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Toft A, Sjödin S, Simonsen AH, Ejlerskov P, Roos P, Musaeus CS, Henriksen EE, Nielsen TT, Brinkmalm A, Blennow K, Zetterberg H, Nielsen JE. Endo-lysosomal protein concentrations in CSF from patients with frontotemporal dementia caused by CHMP2B mutation. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2023; 15:e12402. [PMID: 36815874 PMCID: PMC9936136 DOI: 10.1002/dad2.12402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/02/2023] [Accepted: 01/12/2023] [Indexed: 02/19/2023]
Abstract
Introduction Increasing evidence implicates proteostatic dysfunction as an early event in the development of frontotemporal dementia (FTD). This study aimed to explore potential cerebrospinal fluid (CSF) biomarkers associated with the proteolytic systems in genetic FTD caused by CHMP2B mutation. Methods Combining solid-phase extraction and parallel reaction monitoring mass spectrometry, a panel of 47 peptides derived from 20 proteins was analyzed in CSF from 31 members of the Danish CHMP2B-FTD family. Results Compared with family controls, mutation carriers had significantly higher levels of complement C9, lysozyme and transcobalamin II, and lower levels of ubiquitin, cathepsin B, and amyloid precursor protein. Discussion Lower CSF ubiquitin concentrations in CHMP2B mutation carriers indicate that ubiquitin levels relate to the specific disease pathology, rather than all-cause neurodegeneration. Increased lysozyme and complement proteins may indicate innate immune activation. Altered levels of amyloid precursor protein and cathepsins have previously been associated with impaired lysosomal proteolysis in FTD. Highlights CSF markers of proteostasis were explored in CHMP2B-mediated frontotemporal dementia (FTD).31 members of the Danish CHMP2B-FTD family were included.We used solid-phase extraction and parallel reaction monitoring mass spectrometry.Six protein levels were significantly altered in CHMP2B-FTD compared with controls.Lower CSF ubiquitin levels in patients suggest association with disease mechanisms.
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Affiliation(s)
- Anders Toft
- Neurogenetics Clinic & Research LabDanish Dementia Research CentreRigshospitaletCopenhagenDenmark
| | - Simon Sjödin
- Laboratory of Clinical ChemistrySahlgrenska University HospitalGothenburgSweden
| | - Anja Hviid Simonsen
- Neurogenetics Clinic & Research LabDanish Dementia Research CentreRigshospitaletCopenhagenDenmark
| | - Patrick Ejlerskov
- Neurogenetics Clinic & Research LabDanish Dementia Research CentreRigshospitaletCopenhagenDenmark
| | - Peter Roos
- Neurogenetics Clinic & Research LabDanish Dementia Research CentreRigshospitaletCopenhagenDenmark
| | - Christian Sandøe Musaeus
- Neurogenetics Clinic & Research LabDanish Dementia Research CentreRigshospitaletCopenhagenDenmark
| | - Emil Elbæk Henriksen
- Neurogenetics Clinic & Research LabDanish Dementia Research CentreRigshospitaletCopenhagenDenmark
| | - Troels Tolstrup Nielsen
- Neurogenetics Clinic & Research LabDanish Dementia Research CentreRigshospitaletCopenhagenDenmark
| | - Ann Brinkmalm
- Clinical Neurochemistry LaboratorySahlgrenska University HospitalMölndalSweden
| | - Kaj Blennow
- Clinical Neurochemistry LaboratorySahlgrenska University HospitalMölndalSweden,Department of Psychiatry and NeurochemistryInstitute of Neuroscience and Physiologythe Sahlgrenska Academy at the University of GothenburgMölndalSweden
| | - Henrik Zetterberg
- Clinical Neurochemistry LaboratorySahlgrenska University HospitalMölndalSweden,Department of Psychiatry and NeurochemistryInstitute of Neuroscience and Physiologythe Sahlgrenska Academy at the University of GothenburgMölndalSweden,Department of Neurodegenerative DiseaseUCL Institute of NeurologyQueen SquareLondonUK,UK Dementia Research Institute at UCLLondonUK,Hong Kong Center for Neurodegenerative DiseasesClear Water BayHong KongChina
| | - Jørgen Erik Nielsen
- Neurogenetics Clinic & Research LabDanish Dementia Research CentreRigshospitaletCopenhagenDenmark
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Hossain MB, Islam MK, Adhikary A, Rahaman A, Islam MZ. Bioinformatics Approach to Identify Significant Biomarkers, Drug Targets Shared Between Parkinson's Disease and Bipolar Disorder: A Pilot Study. Bioinform Biol Insights 2022; 16:11779322221079232. [PMID: 35221677 PMCID: PMC8874170 DOI: 10.1177/11779322221079232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 02/01/2022] [Indexed: 11/17/2022] Open
Abstract
Parkinson’s disease (PD) is a neurodegenerative disorder responsible for shaking, rigidity, and trouble in walking and patients’ coordination ability and physical stability deteriorate day by day. Bipolar disorder (BD) is a psychiatric disorder which is the reason behind extreme shiftiness in mood, and frequent mood inversion may reach too high called mania. People with BD have a greater chance of developing PD during the follow-up period. A lot of work has been done to understand the key factors for developing these 2 diseases. But the molecular functionalities that trigger the development of PD in people with BD are not clear yet. In our study, we are intended to identify the molecular biomarkers and pathways shared between BD and PD. We have investigated the RNA-Seq gene expression data sets of PD and BD. A total of 45 common unique genes (32 up-regulated and 13 down-regulated) abnormally expressed in both PD and BD were identified by applying statistical methods on the GEO data sets. Gene ontology (GO) and BioCarta, KEGG, and Reactome pathways analysis of these 45 common dysregulated genes identified numerous altered molecular pathways such as mineral absorption, Epstein-Barr virus infection, HTLV-I infection, antigen processing, and presentation. Analysis of protein-protein interactions revealed 9 significant hub-proteins, namely RPL21, RPL34, CKS2, B2M, TNFRSF10A, DTX2, HLA-B, ATP2A3, and TAPBP. Significant transcription factors (IRF8, SPI1, RUNX1, and FOXA1) and posttranscriptional regulator microRNAs (hsa-miR-491-3p and hsa-miR-1246) are also found by analyzing gene-transcription factors and gene-miRNAs interactions, respectively. Protein-drug interaction analysis revealed hub-protein B2M’s interaction with molecular drug candidates like N-formylmethionine, 3-indolebutyric acid, and doxycycline. Finally, a link between pathological processes of PD and BD is identified at transcriptional level. This study may help us to predict the development of PD among the people suffering from BD and gives some clue to understand significant pathological mechanisms.
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Affiliation(s)
- Md Bipul Hossain
- Department of Information and Communication Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh.,Department of Information and Communication Technology, Islamic University, Kushtia, Bangladesh
| | - Md Kobirul Islam
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Apurba Adhikary
- Department of Information and Communication Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Abidur Rahaman
- Department of Information and Communication Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Zahidul Islam
- Department of Information and Communication Technology, Islamic University, Kushtia, Bangladesh
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Marques TM, van Rumund A, Kersten I, Bruinsma IB, Wessels HJ, Gloerich J, Kaffa C, Esselink RAJ, Bloem BR, Kuiperij HB, Verbeek MM. Identification of cerebrospinal fluid biomarkers for parkinsonism using a proteomics approach. NPJ Parkinsons Dis 2021; 7:107. [PMID: 34848724 PMCID: PMC8633286 DOI: 10.1038/s41531-021-00249-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 10/27/2021] [Indexed: 01/25/2023] Open
Abstract
The aim of our study was to investigate cerebrospinal fluid (CSF) tryptic peptide profiles as potential diagnostic biomarkers for the discrimination of parkinsonian disorders. CSF samples were collected from individuals with parkinsonism, who had an uncertain diagnosis at the time of inclusion and who were followed for up to 12 years in a longitudinal study. We performed shotgun proteomics to identify tryptic peptides in CSF of Parkinson's disease (PD, n = 10), multiple system atrophy patients (MSA, n = 5) and non-neurological controls (n = 10). We validated tryptic peptides with differential levels between PD and MSA using a newly developed selected reaction monitoring (SRM) assay in CSF of PD (n = 46), atypical parkinsonism patients (AP; MSA, n = 17; Progressive supranuclear palsy; n = 8) and non-neurological controls (n = 39). We identified 191 tryptic peptides that differed significantly between PD and MSA, of which 34 met our criteria for SRM development. For 14/34 peptides we confirmed differences between PD and AP. These tryptic peptides discriminated PD from AP with moderate-to-high accuracy. Random forest modelling including tryptic peptides plus either clinical assessments or other CSF parameters (neurofilament light chain, phosphorylated tau protein) and age improved the discrimination of PD vs. AP. Our results show that the discovery of tryptic peptides by untargeted and subsequent validation by targeted proteomics is a suitable strategy to identify potential CSF biomarkers for PD versus AP. Furthermore, the tryptic peptides, and corresponding proteins, that we identified as differential biomarkers may increase our current knowledge about the disease-specific pathophysiological mechanisms of parkinsonism.
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Affiliation(s)
- Tainá M. Marques
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,Radboudumc Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anouke van Rumund
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,Radboudumc Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands
| | - Iris Kersten
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ilona B. Bruinsma
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hans J.C.T. Wessels
- grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jolein Gloerich
- grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Charlotte Kaffa
- grid.10417.330000 0004 0444 9382Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rianne A. J. Esselink
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,Radboudumc Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands
| | - Bastiaan R. Bloem
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,Radboudumc Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands
| | - H. Bea Kuiperij
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marcel M. Verbeek
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,Radboudumc Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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Abstract
PURPOSE OF REVIEW Corticobasal degeneration (CBD) is a rapidly progressive neurodegenerative tauopathy diagnosed postmortem by pathological examination. The clinical presentation of corticobasal syndrome (CBS) is an apraxic, dystonic, and rigid limb with asymmetrical cortical signs and myoclonus. However, less than half of the patients with CBS receive a CBD diagnosis. As tau-lowering therapies have entered clinical trials, improved antemortem diagnosis of CBD is needed. Here, clinicopathological, neuroimaging, and biofluid data in CBS and/or CBD patients are briefly summarized and some knowledge gaps identified. RECENT FINDINGS Developments of MRI-based and nuclear medicine imaging modalities have increased pathophysiological insights of CBS and may improve diagnostic accuracy. In particular, several tau-PET ligands have been evaluated in CBS patients. Cerebrospinal fluid and plasma levels of neurofilament light chain can distinguish CBS from Parkinson's disease but not from other atypical forms of Parkinsonism. SUMMARY Structural and functional imaging approaches provide some aid in the diagnosis of CBD but have low-content validity. None of the currently available tau-PET ligands is suitable for detecting straight filament 4repeat tau disease in clinical routine. Biofluid markers reflecting the distinct tau and/or astrocyte disease of CBD are needed. Examining biosamples along with clinical parameters from longitudinally followed patients with autopsy-confirmed CBD diagnosis shall hopefully delineate improved biomarkers.
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Zhu S, Wuolikainen A, Wu J, Öhman A, Wingsle G, Moritz T, Andersen PM, Forsgren L, Trupp M. Targeted Multiple Reaction Monitoring Analysis of CSF Identifies UCHL1 and GPNMB as Candidate Biomarkers for ALS. J Mol Neurosci 2019; 69:643-657. [PMID: 31721001 PMCID: PMC6858390 DOI: 10.1007/s12031-019-01411-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 09/26/2019] [Indexed: 02/06/2023]
Abstract
The neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD) share some common molecular deficits including disruption of protein homeostasis leading to disease-specific protein aggregation. While insoluble protein aggregates are the defining pathological confirmation of diagnosis, patient stratification based on early molecular etiologies may identify distinct subgroups within a clinical diagnosis that would respond differently in therapeutic development programs. We are developing targeted multiple reaction monitoring (MRM) mass spectrometry methods to rigorously quantify CSF proteins from known disease genes involved in lysosomal, ubiquitin-proteasomal, and autophagy pathways. Analysis of CSF from 21 PD, 21 ALS, and 25 control patients, rigorously matched for gender, age, and age of sample, revealed significant changes in peptide levels between PD, ALS, and control. In patients with PD, levels of two peptides for chromogranin B (CHGB, secretogranin 1) were significantly reduced. In CSF of patients with ALS, levels of two peptides from ubiquitin carboxy-terminal hydrolase like protein 1 (UCHL1) and one peptide each for glycoprotein non-metastatic melanoma protein B (GPNMB) and cathepsin D (CTSD) were all increased. Analysis of patients with ALS separated into two groups based on length of survival after CSF sampling revealed that the increases in GPNMB and UCHL1 were specific for short-lived ALS patients. While analysis of additional cohorts is required to validate these candidate biomarkers, this study suggests methods for stratification of ALS patients for clinical trials and identifies targets for drug efficacy measurements during therapeutic development.
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Affiliation(s)
- Shaochun Zhu
- Department of Clinical Science, Neurosciences, Umeå University, Building 10, NUS, Umeå, Sweden
| | | | - Junfang Wu
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Anders Öhman
- Department of Clinical Science, Neurosciences, Umeå University, Building 10, NUS, Umeå, Sweden
| | - Gunnar Wingsle
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Thomas Moritz
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Peter M Andersen
- Department of Clinical Science, Neurosciences, Umeå University, Building 10, NUS, Umeå, Sweden
| | - Lars Forsgren
- Department of Clinical Science, Neurosciences, Umeå University, Building 10, NUS, Umeå, Sweden
| | - Miles Trupp
- Department of Clinical Science, Neurosciences, Umeå University, Building 10, NUS, Umeå, Sweden.
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6
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Sjödin S, Brinkmalm G, Öhrfelt A, Parnetti L, Paciotti S, Hansson O, Hardy J, Blennow K, Zetterberg H, Brinkmalm A. Endo-lysosomal proteins and ubiquitin CSF concentrations in Alzheimer's and Parkinson's disease. Alzheimers Res Ther 2019; 11:82. [PMID: 31521194 PMCID: PMC6745076 DOI: 10.1186/s13195-019-0533-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/22/2019] [Indexed: 01/17/2023]
Abstract
BACKGROUND Increasing evidence implicates dysfunctional proteostasis and the involvement of the autophagic and endo-lysosomal system and the ubiquitin-proteasome system in neurodegenerative diseases. In Alzheimer's disease (AD), there is an accumulation of autophagic vacuoles within the neurons. In Parkinson's disease (PD), susceptibility has been linked to genes encoding proteins involved in autophagy and lysosomal function, as well as mutations causing lysosomal disorders. Furthermore, both diseases are characterized by the accumulation of protein aggregates. METHODS Proteins associated with endocytosis, lysosomal function, and the ubiquitin-proteasome system were identified in the cerebrospinal fluid (CSF) and targeted by combining solid-phase extraction and parallel reaction monitoring mass spectrometry. In total, 50 peptides from 18 proteins were quantified in three cross-sectional cohorts including AD (N = 61), PD (N = 21), prodromal AD (N = 10), stable mild cognitive impairment (N = 15), and controls (N = 68). RESULTS A pilot study, including subjects selected based on their AD CSF core biomarker concentrations, showed increased concentrations of several targeted proteins in subjects with core biomarker levels indicating AD pathology compared to controls. Next, in a clinically characterized cohort, lower concentrations in CSF of proteins in PD were found compared to subjects with prodromal AD. Further investigation in an additional clinical study again revealed lower concentrations in CSF of proteins in PD compared to controls and AD. CONCLUSION In summary, significantly different peptide CSF concentrations were identified from proteins AP2B1, C9, CTSB, CTSF, GM2A, LAMP1, LAMP2, TCN2, and ubiquitin. Proteins found to have altered concentrations in more than one study were AP2B1, CTSB, CTSF, GM2A, LAMP2, and ubiquitin. Interestingly, given the genetic implication of lysosomal function in PD, we did identify the CSF concentrations of CTSB, CTSF, GM2A, and LAMP2 to be altered. However, we also found differences in proteins associated with endocytosis (AP2B1) and the ubiquitin-proteasome system (ubiquitin). No difference in any peptide CSF concentration was found in clinically characterized subjects with AD compared to controls. In conclusion, CSF analyses of subjects with PD suggest a general lysosomal dysfunction, which resonates well with recent genetic findings, while such changes are minor or absent in AD.
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Affiliation(s)
- Simon Sjödin
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, House V3, SU/Mölndal, SE-43180, Mölndal, Sweden.
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.
| | - Gunnar Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, House V3, SU/Mölndal, SE-43180, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Annika Öhrfelt
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, House V3, SU/Mölndal, SE-43180, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Lucilla Parnetti
- Laboratory of Clinical Neurochemistry, Neurology Clinic, University of Perugia, Perugia, Italy
| | - Silvia Paciotti
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
- Laboratory of Clinical Neurochemistry, Department of Medicine, University of Perugia, Perugia, Italy
| | - Oskar Hansson
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
- Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - John Hardy
- Department of Molecular Neuroscience, University College London Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, UK
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, House V3, SU/Mölndal, SE-43180, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, House V3, SU/Mölndal, SE-43180, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Molecular Neuroscience, University College London Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, UK
| | - Ann Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, House V3, SU/Mölndal, SE-43180, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
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Brinkmalm A, Portelius E, Brinkmalm G, Pannee J, Dahlén R, Gobom J, Blennow K, Zetterberg H. Fluid-based proteomics targeted on pathophysiological processes and pathologies in neurodegenerative diseases. J Neurochem 2018; 151:417-434. [PMID: 30238462 DOI: 10.1111/jnc.14594] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 07/05/2018] [Accepted: 09/15/2018] [Indexed: 12/12/2022]
Abstract
Neurodegenerative dementias constitute a broad group of diseases in which abnormally folded proteins accumulate in specific brain regions and result in tissue reactions that eventually cause neuronal dysfunction and degeneration. Depending on where in the brain this happens, symptoms appear which may be used to classify the disorders on clinical grounds. However, brain changes in neurodegenerative dementias start to accumulate many years prior to symptom onset and there is a poor correlation between the clinical picture and what pathology that is the most likely to cause it. Thus, novel drug candidates having disease-modifying effects that is targeting the underlying pathology and changes the course of the disease needs to be defined using objective biomarker-based measures since the clinical symptoms are often non-specific and overlap between different disorders. Furthermore, the treatment should ideally be initiated as soon as symptoms are evident or when biomarkers confirm an underlying pathology (pre-clinical phase of the disease) to reduce irreversible damage to, for example, neurons, synapses and axons. Clinical trials in the pre-clinical phase bring a greater importance to biomarkers since by definition the clinical effects are difficult or slow to discern in a population that is not yet clinically affected. Here, we discuss neuropathological changes that may underlie neurodegenerative dementias, including how they can be detected and quantified using currently available biofluid-based biomarkers and how more of them could be identified using targeted proteomics approaches. This article is part of the special issue "Proteomics".
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Affiliation(s)
- Ann Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Erik Portelius
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Gunnar Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Josef Pannee
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Rahil Dahlén
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Johan Gobom
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK.,UK Dementia Research Institute at UCL, London, UK
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Sjödin S, Hansson O, Öhrfelt A, Brinkmalm G, Zetterberg H, Brinkmalm A, Blennow K. Mass Spectrometric Analysis of Cerebrospinal Fluid Ubiquitin in Alzheimer's Disease and Parkinsonian Disorders. Proteomics Clin Appl 2017; 11:1700100. [PMID: 28972305 PMCID: PMC5765402 DOI: 10.1002/prca.201700100] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/01/2017] [Indexed: 01/13/2023]
Abstract
PURPOSE Dysfunctional proteostasis, with decreased protein degradation and an accumulation of ubiquitin into aggregated protein inclusions, is a feature of neurodegenerative diseases. Identifying new potential biomarkers in cerebrospinal fluid (CSF) reflecting this process could contribute important information on pathophysiology. EXPERIMENTAL DESIGN A developed method combining SPE and PRM-MS is employed to monitor the concentration of ubiquitin in CSF from subjects with Alzheimer's disease (AD), Parkinson's disease (PD), and progressive supranuclear palsy (PSP). Four independent cross-sectional studies are conducted, studies 1-4, including controls (n = 86) and participants with AD (n = 60), PD (n = 15), and PSP (n = 11). RESULTS The method shows a repeatability and intermediate precision not exceeding 6.1 and 7.9%, respectively. The determined LOD is 0.1 nm and the LOQ range between 0.625 and 80 nm. The CSF ubiquitin concentration is 1.2-1.5-fold higher in AD patients compared with controls in the three independent AD-control studies (Study 1, p < 0.001; Study 2, p < 0.001; and Study 3, p = 0.003). In the fourth study, there is no difference in PD or PSP, compared to controls. CONCLUSION AND CLINICAL RELEVANCE CSF ubiquitin may reflect dysfunctional proteostasis in AD. The described method can be used for further exploration of ubiquitin as a potential biomarker in neurodegenerative diseases.
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Affiliation(s)
- Simon Sjödin
- Department of Psychiatry and NeurochemistryInstitute of Neuroscience and PhysiologyThe Sahlgrenska Academy at University of GothenburgMölndalSweden
| | - Oskar Hansson
- Clinical Memory Research UnitDepartment of Clinical Sciences MalmöLund UniversityLundSweden
- Memory ClinicSkåne University HospitalMalmöSweden
| | - Annika Öhrfelt
- Department of Psychiatry and NeurochemistryInstitute of Neuroscience and PhysiologyThe Sahlgrenska Academy at University of GothenburgMölndalSweden
| | - Gunnar Brinkmalm
- Department of Psychiatry and NeurochemistryInstitute of Neuroscience and PhysiologyThe Sahlgrenska Academy at University of GothenburgMölndalSweden
| | - Henrik Zetterberg
- Department of Psychiatry and NeurochemistryInstitute of Neuroscience and PhysiologyThe Sahlgrenska Academy at University of GothenburgMölndalSweden
- Clinical Neurochemistry LaboratorySahlgrenska University HospitalMölndalSweden
- Department of Molecular NeuroscienceUniversity College London Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLLondonUK
| | - Ann Brinkmalm
- Department of Psychiatry and NeurochemistryInstitute of Neuroscience and PhysiologyThe Sahlgrenska Academy at University of GothenburgMölndalSweden
- Clinical Neurochemistry LaboratorySahlgrenska University HospitalMölndalSweden
| | - Kaj Blennow
- Department of Psychiatry and NeurochemistryInstitute of Neuroscience and PhysiologyThe Sahlgrenska Academy at University of GothenburgMölndalSweden
- Clinical Neurochemistry LaboratorySahlgrenska University HospitalMölndalSweden
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Jellinger KA. Potential clinical utility of multiple system atrophy biomarkers. Expert Rev Neurother 2017; 17:1189-1208. [DOI: 10.1080/14737175.2017.1392239] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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10
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Bastos P, Ferreira R, Manadas B, Moreira PI, Vitorino R. Insights into the human brain proteome: Disclosing the biological meaning of protein networks in cerebrospinal fluid. Crit Rev Clin Lab Sci 2017; 54:185-204. [PMID: 28393582 DOI: 10.1080/10408363.2017.1299682] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cerebrospinal fluid (CSF) is an excellent source of biological information regarding the nervous system, once it is in close contact and accurately reflects alterations in this system. Several studies have analyzed differential protein profiles of CSF samples between healthy and diseased human subjects. However, the pathophysiological mechanisms and how CSF proteins relate to diseases are still poorly known. By applying bioinformatics tools, we attempted to provide new insights on the biological and functional meaning of proteomics data envisioning the identification of putative disease biomarkers. Bioinformatics analysis of data retrieved from 99 mass spectrometry (MS)-based studies on CSF profiling highlighted 1985 differentially expressed proteins across 49 diseases. A large percentage of the modulated proteins originate from exosome vesicles, and the majority are involved in either neuronal cell growth, development, maturation, migration, or neurotransmitter-mediated cellular communication. Nevertheless, some diseases present a unique CSF proteome profile, which were critically analyzed in the present study. For instance, 48 proteins were found exclusively upregulated in the CSF of patients with Alzheimer's disease and are mainly involved in steroid esterification and protein activation cascade processes. A higher number of exclusively upregulated proteins were found in the CSF of patients with multiple sclerosis (76 proteins) and with bacterial meningitis (70 proteins). Whereas in multiple sclerosis, these proteins are mostly involved in the regulation of RNA metabolism and apoptosis, in bacterial meningitis the exclusively upregulated proteins participate in inflammation and antibacterial humoral response, reflecting disease pathogenesis. The exploration of the contribution of exclusively upregulated proteins to disease pathogenesis will certainly help to envision potential biomarkers in the CSF for the clinical management of nervous system diseases.
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Affiliation(s)
- Paulo Bastos
- a Department of Chemistry , University of Aveiro , Aveiro , Portugal.,b Department of Medical Sciences , Institute for Biomedicine - iBiMED, University of Aveiro , Aveiro , Portugal
| | - Rita Ferreira
- c QOPNA, Department of Chemistry , University of Aveiro , Aveiro , Portugal
| | - Bruno Manadas
- d CNC, Center for Neuroscience and Cell Biology, University of Coimbra , Coimbra , Portugal
| | - Paula I Moreira
- d CNC, Center for Neuroscience and Cell Biology, University of Coimbra , Coimbra , Portugal.,e Laboratory of Physiology, Faculty of Medicine , University of Coimbra , Coimbra , Portugal
| | - Rui Vitorino
- b Department of Medical Sciences , Institute for Biomedicine - iBiMED, University of Aveiro , Aveiro , Portugal.,f Departmento de Cirurgia e Fisiologia, Faculdade de Medicina , Unidade de Investigação Cardiovascular, Universidade do Porto , Porto , Portugal
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11
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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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12
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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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13
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Andersen AD, Binzer M, Stenager E, Gramsbergen JB. Cerebrospinal fluid biomarkers for Parkinson's disease - a systematic review. Acta Neurol Scand 2017; 135:34-56. [PMID: 26991855 DOI: 10.1111/ane.12590] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2016] [Indexed: 12/14/2022]
Abstract
Diagnosis of Parkinson's disease (PD) relies on clinical history and physical examination, but misdiagnosis is common in early stages. Identification of biomarkers for PD may allow early and more precise diagnosis and monitoring of dopamine replacement strategies and disease modifying treatments. Developments in analytical chemistry allow the detection of large numbers of molecules in plasma or cerebrospinal fluid, associated with the pathophysiology or pathogenesis of PD. This systematic review includes cerebrospinal fluid biomarker studies focusing on different disease pathways: oxidative stress, neuroinflammation, lysosomal dysfunction and proteins involved in PD and other neurodegenerative disorders, focusing on four clinical domains: their ability to (1) distinguish PD from healthy subjects and other neurodegenerative disorders as well as their relation to (2) disease duration after initial diagnosis, (3) severity of disease (motor symptoms) and (4) cognitive dysfunction. Oligomeric alpha-synuclein might be helpful in the separation of PD from controls. Through metabolomics, changes in purine and tryptophan metabolism have been discovered in patients with PD. Neurofilament light chain (NfL) has a significant role in distinguishing PD from other neurodegenerative diseases. Several oxidative stress markers are related to disease severity, with the antioxidant urate also having a prognostic value in terms of disease severity. Increased levels of amyloid and tau-proteins correlate with cognitive decline and may have prognostic value for cognitive deficits in PD. In the future, larger longitudinal studies, corroborating previous research on viable biomarker candidates or using metabolomics identifying a vast amount of potential biomarkers, could be a good approach.
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Affiliation(s)
- A. D. Andersen
- Department of Neurology; Hospital of Southern Jutland; Sønderborg Denmark
- Institute of Regional Health Research; University of Southern Denmark; Odense Denmark
- Focused Research Group in Neurology; Hospital of Southern Jutland; Sønderborg Denmark
| | - M. Binzer
- Institute of Regional Health Research; University of Southern Denmark; Odense Denmark
- Focused Research Group in Neurology; Hospital of Southern Jutland; Sønderborg Denmark
| | - E. Stenager
- Institute of Regional Health Research; University of Southern Denmark; Odense Denmark
- Focused Research Group in Neurology; Hospital of Southern Jutland; Sønderborg Denmark
- The Multiple Sclerosis Clinic of Southern Jutland; (Vejle, Sonderborg, Esbjerg) Denmark
| | - J. B. Gramsbergen
- Institute of Molecular Medicine, Neurobiological Research; University of Southern Denmark; Odense Denmark
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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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15
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Laurens B, Constantinescu R, Freeman R, Gerhard A, Jellinger K, Jeromin A, Krismer F, Mollenhauer B, Schlossmacher MG, Shaw LM, Verbeek MM, Wenning GK, Winge K, Zhang J, Meissner WG. Fluid biomarkers in multiple system atrophy: A review of the MSA Biomarker Initiative. Neurobiol Dis 2015; 80:29-41. [PMID: 25982836 DOI: 10.1016/j.nbd.2015.05.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 04/29/2015] [Accepted: 05/08/2015] [Indexed: 01/10/2023] Open
Abstract
Despite growing research efforts, no reliable biomarker currently exists for the diagnosis and prognosis of multiple system atrophy (MSA). Such biomarkers are urgently needed to improve diagnostic accuracy, prognostic guidance and also to serve as efficacy measures or surrogates of target engagement for future clinical trials. We here review candidate fluid biomarkers for MSA and provide considerations for further developments and harmonization of standard operating procedures. A PubMed search was performed until April 24, 2015 to review the literature with regard to candidate blood and cerebrospinal fluid (CSF) biomarkers for MSA. Abstracts of 1760 studies were retrieved and screened for eligibility. The final list included 60 studies assessing fluid biomarkers in patients with MSA. Most studies have focused on alpha-synuclein, markers of axonal degeneration or catecholamines. Their results suggest that combining several CSF fluid biomarkers may be more successful than using single markers, at least for the diagnosis. Currently, the clinically most useful markers may comprise a combination of the light chain of neurofilament (which is consistently elevated in MSA compared to controls and Parkinson's disease), metabolites of the catecholamine pathway and proteins such as α-synuclein, DJ-1 and total-tau. Beyond future efforts in biomarker discovery, the harmonization of standard operating procedures will be crucial for future success.
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Affiliation(s)
- Brice Laurens
- Service de Neurologie, CHU de Bordeaux, F-33076 Bordeaux, France
| | - Radu Constantinescu
- Department of Neurology, Sahlgrenska University Hospital, 413 45 Göteborg, Sweden
| | - Roy Freeman
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston
| | - Alexander Gerhard
- Institute of Brain Behaviour and Mental Heath, University of Manchester, UK
| | - Kurt Jellinger
- Institute of Clinical Neurobiology, Kenyongasse 18, A-1070 Vienna, Austria
| | | | - Florian Krismer
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik, Kassel, Germany and Department of Neuropathology, University Medical Center Goettingen, Germany
| | - Michael G Schlossmacher
- Program in Neuroscience, The Ottawa Hospital, University of Ottawa Brain and Mind Research Institute, Ottawa, Ontario, Canada
| | - Leslie M Shaw
- Perelman School of Medicine, University of Pennsylvania
| | - Marcel M Verbeek
- Department of Neurology, Parkinson Center, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, the Netherlands; Department of Laboratory Medicine, Parkinson Center, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Gregor K Wenning
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Kristian Winge
- Department of Neurology, Bispebjerg University Hospital, Copenhagen, Denmark
| | - Jing Zhang
- Department of Pathology, University of WA, Seattle, USA
| | - Wassilios G Meissner
- Service de Neurologie, CHU de Bordeaux, F-33076 Bordeaux, France; Centre de référence atrophie multisystématisée, CHU de Bordeaux, F-33076 Bordeaux, France; Univ. de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, F-33076 Bordeaux, France; CNRS, Institut des Maladies Neurodégénératives, UMR 5293, F-33076 Bordeaux, France.
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16
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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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17
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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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18
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Oeckl P, Steinacker P, Feneberg E, Otto M. Cerebrospinal fluid proteomics and protein biomarkers in frontotemporal lobar degeneration: Current status and future perspectives. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:757-68. [PMID: 25526887 DOI: 10.1016/j.bbapap.2014.12.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 11/18/2014] [Accepted: 12/11/2014] [Indexed: 12/13/2022]
Abstract
Frontotemporal lobar degeneration (FTLD) comprises a spectrum of rare neurodegenerative diseases with an estimated prevalence of 15-22 cases per 100,000 persons including the behavioral variant of frontotemporal dementia (bvFTD), progressive non-fluent aphasia (PNFA), semantic dementia (SD), FTD with motor neuron disease (FTD-MND), progressive supranuclear palsy (PSP) and corticobasal syndrome (CBS). The pathogenesis of the diseases is still unclear and clinical diagnosis of FTLD is hampered by overlapping symptoms within the FTLD subtypes and with other neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). Intracellular protein aggregates in the brain are a major hallmark of FTLD and implicate alterations in protein metabolism or function in the disease's pathogenesis. Cerebrospinal fluid (CSF) which surrounds the brain can be used to study changes in neurodegenerative diseases and to identify disease-related mechanisms or neurochemical biomarkers for diagnosis. In the present review, we will give an overview of the current literature on proteomic studies in CSF of FTLD patients. Reports of targeted and unbiased proteomic approaches are included and the results are discussed in regard of their informative value about disease pathology and the suitability to be used as diagnostic biomarkers. Finally, we will give some future perspectives on CSF proteomics and a list of candidate biomarkers which might be interesting for validation in further studies. This article is part of a Special Issue entitled: Neuroproteomics: Applications in neuroscience and neurology.
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Affiliation(s)
- Patrick Oeckl
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081 Ulm, Germany.
| | - Petra Steinacker
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081 Ulm, Germany.
| | - Emily Feneberg
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081 Ulm, Germany.
| | - Markus Otto
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081 Ulm, Germany.
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19
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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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20
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Oeckl P, Steinacker P, von Arnim CAF, Straub S, Nagl M, Feneberg E, Weishaupt JH, Ludolph AC, Otto M. Intact protein analysis of ubiquitin in cerebrospinal fluid by multiple reaction monitoring reveals differences in Alzheimer's disease and frontotemporal lobar degeneration. J Proteome Res 2014; 13:4518-25. [PMID: 25091646 DOI: 10.1021/pr5006058] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The impairment of the ubiquitin-proteasome system (UPS) is thought to be an early event in neurodegeneration, and monitoring UPS alterations might serve as a disease biomarker. Our aim was to establish an alternate method to antibody-based assays for the selective measurement of free monoubiquitin in cerebrospinal fluid (CSF). Free monoubiquitin was measured with liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MS/MS) in CSF of patients with Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), behavioral variant of frontotemporal dementia (bvFTD), Creutzfeldt-Jakob disease (CJD), Parkinson's disease (PD), primary progressive aphasia (PPA), and progressive supranuclear palsy (PSP). The LC-MS/MS method showed excellent intra- and interassay precision (4.4-7.4% and 4.9-10.3%) and accuracy (100-107% and 100-106%). CSF ubiquitin concentration was increased compared with that of controls (33.0 ± 9.7 ng/mL) in AD (47.5 ± 13.1 ng/mL, p < 0.05) and CJD patients (171.5 ± 103.5 ng/mL, p < 0.001) but not in other neurodegenerative diseases. Receiver operating characteristic curve (ROC) analysis of AD vs control patients revealed an area under the curve (AUC) of 0.832, and the specificity and sensitivity were 75 and 75%, respectively. ROC analysis of AD and FTLD patients yielded an AUC of 0.776, and the specificity and sensitivity were 53 and 100%, respectively. In conclusion, our LC-MS/MS method may facilitate ubiquitin determination to a broader community and might help to discriminate AD, CJD, and FTLD patients.
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Affiliation(s)
- Patrick Oeckl
- Department of Neurology, Ulm University Hospital , Oberer Eselsberg 45, 89081 Ulm, Germany
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21
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Liu Z, Yuan Z, Zhao Q. SELDI-TOF-MS proteomic profiling of serum, urine, and amniotic fluid in neural tube defects. PLoS One 2014; 9:e103276. [PMID: 25054433 PMCID: PMC4108413 DOI: 10.1371/journal.pone.0103276] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/29/2014] [Indexed: 12/13/2022] Open
Abstract
Neural tube defects (NTDs) are common birth defects, whose specific biomarkers are needed. The purpose of this pilot study is to determine whether protein profiling in NTD-mothers differ from normal controls using SELDI-TOF-MS. ProteinChip Biomarker System was used to evaluate 82 maternal serum samples, 78 urine samples and 76 amniotic fluid samples. The validity of classification tree was then challenged with a blind test set including another 20 NTD-mothers and 18 controls in serum samples, and another 19 NTD-mothers and 17 controls in urine samples, and another 20 NTD-mothers and 17 controls in amniotic fluid samples. Eight proteins detected in serum samples were up-regulated and four proteins were down-regulated in the NTD group. Four proteins detected in urine samples were up-regulated and one protein was down-regulated in the NTD group. Six proteins detected in amniotic fluid samples were up-regulated and one protein was down-regulated in the NTD group. The classification tree for serum samples separated NTDs from healthy individuals, achieving a sensitivity of 91% and a specificity of 97% in the training set, and achieving a sensitivity of 90% and a specificity of 97% and a positive predictive value of 95% in the test set. The classification tree for urine samples separated NTDs from controls, achieving a sensitivity of 95% and a specificity of 94% in the training set, and achieving a sensitivity of 89% and a specificity of 82% and a positive predictive value of 85% in the test set. The classification tree for amniotic fluid samples separated NTDs from controls, achieving a sensitivity of 93% and a specificity of 89% in the training set, and achieving a sensitivity of 90% and a specificity of 88% and a positive predictive value of 90% in the test set. These suggest that SELDI-TOF-MS is an additional method for NTDs pregnancies detection.
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Affiliation(s)
- Zhenjiang Liu
- Department of Pediatric Surgery, The Shengjing Hospital, China Medical University, Heping District, Shenyang City, Liaoning Province, People’s Republic of China
- * E-mail:
| | - Zhengwei Yuan
- Department of Pediatric Surgery, The Shengjing Hospital, China Medical University, Heping District, Shenyang City, Liaoning Province, People’s Republic of China
| | - Qun Zhao
- Department of Pediatric Surgery, The Shengjing Hospital, China Medical University, Heping District, Shenyang City, Liaoning Province, People’s Republic of China
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22
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Guldbrandsen A, Vethe H, Farag Y, Oveland E, Garberg H, Berle M, Myhr KM, Opsahl JA, Barsnes H, Berven FS. In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR). Mol Cell Proteomics 2014; 13:3152-63. [PMID: 25038066 PMCID: PMC4223498 DOI: 10.1074/mcp.m114.038554] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this study, the human cerebrospinal fluid (CSF) proteome was mapped using three different strategies prior to Orbitrap LC-MS/MS analysis: SDS-PAGE and mixed mode reversed phase-anion exchange for mapping the global CSF proteome, and hydrazide-based glycopeptide capture for mapping glycopeptides. A maximal protein set of 3081 proteins (28,811 peptide sequences) was identified, of which 520 were identified as glycoproteins from the glycopeptide enrichment strategy, including 1121 glycopeptides and their glycosylation sites. To our knowledge, this is the largest number of identified proteins and glycopeptides reported for CSF, including 417 glycosylation sites not previously reported. From parallel plasma samples, we identified 1050 proteins (9739 peptide sequences). An overlap of 877 proteins was found between the two body fluids, whereas 2204 proteins were identified only in CSF and 173 only in plasma. All mapping results are freely available via the new CSF Proteome Resource (http://probe.uib.no/csf-pr), which can be used to navigate the CSF proteome and help guide the selection of signature peptides in targeted quantitative proteomics.
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Affiliation(s)
- Astrid Guldbrandsen
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Heidrun Vethe
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Yehia Farag
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; ¶Department of Informatics, University of Bergen, Bergen, Norway
| | - Eystein Oveland
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway; ‖Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hilde Garberg
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Magnus Berle
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; **Surgical Clinic, Haukeland University Hospital, Bergen, Norway
| | - Kjell-Morten Myhr
- §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway; ‡‡Norwegian Multiple Sclerosis Registry and Biobank, Haukeland University Hospital, Bergen, Norway
| | - Jill A Opsahl
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway; §§Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway.
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You J, Willcox MD, Madigan MC, Wasinger V, Schiller B, Walsh BJ, Graham PH, Kearsley JH, Li Y. Tear fluid protein biomarkers. Adv Clin Chem 2014; 62:151-96. [PMID: 24772667 DOI: 10.1016/b978-0-12-800096-0.00004-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The tear film covers and protects the ocular surface. It contains various molecules including a large variety of proteins. The protein composition of the tear fluid can change with respect to various local and systemic diseases. Prior to the advent of the proteomic era, tear protein analysis was limited to a few analytical techniques, the most common of which was immunoelectrophoresis, an approach dependent on antibody availability. Using proteomics, hundreds of tear proteins could potentially be identified and subsequently studied. Although detection of low-abundance proteins in the complex tear proteome remains a challenge, advances in sample fractionation and mass spectrometry have greatly enhanced our ability to detect these proteins. With increasing proteomic applications, tears show great potential as biomarkers in the development of clinical assays for various human diseases. In this chapter, we discuss the structure and functions of the tear film and methods for its collection. We also summarize potential tear protein biomarkers identified using proteomic techniques for both ocular and systemic diseases. Finally, modern proteomic techniques for tear biomarker research and future challenges are explored.
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Demartini DR, Schilling LP, da Costa JC, Carlini CR. Alzheimer's and Parkinson's diseases: an environmental proteomic point of view. J Proteomics 2014; 104:24-36. [PMID: 24751585 DOI: 10.1016/j.jprot.2014.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/07/2014] [Accepted: 04/10/2014] [Indexed: 11/25/2022]
Abstract
Alzheimer's and Parkinson's diseases are severe neurodegenerative conditions triggered by complex biochemical routes. Many groups are currently pursuing the search for valuable biomarkers to either perform early diagnostic or to follow the disease's progress. Several studies have reported relevant findings regarding environmental issues and the progression of such diseases. Here the etiology and mechanisms of these diseases are briefly reviewed. Approaches that might reveal candidate biomarkers and environmental stressors associated to the diseases were analyzed under a proteomic perspective. This article is part of a Special Issue entitled: Environmental and structural proteomics.
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Affiliation(s)
- Diogo Ribeiro Demartini
- Center of Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves 9500, Prédio 43431, Sala 214, 91501-970 Porto Alegre, RS, Brazil.
| | - Lucas Porcello Schilling
- Brain Institute of Rio Grande do Sul, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga 6690, 90610-000 Porto Alegre, RS, Brazil
| | - Jaderson Costa da Costa
- Brain Institute of Rio Grande do Sul, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga 6690, 90610-000 Porto Alegre, RS, Brazil.
| | - Célia Regina Carlini
- Center of Biotechnology, Federal University of Rio Grande do Sul, Av. Bento Gonçalves 9500, Prédio 43431, Sala 214, 91501-970 Porto Alegre, RS, Brazil; Brain Institute of Rio Grande do Sul, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga 6690, 90610-000 Porto Alegre, RS, Brazil
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25
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Classical MALDI-MS versus CE-based ESI-MS proteomic profiling in urine for clinical applications. Bioanalysis 2014; 6:247-66. [DOI: 10.4155/bio.13.313] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human urine is an attractive and informative biofluid for medical diagnosis, which has been shown to reflect the (patho)-physiology of not only the urogenital system, but also others such as the cardiovascular system. For this reason, many studies have concentrated on the study of the urine proteome, aiming to find relevant biomarkers that could be applied in a clinical setting. However, this goal can only be achieved after reliable quantitative and qualitative analysis of the urinary proteome. In the last two decades, MS-based platforms have evolved to become indispensable tools for biomarker research. In this review, we will present and compare two of the most clinically relevant analytical platforms that have been used for the study of the urinary proteome, namely CE-based ESI-MS and classical MALDI-MS. These platforms, although not directly comparable, have been extensively used in proteomic profiling and therefore their comparison is fundamentally relevant to this field.
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26
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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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Constantinescu R, Mondello S. Cerebrospinal fluid biomarker candidates for parkinsonian disorders. Front Neurol 2013; 3:187. [PMID: 23346074 PMCID: PMC3549487 DOI: 10.3389/fneur.2012.00187] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 12/21/2012] [Indexed: 01/21/2023] Open
Abstract
The Parkinsonian disorders are a large group of neurodegenerative diseases including idiopathic Parkinson’s disease (PD) and atypical Parkinsonian disorders (APD), such as multiple system atrophy, progressive supranuclear palsy, corticobasal degeneration, and dementia with Lewy bodies. The etiology of these disorders is not known although it is considered to be a combination of genetic and environmental factors. One of the greatest obstacles for developing efficacious disease-modifying treatment strategies is the lack of biomarkers. Reliable biomarkers are needed for early and accurate diagnosis, to measure disease progression, and response to therapy. In this review several of the most promising cerebrospinal biomarker candidates are discussed. Alpha-synuclein seems to be intimately involved in the pathogenesis of synucleinopathies and its levels can be measured in the cerebrospinal fluid and in plasma. In a similar way, tau protein accumulation seems to be involved in the pathogenesis of tauopathies. Urate, a potent antioxidant, seems to be associated to the risk of developing PD and with its progression. Neurofilament light chain levels are increased in APD compared with PD and healthy controls. The new “omics” techniques are potent tools offering new insights in the patho-etiology of these disorders. Some of the difficulties encountered in developing biomarkers are discussed together with future perspectives.
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Affiliation(s)
- Radu Constantinescu
- Department of Neurology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg Gothenburg, Sweden
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28
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Mattison HA, Stewart T, Zhang J. Applying bioinformatics to proteomics: is machine learning the answer to biomarker discovery for PD and MSA? Mov Disord 2012; 27:1595-7. [PMID: 23115026 DOI: 10.1002/mds.25189] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 08/05/2012] [Indexed: 11/10/2022] Open
Abstract
Bioinformatics tools are increasingly being applied to proteomic data to facilitate the identification of biomarkers and classification of patients. In the June, 2012 issue, Ishigami et al. used principal component analysis (PCA) to extract features and support vector machine (SVM) to differentiate and classify cerebrospinal fluid (CSF) samples from two small cohorts of patients diagnosed with either Parkinson's disease (PD) or multiple system atrophy (MSA) based on differences in the patterns of peaks generated with matrix-assisted desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). PCA accurately segregated patients with PD and MSA from controls when the cohorts were combined, but did not perform well when segregating PD from MSA. On the other hand, SVM, a machine learning classification model, correctly classified the samples from patients with early PD or MSA, and the peak at m/z 6250 was identified as a strong contributor to the ability of SVM to distinguish the proteomic profiles of either cohort when trained on one cohort. This study, while preliminary, provides promising results for the application of bioinformatics tools to proteomic data, an approach that may eventually facilitate the ability of clinicians to differentiate and diagnose closely related parkinsonian disorders.
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Affiliation(s)
- Hayley A Mattison
- Department of Pathology, University of Washington, Seattle, Washington 98104, USA
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29
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Angel TE, Jacobs JM, Smith RP, Pasternack MS, Elias S, Gritsenko MA, Shukla A, Gilmore EC, McCarthy C, Camp DG, Smith RD, Warren HS. Cerebrospinal fluid proteome of patients with acute Lyme disease. J Proteome Res 2012; 11:4814-22. [PMID: 22900834 DOI: 10.1021/pr300577p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
During acute Lyme disease, bacteria can disseminate to the central nervous system (CNS), leading to the development of meningitis and other neurologic symptoms. Here we have analyzed pooled cerebrospinal fluid (CSF) allowing a deep view into the proteome for patients diagnosed with early disseminated Lyme disease and CSF inflammation. Additionally, we analyzed individual patient samples and quantified differences in protein abundance employing label-free quantitative mass spectrometry-based methods. We identified 108 proteins that differ significantly in abundance in patients with acute Lyme disease from controls. Comparison between infected patients and control subjects revealed differences in proteins in the CSF associated with cell death localized to brain synapses and others that likely originate from brain parenchyma.
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Affiliation(s)
- Thomas E Angel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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Ishigami N, Tokuda T, Ikegawa M, Komori M, Kasai T, Kondo T, Matsuyama Y, Nirasawa T, Thiele H, Tashiro K, Nakagawa M. Cerebrospinal fluid proteomic patterns discriminate Parkinson's disease and multiple system atrophy. Mov Disord 2012; 27:851-7. [DOI: 10.1002/mds.24994] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 02/27/2012] [Accepted: 03/09/2012] [Indexed: 11/05/2022] Open
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Angel TE, Jacobs JM, Spudich SS, Gritsenko MA, Fuchs D, Liegler T, Zetterberg H, Camp DG, Price RW, Smith RD. The cerebrospinal fluid proteome in HIV infection: change associated with disease severity. Clin Proteomics 2012; 9:3. [PMID: 22433316 PMCID: PMC3353874 DOI: 10.1186/1559-0275-9-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 03/20/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Central nervous system (CNS) infection is a nearly universal feature of untreated systemic HIV infection with a clinical spectrum that ranges from chronic asymptomatic infection to severe cognitive and motor dysfunction. Analysis of cerebrospinal fluid (CSF) has played an important part in defining the character of this evolving infection and response to treatment. To further characterize CNS HIV infection and its effects, we applied advanced high-throughput proteomic methods to CSF to identify novel proteins and their changes with disease progression and treatment. RESULTS After establishing an accurate mass and time (AMT) tag database containing 23,141 AMT tags for CSF peptides, we analyzed 91 CSF samples by LC-MS from 12 HIV-uninfected and 14 HIV-infected subjects studied in the context of initiation of antiretroviral therapy and correlated abundances of identified proteins a) within and between subjects, b) with all other proteins across the entire sample set, and c) with "external" CSF biomarkers of infection (HIV RNA), immune activation (neopterin) and neural injury (neurofilament light chain protein, NFL). We identified a mean of 2,333 +/- 328 (SD) peptides covering 307 +/-16 proteins in the 91 CSF sample set. Protein abundances differed both between and within subjects sampled at different time points and readily separated those with and without HIV infection. Proteins also showed inter-correlations across the sample set that were associated with biologically relevant dynamic processes. One-hundred and fifty proteins showed correlations with the external biomarkers. For example, using a threshold of cross correlation coefficient (Pearson's) ≤ -0.3 and ≥0.3 for potentially meaningful relationships, a total of 99 proteins correlated with CSF neopterin (43 negative and 56 positive correlations) and related principally to neuronal plasticity and survival and to innate immunity. Pathway analysis defined several networks connecting the identified proteins, including one with amyloid precursor protein as a central node. CONCLUSIONS Advanced CSF proteomic analysis enabled the identification of an array of novel protein changes across the spectrum of CNS HIV infection and disease. This initial analysis clearly demonstrated the value of contemporary state-of-the-art proteomic CSF analysis as a discovery tool in HIV infection with likely similar application to other neurological inflammatory and degenerative diseases.
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Affiliation(s)
- Thomas E Angel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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Tufekci KU, Meuwissen R, Genc S, Genc K. Inflammation in Parkinson's disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 88:69-132. [PMID: 22814707 DOI: 10.1016/b978-0-12-398314-5.00004-0] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease that is characterized by the degeneration of dopaminergic neurons in the substantia nigra pars compacta. Inflammatory responses manifested by glial reactions, T cell infiltration, and increased expression of inflammatory cytokines, as well as other toxic mediators derived from activated glial cells, are currently recognized as prominent features of PD. The consistent findings obtained by various animal models of PD suggest that neuroinflammation is an important contributor to the pathogenesis of the disease and may further propel the progressive loss of nigral dopaminergic neurons. Furthermore, although it may not be the primary cause of PD, additional epidemiological, genetic, pharmacological, and imaging evidence support the proposal that inflammatory processes in this specific brain region are crucial for disease progression. Recent in vitro studies, however, have suggested that activation of microglia and subsequently astrocytes via mediators released by injured dopaminergic neurons is involved. However, additional in vivo experiments are needed for a deeper understanding of the mechanisms involved in PD pathogenesis. Further insight on the mechanisms of inflammation in PD will help to further develop alternative therapeutic strategies that will specifically and temporally target inflammatory processes without abrogating the potential benefits derived by neuroinflammation, such as tissue restoration.
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Affiliation(s)
- Kemal Ugur Tufekci
- Department of Neuroscience, Health Science Institute, Dokuz Eylul University, Izmir, Turkey
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Proteomics in Parkinson's disease: An unbiased approach towards peripheral biomarkers and new therapies. J Biotechnol 2011; 156:325-37. [DOI: 10.1016/j.jbiotec.2011.08.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2011] [Revised: 06/24/2011] [Accepted: 08/08/2011] [Indexed: 12/27/2022]
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Biomarkers of Parkinson's disease and Dementia with Lewy bodies. Prog Neurobiol 2011; 95:601-13. [PMID: 21983334 DOI: 10.1016/j.pneurobio.2011.09.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/04/2011] [Accepted: 09/06/2011] [Indexed: 01/22/2023]
Abstract
Parkinson's disease (PD) and Dementia with Lewy bodies (DLB) are progressive and disabling neurodegenerative disorders, in which signs and symptoms overlap with each other and with other neurodegenerative conditions. Currently, diagnosis, measurement of progression, and response to therapeutic intervention rely upon clinical observation. However, there remains a critical need for validated biomarkers in each of these areas. A definitive diagnostic test would improve clinical management and enrollment into clinical trials. An objective measure of progression is vitally important in identifying neuroprotective interventions. Biomarkers may also provide insight into pathogenesis, and might therefore suggest possible novel targets for therapeutic intervention. In addition, certain biomarkers might be of use in monitoring the biochemical and physiological effects of therapeutic interventions. Development of diagnostic biomarkers has focused until recently upon imaging techniques based upon measuring loss of dopamine neurons. Additionally, advances in understanding the genetic contribution to neurodegenerative disorders, in particular in PD, have identified multiple causative genes and risk factors that in some cases may help estimate PD risk. However, recent availability of increasingly sophisticated bioinformatics technology has rendered development of fluid biomarkers feasible, opening the possibility of generally accessible blood or cerebrospinal fluid (CSF) tests that could impact upon diagnosis, management, and research in PD, PDD, and DLB.
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Nyhlén J, Constantinescu R, Zetterberg H. Problems associated with fluid biomarkers for Parkinson's disease. Biomark Med 2011; 4:671-81. [PMID: 20945980 DOI: 10.2217/bmm.10.84] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This article focuses on biochemical markers that may be used in the diagnostics of Parkinson's disease and associated disorders, and to identify early cases and stratify patients into subgroups. We present an updated account of some currently available candidate fluid biomarkers, and discuss their diagnostic performance and limitations. We also discuss some of the general problems with Parkinson's disease biomarkers and possible ways of moving forward. It may be concluded that a diagnostically useful fluid biomarker for Parkinson's disease is yet to be identified. However, some interesting candidates exist and may prove useful in the future, alone or when analyzed together in patterns.
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Affiliation(s)
- Jakob Nyhlén
- Institute of Neuroscience & Physiology, Department of Psychiatry & Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
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