of intracellular calcium homeostasis. However, its detailed mechanisms are not fully understood. Here, we identified proteins after treatment with hydrogen peroxide using isolated neurites by liquid chromatography-matrix-assisted laser desorption/ionization-time of flight/time of flight analysis. Twenty-one proteins were increased after treatment with hydrogen peroxide. Specifically, 5 proteins which were secretogranin-1, heat shock protein family D member 1, Brain acid soluble protein 1, heat shock 70-kDa protein 5 and superoxide dismutase 1, were identified of all experiments and increased in isolated neurites of hydrogen peroxide-treated cells compared to the controls. Furthermore, secretogranin-1 and heat shock protein family D member 1 protein expressions were significantly increased in normal aged and Alzheimer’s transgenic mice brains. These results indicate that secretogranin-1 and heat shock protein family D member 1 might contribute to reactive oxygen species-induced neurite degeneration. Both proteins have been related to neurodegenerative disorders, so their study may shed light on neurite dysfunction.
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Affiliation(s)
- Koji Fukui
- Molecular Cell Biology Laboratory, Department of Systems Engineering and Science, Graduate School of Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan.,Molecular Cell Biology Laboratory, Department of Bioscience and Engineering, College of Systems Engineering and Sciences, Shibaura Institute of Technology
| | - Shunsuke Okihiro
- Molecular Cell Biology Laboratory, Department of Systems Engineering and Science, Graduate School of Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Yuuka Ohfuchi
- Molecular Cell Biology Laboratory, Department of Bioscience and Engineering, College of Systems Engineering and Sciences, Shibaura Institute of Technology
| | - Minae Hashimoto
- Molecular Cell Biology Laboratory, Department of Systems Engineering and Science, Graduate School of Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Yugo Kato
- Molecular Cell Biology Laboratory, Department of Systems Engineering and Science, Graduate School of Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Naoki Yoshida
- Molecular Cell Biology Laboratory, Department of Systems Engineering and Science, Graduate School of Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Kaho Mochizuki
- Molecular Cell Biology Laboratory, Department of Systems Engineering and Science, Graduate School of Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan
| | - Hiroki Tsumoto
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakaecho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Yuri Miura
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakaecho, Itabashi-ku, Tokyo 173-0015, Japan
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18
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Begcevic I, Brinc D, Dukic L, Simundic AM, Zavoreo I, Basic Kes V, Martinez-Morillo E, Batruch I, Drabovich AP, Diamandis EP. Targeted Mass Spectrometry-Based Assays for Relative Quantification of 30 Brain-Related Proteins and Their Clinical Applications. J Proteome Res 2018; 17:2282-2292. [PMID: 29708756 DOI: 10.1021/acs.jproteome.7b00768] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cerebrospinal fluid (CSF) is a promising clinical sample for identification of novel biomarkers for various neurological disorders. Considering its direct contact with brain tissue, CSF represents a valuable source of brain-related and brain-specific proteins. Multiple sclerosis is an inflammatory, demyelinating neurological disease affecting the central nervous system, and so far there are no diagnostic or prognostic disease specific biomarkers available in the clinic. The primary aim of the present study was to develop a targeted mass spectrometry assay for simultaneous quantification of 30 brain-related proteins in CSF and subsequently to demonstrate assay feasibility in neurological samples derived from multiple sclerosis patients. Our multiplex selected reaction monitoring assay had wide dynamic range (median fold range across peptides = 8.16 × 103) and high assay reproducibility (median across peptides CV = 4%). Candidate biomarkers were quantified in CSF samples from neurologically healthy individuals (n = 9) and patients diagnosed with clinically isolated syndrome (n = 29) or early multiple sclerosis (n = 15).
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Affiliation(s)
- Ilijana Begcevic
- Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario M5S 1A8 , Canada.,Department of Pathology & Laboratory Medicine , Mount Sinai Hospital , Toronto , Ontario M5T 3L9 , Canada
| | - Davor Brinc
- Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario M5S 1A8 , Canada.,Department of Pathology & Laboratory Medicine , Mount Sinai Hospital , Toronto , Ontario M5T 3L9 , Canada.,Department of Clinical Biochemistry , University Health Network , Toronto , Ontario M5G 2C4 , Canada
| | - Lora Dukic
- Department of Medical Laboratory Diagnostics , University Hospital "Sveti Duh" , 10000 Zagreb , Croatia
| | - Ana-Maria Simundic
- Department of Medical Laboratory Diagnostics , University Hospital "Sveti Duh" , 10000 Zagreb , Croatia
| | - Iris Zavoreo
- University Department of Neurology , Medical School University Hospital "Sestre milosrdnice" , 10000 Zagreb , Croatia
| | - Vanja Basic Kes
- University Department of Neurology , Medical School University Hospital "Sestre milosrdnice" , 10000 Zagreb , Croatia
| | - Eduardo Martinez-Morillo
- Laboratory of Medicine, Department of Clinical Biochemistry , Hospital Universitario Central de Asturias , 33011 Oviedo , Spain
| | - Ihor Batruch
- Department of Pathology & Laboratory Medicine , Mount Sinai Hospital , Toronto , Ontario M5T 3L9 , Canada
| | - Andrei P Drabovich
- Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario M5S 1A8 , Canada.,Department of Clinical Biochemistry , University Health Network , Toronto , Ontario M5G 2C4 , Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario M5S 1A8 , Canada.,Department of Pathology & Laboratory Medicine , Mount Sinai Hospital , Toronto , Ontario M5T 3L9 , Canada.,Department of Clinical Biochemistry , University Health Network , Toronto , Ontario M5G 2C4 , Canada
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19
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Forthun RB, Aasebø E, Rasinger JD, Bedringaas SL, Berven F, Selheim F, Bruserud Ø, Gjertsen BT. Phosphoprotein DIGE profiles reflect blast differentiation, cytogenetic risk stratification, FLT3/NPM1 mutations and therapy response in acute myeloid leukaemia. J Proteomics 2017; 173:32-41. [PMID: 29175091 DOI: 10.1016/j.jprot.2017.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 09/30/2017] [Accepted: 11/18/2017] [Indexed: 12/12/2022]
Abstract
Acute myeloid leukaemia (AML) is an aggressive blood cancer characterized by a distinct block in differentiation of myeloid progenitors, recurrent chromosomal translocations and gene mutations of which >50% involve signal transduction through dysregulated kinases and phosphatases. In search for novel protein biomarkers for disease stratification we investigated the phosphoproteome in leukaemic cells from 62 AML patients at time of diagnosis using immobilized metal-affinity chromatography, protein separation by two-dimensional differential gel electrophoresis (2D-DIGE) and mass spectrometry before validation by selected reaction monitoring (SRM). Unsupervised clustering found 27 phosphoproteins significantly discriminating patients according to leukaemic cell differentiation (French-American-British (FAB) classification), cytogenetic and mutational (FLT3, NPM1) status or response to chemotherapy. Monocytic differentiation (FAB M4-M5) correlated with enrichment of proteins involved in apoptosis (MOES, ANXA5 and EFHD2). TALDO, a protein associated with thrombocytopenia if down-regulated, was elevated in patients with wild type NPM1 compared to patients with NPM1 mutation. This study demonstrates the potential of quantitative proteomics in AML classification and risk stratification. BIOLOGICAL SIGNIFICANCE Patients diagnosed with AML are currently categorized according to cellular morphology, cytogenetic alterations and mutations, although the majority of these cellular and genetic alterations have no or unsolved impact on therapy selection or prognosis. We therefore explored the phosphoproteome for abundance changes associated with traditional classifiers to unravel patterns that could stratify patients at the protein level. MOES, ANXA5 and EFHD2 were confirmed by SRM to be correlated to monocytic differentiation, whilst TALDO was elevated in NPM1 wild type patients.
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Affiliation(s)
- Rakel Brendsdal Forthun
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Elise Aasebø
- Department of Biomedicine, Proteomic Unit, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway; Department of Clinical Science, Leukemia Research Group, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | | | - Siv Lise Bedringaas
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Frode Berven
- Department of Biomedicine, Proteomic Unit, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Frode Selheim
- Department of Biomedicine, Proteomic Unit, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Øystein Bruserud
- Department of Clinical Science, Leukemia Research Group, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway; Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway
| | - Bjørn Tore Gjertsen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway; Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway.
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20
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Chitrala KN, Guan H, Singh NP, Busbee B, Gandy A, Mehrpouya-Bahrami P, Ganewatta MS, Tang C, Chatterjee S, Nagarkatti P, Nagarkatti M. CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice. Eur J Immunol 2017; 47:1188-1199. [PMID: 28543188 DOI: 10.1002/eji.201646792] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 03/17/2017] [Accepted: 05/10/2017] [Indexed: 02/06/2023]
Abstract
Dysbiosis in gut microbiome has been shown to be associated with inflammatory and autoimmune diseases. Previous studies from our laboratory demonstrated the pivotal role played by CD44 in the regulation of EAE, a murine model of multiple sclerosis. In the current study, we determined whether these effects resulted from an alteration in gut microbiota and the short-chain fatty acid (SCFA) production in CD44 knockout (CD44KO) mice. Fecal transfer from naïve CD44KO but not C57BL/6 wild type (CD44WT) mice, into EAE-induced CD44WT mice, led to significant amelioration of EAE. High-throughput bacterial 16S rRNA gene sequencing, followed by clustering sequences into operational taxonomic units (OTUs) and biochemical analysis, revealed that EAE-induced CD44KO mice showed significant diversity, richness, and evenness when compared to EAE-induced CD44WT mice at the phylum level, with dominant Bacteroidetes (68.5%) and low Firmicutes (26.8%). Further, data showed a significant change in the abundance of SCFAs, propionic acid, and i-butyric acid in EAE-CD44KO compared to EAE-CD44WT mice. In conclusion, our results demonstrate that the attenuation of EAE seen following CD44 gene deletion in mice may result from alterations in the gut microbiota and SCFAs. Furthermore, our studies also demonstrate that the phenotype of gene knock-out animals may be shaped by gut microbiota.
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Affiliation(s)
| | - Hongbing Guan
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, Columbia, SC, USA.,Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, China
| | - Narendra P Singh
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, Columbia, SC, USA
| | - Brandon Busbee
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, Columbia, SC, USA
| | - Alexa Gandy
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, Columbia, SC, USA
| | - Pegah Mehrpouya-Bahrami
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, Columbia, SC, USA
| | - Mitra S Ganewatta
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Chuanbing Tang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Saurabh Chatterjee
- Department of Environmental Health Sciences, University of South Carolina, Columbia, SC, USA
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, Columbia, SC, USA
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology, and Immunology, University of South Carolina, Columbia, SC, USA.,WJB Dorn VA Medical Center, Columbia, SC, USA
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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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23
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Aslam B, Basit M, Nisar MA, Khurshid M, Rasool MH. Proteomics: Technologies and Their Applications. J Chromatogr Sci 2016; 55:182-196. [PMID: 28087761 DOI: 10.1093/chromsci/bmw167] [Citation(s) in RCA: 457] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 07/25/2016] [Accepted: 09/08/2016] [Indexed: 12/12/2022]
Abstract
Proteomics involves the applications of technologies for the identification and quantification of overall proteins present content of a cell, tissue or an organism. It supplements the other "omics" technologies such as genomic and transcriptomics to expound the identity of proteins of an organism, and to cognize the structure and functions of a particular protein. Proteomics-based technologies are utilized in various capacities for different research settings such as detection of various diagnostic markers, candidates for vaccine production, understanding pathogenicity mechanisms, alteration of expression patterns in response to different signals and interpretation of functional protein pathways in different diseases. Proteomics is practically intricate because it includes the analysis and categorization of overall protein signatures of a genome. Mass spectrometry with LC-MS-MS and MALDI-TOF/TOF being widely used equipment is the central among current proteomics. However, utilization of proteomics facilities including the software for equipment, databases and the requirement of skilled personnel substantially increase the costs, therefore limit their wider use especially in the developing world. Furthermore, the proteome is highly dynamic because of complex regulatory systems that control the expression levels of proteins. This review efforts to describe the various proteomics approaches, the recent developments and their application in research and analysis.
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Affiliation(s)
- Bilal Aslam
- Department of Microbiology, Government College University, Faisalabad, Pakistan
| | - Madiha Basit
- Department of Microbiology, Government College University, Faisalabad, Pakistan
| | - Muhammad Atif Nisar
- Department of Microbiology, Government College University, Faisalabad, Pakistan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University, Faisalabad, Pakistan .,College of Allied Health Professionals, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan
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24
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25
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Gebregiworgis T, Nielsen HH, Massilamany C, Gangaplara A, Reddy J, Illes Z, Powers R. A Urinary Metabolic Signature for Multiple Sclerosis and Neuromyelitis Optica. J Proteome Res 2016; 15:659-66. [PMID: 26759122 DOI: 10.1021/acs.jproteome.5b01111] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Urine is a metabolite-rich biofluid that reflects the body's effort to maintain chemical and osmotic homeostasis. Clinical diagnosis routinely relies on urine samples because the collection process is easy and noninvasive. Despite these advantages, urine is an under-investigated source of biomarkers for multiple sclerosis (MS). Nuclear magnetic resonance spectroscopy (NMR) has become a common approach for analyzing urinary metabolites for disease diagnosis and biomarker discovery. For illustration of the potential of urinary metabolites for diagnosing and treating MS patients, and for differentiating between MS and other illnesses, 38 urine samples were collected from healthy controls, MS patients, and neuromyelitis optica-spectrum disorder (NMO-SD) patients and analyzed with NMR, multivariate statistics, one-way ANOVA, and univariate statistics. Urine from MS patients exhibited a statistically distinct metabolic signature from healthy and NMO-SD controls. A total of 27 metabolites were differentially altered in the urine from MS and NMO-SD patients and were associated with synthesis and degradation of ketone bodies, amino acids, propionate and pyruvate metabolism, tricarboxylic acid cycle, and glycolysis. Metabolites altered in urine from MS patients were shown to be related to known pathogenic processes relevant to MS, including alterations in energy and fatty acid metabolism, mitochondrial activity, and the gut microbiota.
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Affiliation(s)
- Teklab Gebregiworgis
- Department of Chemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0304, United States
| | - Helle H Nielsen
- Department of Neurology, Odense University Hospital, Institute of Clinical Research, University of Southern Denmark , Odense, Denmark
| | - Chandirasegaran Massilamany
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, Nebraska 68583-0905, United States
| | - Arunakumar Gangaplara
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, Nebraska 68583-0905, United States
| | - Jay Reddy
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln , Lincoln, Nebraska 68583-0905, United States
| | - Zsolt Illes
- Department of Neurology, Odense University Hospital, Institute of Clinical Research, University of Southern Denmark , Odense, Denmark
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588-0304, United States
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26
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Martins-de-Souza D, Farias AS. Deciphering the biochemistry and identifying biomarkers to multiple sclerosis. Proteomics 2015; 15:3281-2. [PMID: 26314682 DOI: 10.1002/pmic.201500332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 08/20/2015] [Accepted: 08/24/2015] [Indexed: 11/10/2022]
Abstract
Multiple sclerosis is an idiopathic demyelinating disease of the CNS. Despite being extensively studied during the last decades, many molecular aspects of the disease are still to be elucidated. Moreover, biomarkers for treatment and early diagnosis are major issues to be tackled. In this edition of Kroksveen et al. (Proteomics 2015, 15, 3361-3369) present biomarker candidates for the early detection of multiple sclerosis. Despite the need for validation in larger sets of samples, this dataset contributes to resolve open questions associated to multiple sclerosis.
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Affiliation(s)
- Daniel Martins-de-Souza
- UNICAMP's Neurobiology Center, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.,Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Alessandro S Farias
- UNICAMP's Neurobiology Center, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.,Neuroimmunology Unit, Department of Genetics, Evolution, and Bioagents, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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