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Faizan M, Sachan N, Verma O, Sarkar A, Rawat N, Pratap Singh M. Cerebrospinal fluid protein biomarkers in Parkinson's disease. Clin Chim Acta 2024; 556:117848. [PMID: 38417781 DOI: 10.1016/j.cca.2024.117848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Proteomic profiling is an effective way to identify biomarkers for Parkinson's disease (PD). Cerebrospinal fluid (CSF) has direct connectivity with the brain and could be a source of finding biomarkers and their clinical implications. Comparative proteomic profiling has shown that a group of differentially displayed proteins exist. The studies performed using conventional and classical tools also supported the occurrence of these proteins. Many studies have highlighted the potential of CSF proteomic profiling for biomarker identification and their clinical applications. Some of these proteins are useful for disease diagnosis and prediction. Proteomic profiling of CSF also has immense potential to distinguish PD from similar neurodegenerative disorders. A few protein biomarkers help in fundamental knowledge generation and clinical interpretation. However, the specific biomarker of PD is not yet known. The use of proteomic approaches in clinical settings is also rare. A large-scale, multi-centric, multi-population and multi-continental study using multiple proteomic tools is warranted. Such a study can provide valuable, comprehensive and reliable information for a better understanding of PD and the development of specific biomarkers. The current article sheds light on the role of CSF proteomic profiling in identifying biomarkers of PD and their clinical implications. The article also explains the achievements, obstacles and hopes for future directions of this approach.
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Affiliation(s)
- Mohd Faizan
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Nidhi Sachan
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Oyashvi Verma
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Alika Sarkar
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Neeraj Rawat
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Mahendra Pratap Singh
- Systems Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India; Capacity Building and Knowledge Services, ASSIST Division, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India.
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Harvey J, Pishva E, Chouliaras L, Lunnon K. Elucidating distinct molecular signatures of Lewy body dementias. Neurobiol Dis 2023; 188:106337. [PMID: 37918758 DOI: 10.1016/j.nbd.2023.106337] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/15/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023] Open
Abstract
Dementia with Lewy bodies and Parkinson's disease dementia are common neurodegenerative diseases that share similar neuropathological profiles and spectra of clinical symptoms but are primarily differentiated by the order in which symptoms manifest. The question of whether a distinct molecular pathological profile could distinguish these disorders is yet to be answered. However, in recent years, studies have begun to investigate genomic, epigenomic, transcriptomic and proteomic differences that may differentiate these disorders, providing novel insights in to disease etiology. In this review, we present an overview of the clinical and pathological hallmarks of Lewy body dementias before summarizing relevant research into genetic, epigenetic, transcriptional and protein signatures in these diseases, with a particular interest in those resolving "omic" level changes. We conclude by suggesting future research directions to address current gaps and questions present within the field.
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Affiliation(s)
- Joshua Harvey
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, the Netherlands
| | - Leonidas Chouliaras
- Department of Psychiatry, School of Clinical Medicine, University of Cambridge, Cambridge, UK; Specialist Dementia and Frailty Service, Essex Partnership University NHS Foundation Trust, Epping, UK
| | - Katie Lunnon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
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3
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Naskar A, Stezin A, Dharmappa A, Hegde S, Philip M, Kamble N, Saini J, Sandhya K, Tatu U, Yadav R, Pal PK, Alladi PA. Fibrinogen and Complement Factor H Are Promising CSF Protein Biomarkers for Parkinson's Disease with Cognitive Impairment─A Proteomics-ELISA-Based Study. ACS Chem Neurosci 2022; 13:1030-1045. [PMID: 35200010 DOI: 10.1021/acschemneuro.2c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Parkinson's disease (PD) with cognitive impairment (PDCI) is essentially diagnosed through clinical and neuropsychological examinations. There is a need to identify biomarkers to foresee cognitive decline in them. We performed label-free unbiased nontargeted proteomics (Q-TOF LC/MS-MS) on the CSF of non-neurological control; PDCI; PD; and normal pressure hydrocephalus (NPH) patients, followed by targeted ELISA for validation. Of the 281 proteins identified, 42 were differentially altered in PD, PDCI, and NPH. With a certain overlap, 28 proteins were altered in PDCI and 25 proteins were altered in NPH. Five significantly upregulated proteins in PDCI were fibrinogen, gelsolin, complement factor-H, and apolipoproteins A-I and A-IV, whereas carnosine dipeptidase-1, carboxypeptidase-E, dickkopf-3, and secretogranin-3 precursor proteins were downregulated. Those uniquely altered in NPH were the insulin-like growth factor-binding protein, ceruloplasmin, α-1 antitrypsin, VGF nerve growth factor, and neural cell adhesion molecule L1-like protein. The ELISA-derived protein concentrations correlated with neuropsychological scores of certain cognitive domains. In PDCI, the Wisconsin card sorting percentile correlated negatively with fibrinogen. Intraperitoneal injection of native fibrinogen caused motor deficits in C57BL/6J mice as assessed by the pole test. Thus, a battery of proteins such as fibrinogen-α-chain, CFAH, and APOA-I/APOA-IV alongside neuropsychological assessment could be reliable biomarkers to distinguish PDCI and NPH.
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Affiliation(s)
- Aditi Naskar
- Department of Clinical Psychopharmacology & Neurotoxicology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Albert Stezin
- Department of Clinical Neurosciences, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Arpitha Dharmappa
- Department of Clinical Psychology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Shantala Hegde
- Department of Clinical Psychology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Mariamma Philip
- Department of Biostatistics, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Nitish Kamble
- Department of Neurology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Jitender Saini
- Department of Neuroimaging & Interventional Radiology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - K. Sandhya
- Department of Anaesthesiology, Bangalore Medical College and Research Institute, Bengaluru 560002, India
| | - Utpal Tatu
- Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Ravi Yadav
- Department of Neurology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
| | - Phalguni Anand Alladi
- Department of Clinical Psychopharmacology & Neurotoxicology, National Institute of Mental Health and Neuro Sciences, Bengaluru 560029, India
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Berdowska I, Matusiewicz M, Krzystek-Korpacka M. HDL Accessory Proteins in Parkinson’s Disease—Focusing on Clusterin (Apolipoprotein J) in Regard to Its Involvement in Pathology and Diagnostics—A Review. Antioxidants (Basel) 2022; 11:antiox11030524. [PMID: 35326174 PMCID: PMC8944556 DOI: 10.3390/antiox11030524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
Parkinson’s disease (PD)—a neurodegenerative disorder (NDD) characterized by progressive destruction of dopaminergic neurons within the substantia nigra of the brain—is associated with the formation of Lewy bodies containing mainly α-synuclein. HDL-related proteins such as paraoxonase 1 and apolipoproteins A1, E, D, and J are implicated in NDDs, including PD. Apolipoprotein J (ApoJ, clusterin) is a ubiquitous, multifunctional protein; besides its engagement in lipid transport, it modulates a variety of other processes such as immune system functionality and cellular death signaling. Furthermore, being an extracellular chaperone, ApoJ interacts with proteins associated with NDD pathogenesis (amyloid β, tau, and α-synuclein), thus modulating their properties. In this review, the association of clusterin with PD is delineated, with respect to its putative involvement in the pathological mechanism and its application in PD prognosis/diagnosis.
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Affiliation(s)
- Izabela Berdowska
- Correspondence: (I.B.); (M.M.); Tel.: +48-71-784-13-92 (I.B.); +48-71-784-13-70 (M.M.)
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Kwon DH, Hwang JS, Kim SG, Jang YE, Shin TH, Lee G. Cerebrospinal Fluid Metabolome in Parkinson's Disease and Multiple System Atrophy. Int J Mol Sci 2022; 23:ijms23031879. [PMID: 35163800 PMCID: PMC8836409 DOI: 10.3390/ijms23031879] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 11/16/2022] Open
Abstract
Parkinson’s disease (PD) and multiple system atrophy (MSA) belong to the neurodegenerative group of synucleinopathies; differential diagnosis between PD and MSA is difficult, especially at early stages, owing to their clinical and biological similarities. Thus, there is a pressing need to identify metabolic biomarkers for these diseases. The metabolic profile of the cerebrospinal fluid (CSF) is reported to be altered in PD and MSA; however, the altered metabolites remain unclear. We created a single network with altered metabolites in PD and MSA based on the literature and assessed biological functions, including metabolic disorders of the nervous system, inflammation, concentration of ATP, and neurological disorder, through bioinformatics methods. Our in-silico prediction-based metabolic networks are consistent with Parkinsonism events. Although metabolomics approaches provide a more quantitative understanding of biochemical events underlying the symptoms of PD and MSA, limitations persist in covering molecules related to neurodegenerative disease pathways. Thus, omics data, such as proteomics and microRNA, help understand the altered metabolomes mechanism. In particular, integrated omics and machine learning approaches will be helpful to elucidate the pathological mechanisms of PD and MSA. This review discusses the altered metabolites between PD and MSA in the CSF and omics approaches to discover diagnostic biomarkers.
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Affiliation(s)
- Do Hyeon Kwon
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Ji Su Hwang
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Seok Gi Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Yong Eun Jang
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Tae Hwan Shin
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Korea
- Correspondence: (T.H.S.); (G.L.)
| | - Gwang Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Korea
- Correspondence: (T.H.S.); (G.L.)
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Hu L, Dong MX, Huang YL, Lu CQ, Qian Q, Zhang CC, Xu XM, Liu Y, Chen GH, Wei YD. Integrated Metabolomics and Proteomics Analysis Reveals Plasma Lipid Metabolic Disturbance in Patients With Parkinson's Disease. Front Mol Neurosci 2020; 13:80. [PMID: 32714143 PMCID: PMC7344253 DOI: 10.3389/fnmol.2020.00080] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/23/2020] [Indexed: 12/12/2022] Open
Abstract
Parkinson’s disease (PD) is a common neurodegenerative disease in the elderly with a pathogenesis that remains unclear. We aimed to explore its pathogenesis through plasma integrated metabolomics and proteomics analysis. The clinical data of consecutively recruited PD patients and healthy controls were assessed. Fasting plasma samples were obtained and analyzed using metabolomics and proteomics methods. After that, differentially expressed metabolites and proteins were identified for further bioinformatics analysis. No significant difference was found in the clinical data between these two groups. Eighty-three metabolites were differentially expressed in PD patients identified by metabolomics analysis. These metabolites were predominately lipid and lipid-like molecules (63%), among which 25% were sphingolipids. The sphingolipid metabolism pathway was enriched and tended to be activated in the following KEGG pathway analysis. According to the proteomics analysis, forty proteins were identified to be differentially expressed, seven of which were apolipoproteins. Furthermore, five of the six top ranking Gene Ontology terms from cellular components and eleven of the other fourteen Gene Ontology terms from biological processes were directly associated with lipid metabolism. In KEGG pathway analysis, the five enriched pathways were also significantly related with lipid metabolism (p < 0.05). Overall, Parkinson’s disease is associated with plasma lipid metabolic disturbance, including an activated sphingolipid metabolism and decreased apolipoproteins.
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Affiliation(s)
- Ling Hu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Neurology, Renmin Hospital of Wuhan University, Hubei General Hospital, Wuhan, China
| | - Mei-Xue Dong
- Department of Neurology, Renmin Hospital of Wuhan University, Hubei General Hospital, Wuhan, China
| | - Yan-Ling Huang
- Department of Neurology, Chongqing University Central Hospital, Chongqing Emergency Medical Center, Chongqing, China
| | - Chang-Qi Lu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qian Qian
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chun-Cheng Zhang
- Department of Neurology, The People's Hospital of Tongliang District, Chongqing, China
| | - Xiao-Min Xu
- Department of Neurology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yang Liu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guang-Hui Chen
- Department of Neurology, Renmin Hospital of Wuhan University, Hubei General Hospital, Wuhan, China
| | - You-Dong Wei
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Liu YX, Zhou JN, Liu KH, Fu XP, Zhang ZW, Zhang QH, Yue W. CIRP regulates BEV-induced cell migration in gliomas. Cancer Manag Res 2019; 11:2015-2025. [PMID: 30881126 PMCID: PMC6417006 DOI: 10.2147/cmar.s191249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Purpose A better understanding of the underlying molecular mechanisms in treatment failure of bevacizumab (BEV) for malignant glioma would contribute to overcome therapeutic resistance. Methods Here, we used a quantitative proteomic method to identify molecular signatures of glioblastoma cell after BEV treatment by two-dimensional liquid chromatography-tandem mass spectrometry analysis and 6-plex iTRAQ quantification. Next, the function of cold-inducible RNA-binding protein (CIRP), one of the most significantly affected proteins by drug treatment, was evaluated in drug resistance of glioma cells by invasion assays and animal xenograft assays. Target molecules bound by CIRP were determined using RNA-binding protein immunoprecipitation and microarray analysis. Then, these mRNAs were identified by quantitative real-time PCR. Results Eighty-seven proteins were identified with significant fold changes. The biological functional analysis indicated that most of the proteins were involved in the process of cellular signal transduction, cell adhesion, and protein transport. The expression of CIRP greatly decreased after BEV treatment, and ectopic expression of CIRP abolished cell migration in BEV-treated glioma cells. In addition, CIRP could bind mRNA of CXCL12 and inhibit BEV-induced increase of CXCL12 in glioma cells. Conclusion These data suggested that CIRP may take part in BEV-induced migration of gliomas by binding of migration-relative RNAs.
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Affiliation(s)
- Yu-Xiao Liu
- Department of Neurosurgery, The Fourth Medical Centre of Chinese PLA General Hospital, Beijing 100048, China,
| | - Jun-Nian Zhou
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, Beijing 100850, China, .,Experimental Hematology and Biochemistry Lab, Beijing Institute of Radiation Medicine, Beijing 100850, China.,South China Research Center for Stem Cell & Regenerative Medicine, SCIB, Guangzhou 510005, China
| | - Ke-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiang-Pin Fu
- Department of Neurosurgery, The Fourth Medical Centre of Chinese PLA General Hospital, Beijing 100048, China,
| | - Zhi-Wen Zhang
- Department of Neurosurgery, The Fourth Medical Centre of Chinese PLA General Hospital, Beijing 100048, China,
| | - Qin-Hong Zhang
- Department of Neurosurgery, The Fourth Medical Centre of Chinese PLA General Hospital, Beijing 100048, China,
| | - Wen Yue
- Stem Cell and Regenerative Medicine Lab, Institute of Health Service and Transfusion Medicine, Beijing 100850, China,
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Spodzieja M, Rodziewicz-Motowidło S, Szymanska A. Hyphenated Mass Spectrometry Techniques in the Diagnosis of Amyloidosis. Curr Med Chem 2019; 26:104-120. [DOI: 10.2174/0929867324666171003113019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 07/25/2016] [Accepted: 09/01/2016] [Indexed: 12/18/2022]
Abstract
Amyloidoses are a group of diseases caused by the extracellular deposition of proteins forming amyloid fibrils. The amyloidosis is classified according to the main protein or peptide that constitutes the amyloid fibrils. The most effective methods for the diagnosis of amyloidosis are based on mass spectrometry. Mass spectrometry enables confirmation of the identity of the protein precursor of amyloid fibrils in biological samples with very high sensitivity and specificity, which is crucial for proper amyloid typing. Due to the fact that biological samples are very complex, mass spectrometry is usually connected with techniques such as liquid chromatography or capillary electrophoresis, which enable the separation of proteins before MS analysis. Therefore mass spectrometry constitutes an important part of the so called “hyphenated techniques” combining, preferentially in-line, different analytical methods to provide comprehensive information about the studied problem. Hyphenated methods are very useful in the discovery of biomarkers in different types of amyloidosis. In systemic forms of amyloidosis, the analysis of aggregated proteins is usually performed based on the tissues obtained during a biopsy of an affected organ or a subcutaneous adipose tissue. In some cases, when the diagnostic biopsy is not possible due to the fact that amyloid fibrils are formed in organs like the brain (Alzheimer’s disease), the study of biomarkers presented in body fluids can be carried out. Currently, large-scale studies are performed to find and validate more effective biomarkers, which can be used in diagnostic procedures. We would like to present the methods connected with mass spectrometry which are used in the diagnosis of amyloidosis based on the analysis of proteins occurring in tissues, blood and cerebrospinal fluid.
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Affiliation(s)
- Marta Spodzieja
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sylwia Rodziewicz-Motowidło
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Aneta Szymanska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
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9
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Cilento EM, Jin L, Stewart T, Shi M, Sheng L, Zhang J. Mass spectrometry: A platform for biomarker discovery and validation for Alzheimer's and Parkinson's diseases. J Neurochem 2019; 151:397-416. [PMID: 30474862 DOI: 10.1111/jnc.14635] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/15/2018] [Accepted: 11/19/2018] [Indexed: 12/16/2022]
Abstract
Accurate, reliable, and objective biomarkers for Alzheimer's disease (AD), Parkinson's disease (PD), and related age-associated neurodegenerative disorders are urgently needed to assist in both diagnosis, particularly at early stages, and monitoring of disease progression. Technological advancements in protein detection platforms over the last few decades have resulted in a plethora of reported molecular biomarker candidates for both AD and PD; however, very few of these candidates are developed beyond the discovery phase of the biomarker development pipeline, a reflection of the current bottleneck within the field. In this review, the expanded use of selected reaction monitoring (SRM) targeted mass spectrometry will be discussed in detail as a platform for systematic verification of large panels of protein biomarker candidates prior to costly validation testing. We also advocate for the coupling of discovery-based proteomics with modern targeted MS-based approaches (e.g., SRM) within a single study in future workflows to expedite biomarker development and validation for AD and PD. It is our hope that improving the efficiency within the biomarker development process by use of an SRM pipeline may ultimately hasten the development of biomarkers that both decrease misdiagnosis of AD and PD and ultimately lead to detection at early stages of disease and objective assessment of disease progression. This article is part of the special issue "Proteomics".
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Affiliation(s)
- Eugene M Cilento
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Lorrain Jin
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Tessandra Stewart
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Min Shi
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Lifu Sheng
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Jing Zhang
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA.,Department of Pathology, School of Basic Medicine, Peking University Health Science Center, Peking University Third Hospital and Peking Key Laboratory for Early Diagnosis of Neurodegenerative Disorders, Beijing, China
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Lachén-Montes M, González-Morales A, Fernández-Irigoyen J, Santamaría E. Deployment of Label-Free Quantitative Olfactory Proteomics to Detect Cerebrospinal Fluid Biomarker Candidates in Synucleinopathies. Methods Mol Biol 2019; 2044:273-289. [PMID: 31432419 DOI: 10.1007/978-1-4939-9706-0_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nowadays, diagnosis of neurodegenerative disorders is mainly based on neuroimaging and clinical symptoms, although postmortem neuropathological confirmation remains the gold standard diagnostic technique. Therefore, cerebrospinal fluid (CSF) proteome is considered a valuable molecular repository for diagnosing and targeting the neurodegenerative process. It is well known that olfactory dysfunction is among the earliest features of synucleinopathies such as Parkinson's disease (PD). Consequently, we consider that the application of tissue proteomics in primary olfactory structures is an ideal approach to explore early pathophysiological changes, detecting olfactory proteins that might be tested in CSF as potential biomarkers. Data mining of mass spectrometry-generated datasets has revealed that 30% of the olfactory bulb (OB) proteome is also localized in CSF. In this chapter, we describe a method that utilizes label-free quantitative proteomics and computational analysis to characterize human OB proteomes and potential cerebrospinal fluid (CSF) biomarkers associated with neurodegenerative syndromes. For that, we applied peptide fractionation methods, followed by tandem mass spectrometry (nanoLC-MS/MS), in silico analysis, and semi-quantitative orthogonal techniques in OB derived from PD subjects. After obtaining the differential OB proteome across Lewy-type alpha-synucleinopathy (LTS) stages and further validating the method, this workflow was applied to probe changes in NEGR1 (neuronal growth regulator 1) and GNPDA2 (glucosamine-6-phosphate deaminase 2) protein levels in CSF derived from parkinsonian subjects with respect to controls, observing an inverse correlation between both proteins and α-synuclein, the principal component analysis of Lewy pathology.
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Affiliation(s)
- Mercedes Lachén-Montes
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Andrea González-Morales
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Enrique Santamaría
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain.
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Lachén-Montes M, González-Morales A, Fernández-Irigoyen J, Santamaría E. Determination of Cerebrospinal Fluid Proteome Variations by Isobaric Labeling Coupled with Strong Cation-Exchange Chromatography and Tandem Mass Spectrometry. Methods Mol Biol 2019; 2044:155-168. [PMID: 31432412 DOI: 10.1007/978-1-4939-9706-0_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cerebrospinal fluid (CSF) is in direct contact with the brain and represents a valuable source of mediators that reflect metabolic processes occurring in the central nervous system (CNS). In this sense, mass spectrometry (MS) methods have proven to be sensitive in quantifying the proteomic profiles of CSF, therefore being able to detect biomarker candidates for neurological disorders. In particular, a key development has been the use of multiplexing technologies to easily identify and quantify complex protein mixtures. This chapter describes a workflow suitable for the analysis of CSF proteome using isobaric labeling coupled to strong cation-exchange chromatography fractionation for its potential use as a biomarker discovery platform. In this case, the isobaric tags for relative and absolute quantitation (iTRAQ) label all proteins in a sample via free amines at the N-terminus and on the side chain of lysine residues. Then, the labeled samples are pooled and chromatographically fractionated. These fractions with the pooled samples are afterward analyzed by tandem mass spectrometry (MS/MS), and proteins are quantified by the relative intensities of the reporter ions in the MS/MS spectra, simultaneously obtaining the amino acid sequence. This method complements the neuroproteomic toolbox to identify new protein biomarkers not only for the early clinical diagnosis and disease staging of CNS-related disorders but also to elucidate the molecular mechanisms related to the pathophysiology of these symptoms.
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Affiliation(s)
- Mercedes Lachén-Montes
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Andrea González-Morales
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Enrique Santamaría
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain.
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12
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Unveiling the olfactory proteostatic disarrangement in Parkinson's disease by proteome-wide profiling. Neurobiol Aging 2018; 73:123-134. [PMID: 30342273 DOI: 10.1016/j.neurobiolaging.2018.09.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 09/03/2018] [Accepted: 09/14/2018] [Indexed: 01/07/2023]
Abstract
Olfactory dysfunction is one of the earliest features in Lewy-type alpha-synucleinopathies (LTSs) such as Parkinson's disease (PD). However, the underlying molecular mechanisms associated to smell impairment are poorly understood. Applying mass spectrometry-based quantitative proteomics in postmortem olfactory bulbs across limbic, early-neocortical, and neocortical LTS stages of parkinsonian patients, a proteostasis impairment, was observed, identifying 268 differentially expressed proteins between controls and PD phenotypes. In addition, network-driven proteomics revealed a modulation in ERK1/2, MKK3/6, and PDK1/PKC signaling axes. Moreover, a cross-disease study of selected olfactory molecules in sporadic Alzheimer's disease (AD) cases revealed different protein derangements in the modulation of secretagogin (SCGN), calcyclin-binding protein (CACYBP), and glucosamine 6 phosphate isomerase 2 (GNPDA2) between PD and AD. An inverse correlation between GNPDA2 and α-synuclein protein levels was also reflected in PD cerebrospinal fluid. Interestingly, PD patients exhibited significantly lower serum GNPDA2 levels than controls (n = 82/group). Our study provides important avenues for understanding the olfactory bulb proteostasis imbalance in PD, deciphering mechanistic clues to the equivalent smell deficits observed in AD and PD pathologies.
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13
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Oeckl P, Steinacker P, Otto M. Comparison of Internal Standard Approaches for SRM Analysis of Alpha-Synuclein in Cerebrospinal Fluid. J Proteome Res 2017; 17:516-523. [PMID: 29183121 DOI: 10.1021/acs.jproteome.7b00660] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Absolute protein quantification by selected reaction monitoring (SRM, also MRM) is an alternative to immunoassays, and the gold standard here is the addition of stable-isotope labeled (SIL) proteins (PSAQ). Cerebrospinal fluid (CSF) is the preferred source of biomarkers for neurological diseases, and recent improvements in mass spectrometry enable the quantification of disease-relevant proteins in CSF. We used alpha-synuclein SRM to investigate alternatives to the PSAQ approach in human CSF regarding precision and accuracy, including SIL peptides, winged SIL (WiSIL) peptides, and quantitative protein epitope signature tags (QPrESTs). All approaches yielded precise results in CSF with CV values <15% in several runs for all four measured peptides. PSAQ and QPrEST also showed good accuracy (deviation ≤15%), whereas SIL and WiSIL peptides yielded deviations up to 54% that greatly depended on the measured peptide. Total protein concentration in CSF did not affect precision and accuracy. Thus, our study indicates that all four approaches are suitable for relative quantification of alpha-synuclein in CSF. QPrESTs are a valuable alternative to PSAQ in terms of precision and accuracy, although SIL and WiSIL peptides can yield accurate results as well when peptides are selected consciously.
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Affiliation(s)
- Patrick Oeckl
- Department of Neurology, Ulm University Hospital , D-89081 Ulm, Germany
| | - Petra Steinacker
- Department of Neurology, Ulm University Hospital , D-89081 Ulm, Germany
| | - Markus Otto
- Department of Neurology, Ulm University Hospital , D-89081 Ulm, Germany
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14
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Datta A, Chai YL, Tan JM, Lee JH, Francis PT, Chen CP, Sze SK, Lai MKP. An iTRAQ-based proteomic analysis reveals dysregulation of neocortical synaptopodin in Lewy body dementias. Mol Brain 2017; 10:36. [PMID: 28800743 PMCID: PMC5553757 DOI: 10.1186/s13041-017-0316-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/21/2017] [Indexed: 02/08/2023] Open
Abstract
Lewy body dementias are the second most common cause of neurodegenerative dementia in the elderly after Alzheimer's disease (AD). The two clinical subgroups of Lewy body dementias, namely, dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD), are differentiated by the chronology of cognitive symptoms relative to parkinsonism. At present, there remains a debate on whether DLB and PDD are separate disease entities, or fall within the same spectrum of Lewy body dementias. In this study, we compared the detergent-soluble proteome via an 8-plex isobaric tag for relative and absolute quantitation (iTRAQ) analysis of pooled lysates from the prefrontal cortex (BA9) of DLB (n = 19) and PDD (n = 21) patients matched a priori for amyloid (total Aβ42) burden, semi-quantitative scores for Lewy bodies and neurofibrillary tangles together with age-matched control (n = 21) subjects. A total of 1914 proteins were confidently identified by iTRAQ (false discovery rate = 0%). None of the proteins showed a significant yet opposite regulation in between DLB and PDD when compared to aged controls in the proteomic data set as well as following immunoblot analysis of the pooled and individual lysates involving all 61 subjects. The postsynaptic protein, synaptopodin (SYNPO) was significantly down-regulated in both DLB and PDD subgroups, suggesting a defective synaptic transmission in the demented patients. In conclusion, the largely similar proteome of DLB and PDD matched for amyloid burden suggests that variations in concomitant AD-related pathology, abnormal post-translational modifications or protein-protein interactions, defective intracellular trafficking or misfolding of proteins could play a part in driving the clinically observed differences between these two subgroups of Lewy body dementias. This further indicates that amyloid-targeting therapeutic strategies may show different efficacies in DLB versus PDD.
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Affiliation(s)
- Arnab Datta
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore. .,Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, Building 10 Room 6N318, Bethesda, MD 20814, USA.
| | - Yuek Ling Chai
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore
| | - Jing Min Tan
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore
| | - Jasinda H Lee
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore
| | - Paul T Francis
- Wolfson Centre for Age-related Diseases, King's College London, Guy's Campus, St Thomas Street, London SE1 1UL, UK
| | - Christopher P Chen
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Mitchell K P Lai
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore. .,Wolfson Centre for Age-related Diseases, King's College London, Guy's Campus, St Thomas Street, London SE1 1UL, UK.
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15
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Abstract
INTRODUCTION Parkinson's disease (PD) is an insidious disorder affecting more than 1-2% of the population over the age of 65. Understanding the etiology of PD may create opportunities for developing new treatments. Genomic and transcriptomic studies are useful, but do not provide evidence for the actual status of the disease. Conversely, proteomic studies deal with proteins, which are real time players, and can hence provide information on the dynamic nature of the affected cells. The number of publications relating to the proteomics of PD is vast. Therefore, there is a need to evaluate the current proteomics literature and establish the connections between the past and the present to foresee the future. Areas covered: PubMed and Web of Science were used to retrieve the literature associated with PD proteomics. Studies using human samples, model organisms and cell lines were selected and reviewed to highlight their contributions to PD. Expert commentary: The proteomic studies associated with PD achieved only limited success in facilitating disease diagnosis, monitoring and progression. A global system biology approach using new models is needed. Future research should integrate the findings of proteomics with other omics data to facilitate both early diagnosis and the treatment of PD.
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Affiliation(s)
- Murat Kasap
- a Department of Medical Biology/DEKART Proteomics Laboratory , Kocaeli University Medical School , Kocaeli , Turkey
| | - Gurler Akpinar
- a Department of Medical Biology/DEKART Proteomics Laboratory , Kocaeli University Medical School , Kocaeli , Turkey
| | - Aylin Kanli
- a Department of Medical Biology/DEKART Proteomics Laboratory , Kocaeli University Medical School , Kocaeli , Turkey
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16
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Magdalinou NK, Noyce AJ, Pinto R, Lindstrom E, Holmén-Larsson J, Holtta M, Blennow K, Morris HR, Skillbäck T, Warner TT, Lees AJ, Pike I, Ward M, Zetterberg H, Gobom J. Identification of candidate cerebrospinal fluid biomarkers in parkinsonism using quantitative proteomics. Parkinsonism Relat Disord 2017; 37:65-71. [PMID: 28214264 DOI: 10.1016/j.parkreldis.2017.01.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 01/02/2017] [Accepted: 01/27/2017] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Neurodegenerative parkinsonian syndromes have significant clinical and pathological overlap, making early diagnosis difficult. Cerebrospinal fluid (CSF) biomarkers may aid the differentiation of these disorders, but other than α-synuclein and neurofilament light chain protein, which have limited diagnostic power, specific protein biomarkers remain elusive. OBJECTIVES To study disease mechanisms and identify possible CSF diagnostic biomarkers through discovery proteomics, which discriminate parkinsonian syndromes from healthy controls. METHODS CSF was collected consecutively from 134 participants; Parkinson's disease (n = 26), atypical parkinsonian syndromes (n = 78, including progressive supranuclear palsy (n = 36), multiple system atrophy (n = 28), corticobasal syndrome (n = 14)), and elderly healthy controls (n = 30). Participants were divided into a discovery and a validation set for analysis. The samples were subjected to tryptic digestion, followed by liquid chromatography-mass spectrometry analysis for identification and relative quantification by isobaric labelling. Candidate protein biomarkers were identified based on the relative abundances of the identified tryptic peptides. Their predictive performance was evaluated by analysis of the validation set. RESULTS 79 tryptic peptides, derived from 26 proteins were found to differ significantly between atypical parkinsonism patients and controls. They included acute phase/inflammatory markers and neuronal/synaptic markers, which were respectively increased or decreased in atypical parkinsonism, while their levels in PD subjects were intermediate between controls and atypical parkinsonism. CONCLUSION Using an unbiased proteomic approach, proteins were identified that were able to differentiate atypical parkinsonian syndrome patients from healthy controls. Our study indicates that markers that may reflect neuronal function and/or plasticity, such as the amyloid precursor protein, and inflammatory markers may hold future promise as candidate biomarkers in parkinsonism.
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Affiliation(s)
- N K Magdalinou
- Reta Lila Weston Institute of Neurological Studies, UCL Institute of Neurology, Queen Square, London, UK.
| | - A J Noyce
- Reta Lila Weston Institute of Neurological Studies, UCL Institute of Neurology, Queen Square, London, UK
| | - R Pinto
- Institute of Chemistry University of Umeå, Umeå, Sweden
| | - E Lindstrom
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - J Holmén-Larsson
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - M Holtta
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - K Blennow
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - H R Morris
- Department of Clinical Neuroscience, UCL Institute of Neurology, Royal Free Hospital, London, UK
| | - T Skillbäck
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - T T Warner
- Reta Lila Weston Institute of Neurological Studies, UCL Institute of Neurology, Queen Square, London, UK
| | - A J Lees
- Reta Lila Weston Institute of Neurological Studies, UCL Institute of Neurology, Queen Square, London, UK
| | - I Pike
- Proteome Sciences Plc, London, UK
| | - M Ward
- Proteome Sciences Plc, London, UK
| | - H Zetterberg
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden; Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - J Gobom
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
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17
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Kang UB, Marto JA. Leucine-rich repeat kinase 2 and Parkinson's disease. Proteomics 2016; 17. [PMID: 27723254 DOI: 10.1002/pmic.201600092] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 09/13/2016] [Accepted: 10/06/2016] [Indexed: 12/21/2022]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a large multidomain protein that is expressed in many tissues and participates in numerous biological pathways. Mutations in LRRK2 are recognized as genetic risk factors for familial Parkinson's disease (PD) and may also represent causal factors in the more common sporadic form of PD. The structure of LRRK2 comprises a combination of GTPase, kinase, and scaffolding domains. This functional diversity, combined with a potentially central role in genetic and idiopathic PD motivates significant effort to further credential LRRK2 as a therapeutic target. Here, we review the current understanding for LRRK2 function in normal physiology and PD, with emphasis on insight gained from proteomic approaches.
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Affiliation(s)
- Un-Beom Kang
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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18
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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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19
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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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20
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Delgado-Alvarado M, Gago B, Navalpotro-Gomez I, Jiménez-Urbieta H, Rodriguez-Oroz MC. Biomarkers for dementia and mild cognitive impairment in Parkinson's disease. Mov Disord 2016; 31:861-81. [PMID: 27193487 DOI: 10.1002/mds.26662] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 04/15/2016] [Accepted: 04/18/2016] [Indexed: 12/27/2022] Open
Abstract
Cognitive decline is one of the most frequent and disabling nonmotor features of Parkinson's disease. Around 30% of patients with Parkinson's disease experience mild cognitive impairment, a well-established risk factor for the development of dementia. However, mild cognitive impairment in patients with Parkinson's disease is a heterogeneous entity that involves different types and extents of cognitive deficits. Because it is not currently known which type of mild cognitive impairment confers a higher risk of progression to dementia, it would be useful to define biomarkers that could identify these patients to better study disease progression and possible interventions. In this sense, the identification among patients with Parkinson's disease and mild cognitive impairment of biomarkers associated with dementia would allow the early detection of this process. This review summarizes studies from the past 25 years that have assessed the potential biomarkers of dementia and mild cognitive impairment in Parkinson's disease patients. Despite the potential importance, no biomarker has as yet been validated. However, features such as low levels of epidermal and insulin-like growth factors or uric acid in plasma/serum and of Aß in CSF, reduction of cerebral cholinergic innervation and metabolism measured by PET mainly in posterior areas, and hippocampal atrophy in MRI might be indicative of distinct deficits with a distinct risk of dementia in subgroups of patients. Longitudinal studies combining the existing techniques and new approaches are needed to identify patients at higher risk of dementia. © 2016 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Manuel Delgado-Alvarado
- Biodonostia Health Research Institute, San Sebastián, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Belén Gago
- Biodonostia Health Research Institute, San Sebastián, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Irene Navalpotro-Gomez
- Biodonostia Health Research Institute, San Sebastián, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Haritz Jiménez-Urbieta
- Biodonostia Health Research Institute, San Sebastián, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - María C Rodriguez-Oroz
- Biodonostia Health Research Institute, San Sebastián, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Neurology Department, University Hospital Donostia, San Sebastián, Spain.,Ikerbasque (Basque Foundation for Science), Bilbao, Spain.,Basque Center on Cognition, Brain and Language (BCBL), San Sebastián, Spain.,Physiology Department, Medical School University of Navarra, Pamplona, Spain
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21
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Blennow K, Biscetti L, Eusebi P, Parnetti L. Cerebrospinal fluid biomarkers in Alzheimer's and Parkinson's diseases-From pathophysiology to clinical practice. Mov Disord 2016; 31:836-47. [DOI: 10.1002/mds.26656] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/22/2016] [Accepted: 03/25/2016] [Indexed: 01/05/2023] Open
Affiliation(s)
- Kaj Blennow
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg; Mölndal Campus Mölndal Sweden
| | - Leonardo Biscetti
- Section of Neurology, Department of Medicine, Center for Memory Disturbances, University of Perugia; Sant'Andrea delle Fratte Perugia Italy
| | - Paolo Eusebi
- Section of Neurology, Department of Medicine, Center for Memory Disturbances, University of Perugia; Sant'Andrea delle Fratte Perugia Italy
| | - Lucilla Parnetti
- Section of Neurology, Department of Medicine, Center for Memory Disturbances, University of Perugia; Sant'Andrea delle Fratte Perugia Italy
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22
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Halbgebauer S, Öckl P, Wirth K, Steinacker P, Otto M. Protein biomarkers in Parkinson's disease: Focus on cerebrospinal fluid markers and synaptic proteins. Mov Disord 2016; 31:848-60. [PMID: 27134134 DOI: 10.1002/mds.26635] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/06/2016] [Accepted: 03/09/2016] [Indexed: 01/06/2023] Open
Abstract
Despite extensive research, to date, no validated biomarkers for PD have been found. This review seeks to summarize studies approaching the detection of biomarker candidates for PD and introduce promising ones in more detail, with special attention to synaptic proteins. To this end, we performed a PubMed search and included studies using proteomic tools (2-dimensional difference in gel electrophoresis and/or mass spectrometry) for the comparison of samples from PD and control patients. We found 27 studies reporting more than 500 differentially expressed proteins in which a total of 28 were detected in 2 and 17 in 3 or more independent studies, including posttranslationally modified proteins. In addition, of these 500 proteins, 25 were found to be brain specific, and 14 were enriched in synapses. Special attention was given to the applicability of the biomarker regarding sampling procedures, that is, using CSF/serum material for diagnosis. Furthermore, presynaptic proteins involved in vesicle membrane fusion seem to be interesting candidates for future analyses. Nonetheless, even though such promising biomarker candidates for PD exist, validation of these biomarkers in large-scale clinical studies is necessary to evaluate the diagnostic potential. © 2016 International Parkinson and Movement Disorder Society.
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Affiliation(s)
| | - Patrick Öckl
- Department of Neurology, University of Ulm, Ulm, Germany
| | | | | | - Markus Otto
- Department of Neurology, University of Ulm, Ulm, Germany
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23
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Wu C, Duan J, Liu T, Smith RD, Qian WJ. Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:57-68. [PMID: 26868616 DOI: 10.1016/j.jchromb.2016.01.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 02/07/2023]
Abstract
Human biofluids, especially blood plasma or serum, hold great potential as the sources of candidate biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge for detecting promising low-abundance proteins. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high- and moderate-abundance proteins, thus enabling much more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomic applications in human biofluids. The limitations and future perspectives of immunoaffinity separation methods are also discussed.
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Affiliation(s)
- Chaochao Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jicheng Duan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
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24
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Kwasnik A, Tonry C, Ardle AM, Butt AQ, Inzitari R, Pennington SR. Proteomes, Their Compositions and Their Sources. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:3-21. [DOI: 10.1007/978-3-319-41448-5_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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25
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Galasko D. Expanding the Repertoire of Biomarkers for Alzheimer's Disease: Targeted and Non-targeted Approaches. Front Neurol 2015; 6:256. [PMID: 26733934 PMCID: PMC4680926 DOI: 10.3389/fneur.2015.00256] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/23/2015] [Indexed: 01/12/2023] Open
Abstract
The first biofluid markers developed for Alzheimer’s disease (AD) used targeted approaches for discovery. These initial biomarkers were directed at key protein constituents of the hallmark brain lesions in AD. Biomarkers for plaques targeted the amyloid beta protein (Aβ) and for tangles, the microtubule-associated protein tau. Cerebrospinal fluid levels of Aβ and tau have excellent diagnostic utility and can be used to monitor aspects of therapeutic development. Recent research has extended our current concepts of AD, which now include a slow buildup of pathology during a long pre-symptomatic period, a complex cascade of pathological pathways in the brain that may accelerate once symptoms develop, the potential of aggregated proteins to spread across brain pathways, and interactions with vascular and other age-associated brain pathologies. There are many potential roles for biomarkers within this landscape. A more diverse set of biomarkers would provide a better picture of the staging and state of pathological events in the brain across the stages of AD. The aim of this review is to focus on methods of biomarker discovery that may help to expand the currently accepted biomarkers. Opportunities and approaches for targeted and non-targeted (or −omic) biomarker discovery are highlighted, with examples from recent studies. How biomarker discoveries can be developed and integrated to become useful tools in diagnostic and therapeutic efforts is discussed.
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Affiliation(s)
- Douglas Galasko
- Department of Neurosciences, Shiley-Marcos Alzheimer's Disease Research Center, University of California, San Diego , La Jolla, CA , USA
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26
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Bergman N, Bergquist J. Recent developments in proteomic methods and disease biomarkers. Analyst 2015; 139:3836-51. [PMID: 24975697 DOI: 10.1039/c4an00627e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteomic methodologies for identification and analysis of biomarkers have gained more attention during recent years and have evolved rapidly. Identification and detection of disease biomarkers are important to foresee outbreaks of certain diseases thereby avoiding surgery and other invasive and expensive medical treatments for patients. Thus, more research into discovering new biomarkers and new methods for faster and more accurate detection is needed. It is often difficult to detect and measure biomarkers because of their low concentrations and the complexity of their respective matrices. Therefore it is hard to find and validate methods for accurate screening methods suitable for clinical use. The most recent developments during the last three years and also some historical considerations of proteomic methodologies for identification and validation of disease biomarkers are presented in this review.
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Affiliation(s)
- Nina Bergman
- Analytical Chemistry, BMC, Department of Chemistry, Uppsala University, Sweden.
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27
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Guo Z, Zhang Y, Zou L, Wang D, Shao C, Wang Y, Sun W, Zhang L. A Proteomic Analysis of Individual and Gender Variations in Normal Human Urine and Cerebrospinal Fluid Using iTRAQ Quantification. PLoS One 2015. [PMID: 26222143 PMCID: PMC4519152 DOI: 10.1371/journal.pone.0133270] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Urine and cerebrospinal fluid (CSF) are two important biofluids used for disease biomarker discovery. For differential proteomic analysis, it is essential to evaluate individual and gender variations. In this study, we characterized urinary and CSF proteomes of 14 healthy volunteers with regard to individual and gender variations using 2DLC-MS/MS analysis and 8-plex iTRAQ quantification. A total of 968/512 urinary/CSF proteins were identified, with 406/280 quantified in all individuals. The median inter-individual coefficients of variation (CVs) were 0.262 and 0.183 for urinary and CSF proteomes, respectively. Cluster analysis showed that male and female urinary proteomes exhibited different patterns, though CSF proteome showed no remarkable gender differences. In comparison with CSF proteome, urinary proteome showed higher individual variation. Further analysis revealed that individual variation was not correlated with protein abundance. The minimum sample size for proteomic analysis with a 2-fold change was 10 (4/5 for males/females using iTRAQ quantification) for urinary or 8 for CSF proteome. Intracellular proteins leaked from exfoliative cells tended to have higher CVs, and extracellular proteins secreted from urinary tract or originating from plasma tended to have lower CVs. The above results might be beneficial for differential proteomic analysis and biomarker discovery.
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Affiliation(s)
- Zhengguang Guo
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, China, 100005
| | - Yang Zhang
- Department of Neurosurgery/China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, 6 Tian Tan Xi Li, Beijing, China, 100050
| | - Lili Zou
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, China, 100005
| | - Danqi Wang
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, China, 100005
| | - Chen Shao
- National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, China, 100005
| | - Yajie Wang
- Core Laboratory for Clinical Medical Research, Beijing Tiantan Hospital, Capital Medical University, 6 Tian Tan Xi Li, Beijing, China, 100050
- Department of Clinical Laboratory Diagnosis, Beijing Tiantan Hospital, Capital Medical University, 6 Tian Tan Xi Li, Beijing, China, 100050
| | - Wei Sun
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, China, 100005
- * E-mail: (WS); (LZ)
| | - Liwei Zhang
- Department of Neurosurgery/China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, 6 Tian Tan Xi Li, Beijing, China, 100050
- * E-mail: (WS); (LZ)
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28
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Zhang Y, Guo Z, Zou L, Yang Y, Zhang L, Ji N, Shao C, Sun W, Wang Y. A comprehensive map and functional annotation of the normal human cerebrospinal fluid proteome. J Proteomics 2015; 119:90-9. [DOI: 10.1016/j.jprot.2015.01.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 12/25/2014] [Accepted: 01/13/2015] [Indexed: 01/11/2023]
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29
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Nascimento JM, Martins-de-Souza D. The proteome of schizophrenia. NPJ SCHIZOPHRENIA 2015; 1:14003. [PMID: 27336025 PMCID: PMC4849438 DOI: 10.1038/npjschz.2014.3] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 12/24/2022]
Abstract
On observing schizophrenia from a clinical point of view up to its molecular basis, one may conclude that this is likely to be one of the most complex human disorders to be characterized in all aspects. Such complexity is the reflex of an intricate combination of genetic and environmental components that influence brain functions since pre-natal neurodevelopment, passing by brain maturation, up to the onset of disease and disease establishment. The perfect function of tissues, organs, systems, and finally the organism depends heavily on the proper functioning of cells. Several lines of evidence, including genetics, genomics, transcriptomics, neuropathology, and pharmacology, have supported the idea that dysfunctional cells are causative to schizophrenia. Together with the above-mentioned techniques, proteomics have been contributing to understanding the biochemical basis of schizophrenia at the cellular and tissue level through the identification of differentially expressed proteins and consequently their biochemical pathways, mostly in the brain tissue but also in other cells. In addition, mass spectrometry-based proteomics have identified and precisely quantified proteins that may serve as biomarker candidates to prognosis, diagnosis, and medication monitoring in peripheral tissue. Here, we review all data produced by proteomic investigation in the last 5 years using tissue and/or cells from schizophrenic patients, focusing on postmortem brain tissue and peripheral blood serum and plasma. This information has provided integrated pictures of the biochemical systems involved in the pathobiology, and has suggested potential biomarkers, and warrant potential targets to alternative treatment therapies to schizophrenia.
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Affiliation(s)
- Juliana M Nascimento
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
- D’Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
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30
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Lin CH, Wu RM. Biomarkers of cognitive decline in Parkinson's disease. Parkinsonism Relat Disord 2015; 21:431-43. [PMID: 25737398 DOI: 10.1016/j.parkreldis.2015.02.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 02/10/2015] [Accepted: 02/12/2015] [Indexed: 10/24/2022]
Abstract
Cognitive impairment is a frequent and devastating non-motor symptom of Parkinson's disease (PD). Impaired cognition has a major impact on either quality of life or mortality in patients with PD. Notably, the rate of cognitive decline and pattern of early cognitive deficits in PD are highly variable between individuals. Given that the underlying mechanisms of cognitive decline or dementia associated with PD remain unclear, there is currently no mechanism-based treatment available. Identification of biological markers, including neuroimaging, biofluids and common genetic variants, that account for the heterogeneity of PD related cognitive decline could provide important insights into the pathological processes that underlie cognitive impairment in PD. These combined biomarker approaches will enable early diagnosis and provide indicators of cognitive progression in PD patients. This review summarizes recent advances in the development of biomarkers for cognitive impairments in PD.
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Affiliation(s)
- Chin-Hsien Lin
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Ruey-Meei Wu
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei 100, Taiwan.
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31
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Shevchenko G, Konzer A, Musunuri S, Bergquist J. Neuroproteomics tools in clinical practice. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:705-17. [PMID: 25680928 DOI: 10.1016/j.bbapap.2015.01.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/30/2015] [Indexed: 12/13/2022]
Abstract
Neurodegenerative disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) are characterized by neuronal impairment that leads to disease-specific changes in the neuronal proteins. The early diagnosis of these disorders is difficult, thus, the need for identifying, developing and using valid clinically applicable biomarkers that meet the criteria of precision, specificity and repeatability is very vital. The application of rapidly emerging technology such as mass spectrometry (MS) in proteomics has opened new avenues to accelerate biomarker discovery, both for diagnostic as well as for prognostic purposes. This review summarizes the most recent advances in the mass spectrometry-based neuroproteomics and analyses the current and future directions in the biomarker discovery for the neurodegenerative diseases. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Affiliation(s)
- Ganna Shevchenko
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden
| | - Anne Konzer
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden
| | - Sravani Musunuri
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden
| | - Jonas Bergquist
- Analytical Chemistry, Department of Chemistry-BMC and SciLife Lab, Uppsala University, 75124 Uppsala, Sweden.
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32
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The Potential of Proteomics in Understanding Neurodegeneration. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2015; 121:25-58. [DOI: 10.1016/bs.irn.2015.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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33
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Conti A, Alessio M. Proteomics for Cerebrospinal Fluid Biomarker Identification in Parkinsons Disease: Methods and Critical Aspects. AIMS MEDICAL SCIENCE 2015. [DOI: 10.3934/medsci.2015.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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34
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Hölttä M, Minthon L, Hansson O, Holmén-Larsson J, Pike I, Ward M, Kuhn K, Rüetschi U, Zetterberg H, Blennow K, Gobom J. An Integrated Workflow for Multiplex CSF Proteomics and Peptidomics—Identification of Candidate Cerebrospinal Fluid Biomarkers of Alzheimer’s Disease. J Proteome Res 2014; 14:654-63. [DOI: 10.1021/pr501076j] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mikko Hölttä
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
| | - Lennart Minthon
- Clinical
Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, 221 00 Lund, Sweden
| | - Oskar Hansson
- Clinical
Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, 221 00 Lund, Sweden
| | - Jessica Holmén-Larsson
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
| | - Ian Pike
- Proteome
Sciences
PLC, KT11 3EP London, United Kingdom
| | - Malcolm Ward
- Proteome
Sciences
PLC, KT11 3EP London, United Kingdom
| | - Karsten Kuhn
- Proteome Science R&D GmbH&CoKG, 60438 Frankfurt am Main, Germany
| | - Ulla Rüetschi
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
| | - Henrik Zetterberg
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
- UCL Institute of Neurology, Queen Square, WC1N 3BG London, United Kingdom
| | - Kaj Blennow
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
| | - Johan Gobom
- Clinical
Neurochemistry Laboratory, Institute of Neuroscience and Physiology,
Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, 431 80 Mölndal, Sweden
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35
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Fernández-Irigoyen J, Zelaya MV, Tuñon T, Santamaría E. Anatomo-proteomic characterization of human basal ganglia: focus on striatum and globus pallidus. Mol Brain 2014; 7:83. [PMID: 25406675 PMCID: PMC4236423 DOI: 10.1186/s13041-014-0083-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 11/04/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The basal ganglia (BG) are a complex network of subcortical nuclei involved in the coordination and integration of the motor activity. Although these independent anatomical structures are functionally related, the proteome present in each isolated nucleus remains largely unexplored. In order to analyse the BG proteome in a large-scale format, we used a multi-dimensional fractionation approach which combines isolation of anatomically-defined nuclei, and protein/peptide chromatographic fractionation strategies coupled to mass spectrometry. RESULTS Using this workflow, we have obtained a proteomic expression profile across striatum and globus pallidus structures among which 1681 proteins were located in caudate nucleus (CN), 1329 in putamen, 1419 in medial globus pallidus (GPi), and 1480 in lateral globus pallidus (GPe), establishing a BG reference proteome to a depth of 2979 unique proteins. Protein interactome mapping highlighted significant clustering of common proteins in striatal and pallidal structures, contributing to oxidative phosphorylation, protein degradation and neurotrophin signalling pathways. In silico analyses emphasized specific pathways represented in striatal and pallidal structures highlighting 5-hydroxytryptamine degradation, synaptic vesicle trafficking, and dopamine, metabotropic glutamate and muscarinic acetylcholine receptor pathways. Additional bioinformatic analyses also revealed that: i) nearly 4% of identified proteins have been previously associated to neurodegenerative syndromes, ii) 11% of protein set tends to localize to synaptic terminal, and iii) 20% of identified proteins were also localized in cerebrospinal fluid (CSF). CONCLUSIONS Overall, the anatomo-proteomic profiling of BG complements the anatomical atlas of the human brain transcriptome, increasing our knowledge about the molecular basis of the BG and the etiology of the movement disorders.
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Affiliation(s)
- Joaquín Fernández-Irigoyen
- />Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Irunlarrea Street, 31008 Pamplona, Spain
| | - María Victoria Zelaya
- />Neurological Tissue Bank, Navarrabiomed, Fundación Miguel Servet, 31008 Pamplona, Spain
| | - Teresa Tuñon
- />Pathological Anatomy Department, Navarra Hospital Complex, Pamplona, Spain
| | - Enrique Santamaría
- />Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Irunlarrea Street, 31008 Pamplona, Spain
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36
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Magdalinou N, Lees AJ, Zetterberg H. Cerebrospinal fluid biomarkers in parkinsonian conditions: an update and future directions. J Neurol Neurosurg Psychiatry 2014; 85:1065-75. [PMID: 24691581 PMCID: PMC4173749 DOI: 10.1136/jnnp-2013-307539] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Parkinsonian diseases comprise a heterogeneous group of neurodegenerative disorders, which show significant clinical and pathological overlap. Accurate diagnosis still largely relies on clinical acumen; pathological diagnosis remains the gold standard. There is an urgent need for biomarkers to diagnose parkinsonian disorders, particularly in the early stages when diagnosis is most difficult. In this review, several of the most promising cerebrospinal fluid candidate markers will be discussed. Their strengths and limitations will be considered together with future developments in the field.
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Affiliation(s)
- Nadia Magdalinou
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Andrew J Lees
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Henrik Zetterberg
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
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37
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Percy AJ, Yang J, Chambers AG, Simon R, Hardie DB, Borchers CH. Multiplexed MRM with Internal Standards for Cerebrospinal Fluid Candidate Protein Biomarker Quantitation. J Proteome Res 2014; 13:3733-3747. [DOI: 10.1021/pr500317d] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew J. Percy
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Juncong Yang
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Andrew G. Chambers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Romain Simon
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Darryl B. Hardie
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Christoph H. Borchers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
- Department
of Biochemistry and Microbiology, University of Victoria, Petch Building
Room 207, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
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38
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Gupta MK, Jayaram S, Madugundu AK, Chavan S, Advani J, Pandey A, Thongboonkerd V, Sirdeshmukh R. Chromosome-centric Human Proteome Project: Deciphering Proteins Associated with Glioma and Neurodegenerative Disorders on Chromosome 12. J Proteome Res 2014; 13:3178-90. [DOI: 10.1021/pr500023p] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Manoj Kumar Gupta
- Institute
of Bioinformatics, International
Tech Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Savita Jayaram
- Institute
of Bioinformatics, International
Tech Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Anil K. Madugundu
- Institute
of Bioinformatics, International
Tech Park, Bangalore 560066, India
| | - Sandip Chavan
- Institute
of Bioinformatics, International
Tech Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Jayshree Advani
- Institute
of Bioinformatics, International
Tech Park, Bangalore 560066, India
| | - Akhilesh Pandey
- Institute
of Bioinformatics, International
Tech Park, Bangalore 560066, India
- McKusick-Nathans
Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205 United States
| | | | - Ravi Sirdeshmukh
- Institute
of Bioinformatics, International
Tech Park, Bangalore 560066, India
- Mazumdar
Shaw Centre for Translational Research, Narayana Health, Bangalore 560099, India
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39
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Feneberg E, Steinacker P, Lehnert S, Schneider A, Walther P, Thal DR, Linsenmeier M, Ludolph AC, Otto M. Limited role of free TDP-43 as a diagnostic tool in neurodegenerative diseases. Amyotroph Lateral Scler Frontotemporal Degener 2014; 15:351-6. [PMID: 24834468 DOI: 10.3109/21678421.2014.905606] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
TAR DNA-binding protein 43 (TDP-43) is one of the neuropathological hallmarks in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). It is present in patients' blood and cerebrospinal fluid (CSF); however, the source and clinical relevance of TDP-43 measurements in body fluids is uncertain. We investigated paired CSF and serum samples, blood lymphocytes, brain urea fractions and purified exosomes from CSF for TDP-43 by one- (1D), and two-dimensional (2D) Western immunoblotting (WB) and quantitative mass spectrometry (MRM) in patients with ALS, FTLD and non-neurodegenerative diseases. By means of 2D-WB we were able to demonstrate a similar isoform pattern of TDP-43 in lymphocytes, serum and CSF in contrast to that of brain urea fractions with TDP-43 pathology. We found that the TDP-43 CSF to blood concentration ratio is about 1:200. As a possible brain specific fraction we found TDP-43 in exosome preparations from CSF by immunoblot and MRM. We conclude that TDP-43 in CSF originates mainly from blood. Measurements of TDP-43 in CSF and blood are of minor importance as a diagnostic tool, but may be important for monitoring therapy effects of TDP-43 modifying drugs.
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Fernández-Irigoyen J, Zelaya MV, Santamaría E. Applying mass spectrometry-based qualitative proteomics to human amygdaloid complex. Front Cell Neurosci 2014; 8:80. [PMID: 24688456 PMCID: PMC3960493 DOI: 10.3389/fncel.2014.00080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 02/27/2014] [Indexed: 11/13/2022] Open
Abstract
The amygdaloid complex is a key brain structure involved in the expression of behaviors and emotions such as learning, fear, and anxiety. Brain diseases including depression, epilepsy, autism, schizophrenia, and Alzheimer's disease, have been associated with amygdala dysfunction. For several decades, neuroanatomical, neurophysiological, volumetric, and cognitive approaches have been the gold standard techniques employed to characterize the amygdala functionality. However, little attention has been focused specifically on the molecular composition of the human amygdala from the perspective of proteomics. We have performed a global proteome analysis employing protein and peptide fractionation methods followed by nano-liquid chromatography tandem mass spectrometry (nanoLC-MS/MS), detecting expression of at least 1820 protein species in human amygdala, corresponding to 1814 proteins which represent a nine-fold increase in proteome coverage with respect to previous proteomic profiling of the rat amygdala. Gene ontology analysis were used to determine biological process represented in human amygdala highlighting molecule transport, nucleotide binding, and oxidoreductase and GTPase activities. Bioinformatic analyses have revealed that nearly 4% of identified proteins have been previously associated to neurodegenerative syndromes, and 26% of amygdaloid proteins were also found to be present in cerebrospinal fluid (CSF). In particular, a subset of amygdaloid proteins was mainly involved in axon guidance, synaptic vesicle release, L1CAM interactome, and signaling pathways transduced by NGF and NCAM1. Taken together, our data contributes to the repertoire of the human brain proteome, serving as a reference library to provide basic information for understanding the neurobiology of the human amygdala.
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Affiliation(s)
| | - María V Zelaya
- Neurological Tissue Bank, Navarrabiomed, Fundación Miguel Servet Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Group, Proteomics Unit, Navarrabiomed, Fundación Miguel Servet Pamplona, Spain
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Abstract
PURPOSE OF REVIEW Parkinson disease is the second most common neurodegenerative disease after Alzheimer disease, and current demographic trends indicate a life-time risk approaching 4% and predict a doubling of prevalence by 2030. Strategies are being developed to apply recent advances in our understanding of the cause of Parkinson disease to the development of biomarkers that will enable the identification of at-risk individuals, enable early diagnosis and reflect the progression of disease. The latter will be particularly important for the testing of disease-modifying therapies. This review summarizes recent advances in Parkinson disease biomarker development. RECENT FINDINGS Recent reports continue to reflect the application of a variety of clinical, imaging or biochemical measurements, alone or in combination, to general Parkinson disease populations. Probably the most promising is the assay of alpha-synuclein in the diagnosis and evolution of Parkinson disease. At present, detection techniques are still being refined, but once accurate and reproducible assays are available, it will be important to define the relationship of these to early diagnosis and progression. Alpha-synuclein concentrations may also be modulated by certain disease-modifying agents in development and so may represent a measure of their efficacy. It has to be accepted that no single measure currently fulfils all the necessary criteria for a biomarker in Parkinson disease, but combinations of measures are more likely to deliver benefit. SUMMARY The Parkinson disease biomarker field is approaching a stage when certain combinations of clinical, imaging and biochemical measures may identify a proportion of individuals at risk for developing the disease. However, their general applicability may be limited. Attention is now turning to stratification of Parkinson disease into certain at-risk groups defined by genotype. The application of multimodal screening to these populations may be more rewarding in the short term.
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New insight into neurodegeneration: the role of proteomics. Mol Neurobiol 2013; 49:1181-99. [PMID: 24323427 DOI: 10.1007/s12035-013-8590-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 11/06/2013] [Indexed: 12/11/2022]
Abstract
Recent advances within the field of proteomics, including both upstream and downstream protocols, have fuelled a transition from simple protein identification to functional analysis. A battery of proteomics approaches is now being employed for the analysis of protein expression levels, the monitoring of cellular activities and for gaining an increased understanding into biochemical pathways. Combined, these approaches are changing the way we study disease by allowing accurate and targeted, large scale protein analysis, which will provide invaluable insight into disease pathogenesis. Neurodegenerative disorders, including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS), prion disease, and other diseases that affect the neuromuscular system, are a leading cause of disability in the aging population. There are no effective intervention strategies for these disorders and diagnosis is challenging as it relies primarily on clinical symptomatic features, which often overlap at early stages of disease. There is, therefore, an urgent need to develop reliable biomarkers to improve early and specific diagnosis, to track disease progression, to measure molecular responses towards treatment regimes and ultimately devise new therapeutic strategies. To accomplish this, a better understanding of disease mechanisms is needed. In this review we summarize recent advances in the field of proteomics applicable to neurodegenerative disorders, and how these advances are fueling our understanding, diagnosis, and treatment of these complex disorders.
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Gebriel M, Prabhudesai S, Uleberg KE, Larssen E, Piston D, Bjørnstad AH, Møller SG. Zebrafish brain proteomics reveals central proteins involved in neurodegeneration. J Neurosci Res 2013; 92:104-15. [PMID: 24123299 DOI: 10.1002/jnr.23297] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 08/05/2013] [Accepted: 08/12/2013] [Indexed: 12/13/2022]
Abstract
Understanding the complex biology of the brain requires analyzing its structural and functional complexity at the protein level. The large-scale analysis of the brain proteome, coupled with characterization of central brain proteins, provides insight into fundamental brain processes and processes linked to neurodegenerative diseases. Here we provide a map of the zebrafish brain proteome by using two-dimensional gel electrophoresis (2DE), followed by the identification of 95 brain proteins using mass spectrometry (LC-ESI MS/MS). Our data show extensive phosphorylation of brain proteins but less prominent glycosylation. Furthermore, ~51% of the identified proteins are predicted to have one or more ubiquitination sites whereas ~90% are predicted to have one or more SUMOylation sites. Our findings provide a valuable proteome map of the zebrafish brain and associated posttranslational modifications demonstrating that zebrafish proteomic approaches can aid in our understanding of proteins central to important neuronal processes and those associated with neurodegenerative disorders.
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Affiliation(s)
- Mohammed Gebriel
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway
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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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Abstract
Clinical diagnosis of Parkinson disease (PD) is difficult in early stages of disease, with high risk of misdiagnosis. The long preclinical phase of PD provides the possibility for early therapeutic intervention once disease-modifying therapies have been developed, but lack of biomarkers for early diagnosis and monitoring of disease progression represents a major obstacle to achievement of this goal. Accordingly, research efforts aimed at identification of novel biomarkers have been increasing in the past 5 years. Cerebrospinal fluid (CSF) is an accessible source of brain-derived proteins, which mirror molecular changes that take place in the CNS. In this Review, we discuss evidence from numerous studies that have focused on identification of candidate CSF biomarkers for PD. Notably, molecular pathways related to α-synuclein, tau and β-amyloid peptides have received considerable attention. CSF levels of the protein DJ-1 are also of interest, although further investigation of this candidate marker is required. These studies support the usefulness of a combination of various CSF biomarkers of PD to increase diagnostic accuracy during early phases of the disease, and to differentiate PD from other neurodegenerative disorders.
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Jellinger KA. Neurobiology of cognitive impairment in Parkinson’s disease. Expert Rev Neurother 2012; 12:1451-1466. [DOI: 10.1586/ern.12.131] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Jesse S, Lehnert S, Jahn O, Parnetti L, Soininen H, Herukka SK, Steinacker P, Tawfik S, Tumani H, von Arnim CAF, Neumann M, Kretzschmar HA, Kulaksiz H, Lenter M, Wiltfang J, Ferger B, Hengerer B, Otto M. Differential sialylation of serpin A1 in the early diagnosis of Parkinson's disease dementia. PLoS One 2012; 7:e48783. [PMID: 23144969 PMCID: PMC3493604 DOI: 10.1371/journal.pone.0048783] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 10/01/2012] [Indexed: 12/27/2022] Open
Abstract
The prevalence of Parkinson’s disease (PD) increases with age. Up to 50% of PD show cognitive decline in terms of a mild cognitive impairment already in early stages that predict the development of dementia, which can occur in up to 80% of PD patients over the long term, called Parkinson’s disease dementia (PDD). So far, diagnosis of PD/PDD is made according to clinical and neuropsychological examinations while laboratory data is only used for exclusion of other diseases. The aim of this study was the identification of possible biomarkers in cerebrospinal fluid (CSF) of PD, PDD and controls (CON) which predict the development of dementia in PD. For this, a proteomic approach optimized for CSF was performed using 18 clinically well characterized patients in a first step with subsequent validation using 84 patients. Here, we detected differentially sialylated isoforms of Serpin A1 as marker for differentiation of PD versus PDD in CSF. Performing 2D-immunoblots, all PDD patients could be identified correctly (sensitivity 100%). Ten out of 24 PD patients showed Serpin A1 isoforms in a similar pattern like PDD, indicating a specificity of 58% for the test-procedure. In control samples, no additional isoform was detected. On the basis of these results, we conclude that differentially sialylated products of Serpin A1 are an interesting biomarker to indicate the development of a dementia during the course of PD.
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Affiliation(s)
- Sarah Jesse
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Stefan Lehnert
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Olaf Jahn
- Proteomics Group, Max-Planck-Institute for Experimental Medicine, Goettingen, Germany
- DFG Research Center for Molecular Physiology of the Brain, Goettingen, Germany
| | | | - Hilkka Soininen
- Department of Neurology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Sanna-Kaisa Herukka
- Department of Neurology, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | | | - Saskia Tawfik
- Department of Neurology, University of Ulm, Ulm, Germany
| | | | | | - Manuela Neumann
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | | | - Hasan Kulaksiz
- Department of Internal Medicine, University of Ulm, Ulm, Germany
| | - Martin Lenter
- CNS Diseases Research, Boehringer Ingelheim GmbH & Co. KG, Biberach an der Riss, Germany
| | - Jens Wiltfang
- Department of Psychiatry, University of Essen-Duisburg, Essen-Duisburg, Germany
| | - Boris Ferger
- CNS Diseases Research, Boehringer Ingelheim GmbH & Co. KG, Biberach an der Riss, Germany
| | - Bastian Hengerer
- CNS Diseases Research, Boehringer Ingelheim GmbH & Co. KG, Biberach an der Riss, Germany
| | - Markus Otto
- Department of Neurology, University of Ulm, Ulm, Germany
- * E-mail:
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Waragai M, Sekiyama K, Fujita M, Tokuda T, Hashimoto M. Biomarkers for the diagnosis and management of Parkinson's disease. ACTA ACUST UNITED AC 2012; 7:71-83. [PMID: 23530844 DOI: 10.1517/17530059.2013.733694] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Parkinson's disease (PD) is the most common neurodegenerative disease leading to movement disorders, and is characterized neuropathologically by the progressive loss of dopaminergic neurons, intracellular α-synuclein deposition and the formation of Lewy bodies. The difficulty of making a definitive diagnosis of PD itself, as opposed to other neurodegenerative diseases associated with parkinsonism, is a central issue in clinical PD research. However, recent advances in diagnostic methods, encompassing imaging techniques, genetic testing and measurement of biological markers may permit earlier diagnosis, and thus potentially improved management of PD. AREAS COVERED In addition to clinical symptoms and imaging techniques, a number of genetic and biological markers obtained from body fluids such as cerebrospinal fluids may hold promise for the early detection of PD. It is often difficult to make an accurate diagnosis and to distinguish PD from other diseases with features of parkinsonism, particularly during the early stages of the disease. In this regard, biomarkers which are specific for PD, in combination with observation of clinical symptoms, may facilitate the early diagnosis and improved management of PD. EXPERT OPINION Good biomarkers for PD could be helpful for early diagnosis, management and tracking of disease progression. Furthermore, combined analysis using several kinds of biomarkers may allow the detection of preclinical PD, which in turn may facilitate a prevention of disease onset with the use of disease-modifying drugs.
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Affiliation(s)
- Masaaki Waragai
- Tokyo Metropolitan Institute of Medical Science, Division of Sensory and Motor Systems, Tokyo 156-0057, Japan.
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Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM. J Proteomics 2012; 78:312-25. [PMID: 23059536 DOI: 10.1016/j.jprot.2012.09.037] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 09/14/2012] [Accepted: 09/30/2012] [Indexed: 12/25/2022]
Abstract
In the present study, we aimed to discover cerebrospinal fluid (CSF) proteins with significant abundance difference between early multiple sclerosis patients and controls, and do an initial verification of these proteins using selected reaction monitoring (SRM). iTRAQ and Orbitrap MS were used to compare the CSF proteome of patients with clinically isolated syndrome (CIS) (n=5), patients with relapsing-remitting multiple sclerosis that had CIS at the time of lumbar puncture (n=5), and controls with other inflammatory neurological disease (n=5). Of more than 1200 identified proteins, five proteins were identified with significant abundance difference between the patients and controls. In the initial verification using SRM we analyzed a larger patient and control cohort (n=132) and also included proteins reported as differentially abundant in multiple sclerosis in the literature. We found significant abundance difference for 11 proteins after verification, of which the five proteins alpha-1-antichymotrypsin, contactin-1, apolipoprotein D, clusterin, and kallikrein-6 were significantly differentially abundant in several of the group comparisons. This initial study form the basis for further biomarker verification studies in even larger sample cohorts, to determine if these proteins have relevance as diagnostic or prognostic biomarkers for multiple sclerosis.
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