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Yang JC, Chen SP, Wang YF, Chang CH, Chang KH, Fuh JL, Chow LH, Han CL, Chen YJ, Wang SJ. Cerebrospinal Fluid Proteome Map Reveals Molecular Signatures of Reversible Cerebral Vasoconstriction Syndrome. Mol Cell Proteomics 2024; 23:100794. [PMID: 38839039 DOI: 10.1016/j.mcpro.2024.100794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 04/08/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024] Open
Abstract
Reversible cerebral vasoconstriction syndrome (RCVS) is a complex neurovascular disorder characterized by repetitive thunderclap headaches and reversible cerebral vasoconstriction. The pathophysiological mechanism of this mysterious syndrome remains underexplored and there is no clinically available molecular biomarker. To provide insight into the pathogenesis of RCVS, this study reported the first landscape of dysregulated proteome of cerebrospinal fluid (CSF) in patients with RCVS (n = 21) compared to the age- and sex-matched controls (n = 20) using data-independent acquisition mass spectrometry. Protein-protein interaction and functional enrichment analysis were employed to construct functional protein networks using the RCVS proteome. An RCVS-CSF proteome library resource of 1054 proteins was established, which illuminated large groups of upregulated proteins enriched in the brain and blood-brain barrier (BBB). Personalized RCVS-CSF proteomic profiles from 17 RCVS patients and 20 controls reveal proteomic changes involving the complement system, adhesion molecules, and extracellular matrix, which may contribute to the disruption of BBB and dysregulation of neurovascular units. Moreover, an additional validation cohort validated a panel of biomarker candidates and a two-protein signature predicted by machine learning model to discriminate RCVS patients from controls with an area under the curve of 0.997. This study reveals the first RCVS proteome and a potential pathogenetic mechanism of BBB and neurovascular unit dysfunction. It also nominates potential biomarker candidates that are mechanistically plausible for RCVS, which may offer potential diagnostic and therapeutic opportunities beyond the clinical manifestations.
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Affiliation(s)
- Jhih-Ci Yang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Shih-Pin Chen
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan; Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan; Division of Translational Research, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan; Institute of Clinical Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Yen-Feng Wang
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan; Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan; College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chan-Hua Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Department of Chemistry, National Central University, Taoyuan, Taiwan
| | - Kun-Hao Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan; Department of Chemistry, Institute of Chemistry, Academia Sinica, Naitonal Tsing Hua University, Hsinchu, Taiwan
| | - Jong-Ling Fuh
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan; Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan; College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Lok-Hi Chow
- College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Anesthesiology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chia-Li Han
- Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Chemistry, National Taiwan University, Taipei, Taiwan.
| | - Shuu-Jiun Wang
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan; Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan; College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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2
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Kozioł A, Pupek M, Lewandowski Ł. Application of metabolomics in diagnostics and differentiation of meningitis: A narrative review with a critical approach to the literature. Biomed Pharmacother 2023; 168:115685. [PMID: 37837878 DOI: 10.1016/j.biopha.2023.115685] [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: 08/08/2023] [Revised: 09/28/2023] [Accepted: 10/08/2023] [Indexed: 10/16/2023] Open
Abstract
Due to its high mortality rate associated with various life-threatening sequelae, meningitis poses a vital problem in contemporary medicine. Numerous algorithms, many of which were derived with the aid of artificial intelligence, were brought up in a strive for perfection in predicting the status of sepsis-related survival or exacerbation. This review aims to provide key insights on the contextual utilization of metabolomics. The aim of this the metabolomic approach set of methods can be used to investigate both bacterial and host metabolite sets from both the host and its microbes in several types of specimens - even in one's breath, mainly with use of two methods - Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR). Metabolomics, and has been used to elucidate the mechanisms underlying disease development and metabolic identification changes in a wide range of metabolite contents, leading to improved methods of diagnosis, treatment, and prognosis of meningitis. Mass spectrometry (MS) and Nuclear Magnetic Resonance (NMR) are the main analytical platforms used in metabolomics. Its high sensitivity accounts for the usefulness of metabolomics in studies into meningitis, its sequelae, and concomitant comorbidities. Metabolomics approaches are a double-edged sword, due to not only their flexibility, but also - high complexity, as even minor changes in the multi-step methods can have a massive impact on the results. Information on the differential diagnosis of meningitis act as a background in presenting the merits and drawbacks of the use of metabolomics in context of meningeal infections.
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Affiliation(s)
- Agata Kozioł
- Department of Immunochemistry and Chemistry, Wrocław Medical University, M. Skłodowskiej-Curie Street 48/50, 50-369 Wrocław, Poland
| | - Małgorzata Pupek
- Department of Immunochemistry and Chemistry, Wrocław Medical University, M. Skłodowskiej-Curie Street 48/50, 50-369 Wrocław, Poland.
| | - Łukasz Lewandowski
- Department of Medical Biochemistry, Wrocław Medical University, T. Chałubińskiego Street 10, 50-368 Wrocław, Poland
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3
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Gavriilaki M, Papaliagkas V, Stamperna A, Moschou M, Notas K, Papagiannopoulos S, Arnaoutoglou M, Kimiskidis VK. Biomarkers of therapeutic efficacy in adolescents and adults with 5q spinal muscular atrophy: a systematic review. Acta Neurol Belg 2023; 123:1735-1745. [PMID: 35861914 DOI: 10.1007/s13760-022-02028-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/07/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND The therapeutic landscape of spinal muscular atrophy (SMA) was dramatically transformed with the introduction of three disease-modifying therapies (DMTs). A systematic review was performed to assess available evidence regarding quantitative therapeutic biomarkers used in SMA patients older than 11 years under treatment with DMTs. METHODS Latest literature search in MEDLINE, EMBASE, Cochrane databases and gray literature resources was performed in June 2021. Studies reporting only motor function or muscle strength scales or pulmonary function tests were excluded. Primary outcome was the change from baseline score of any serum, cerebrospinal fluid (CSF) or neurophysiologic biomarker examined. RESULTS Database and gray literature search yielded a total of 8050 records. We identified 14 records published from 2019 until 2021 examining 18 putative serum, CSF or neurophysiologic biomarkers along with routine CSF parameters in 295 SMA nusinersen-treated type 2-4 patients older than 11 years of age. There is evidence based on real-world observational studies suggesting that serum creatinine, creatine kinase activity levels along with CSF Αβ42, glial fibrillary acidic protein concentration as well as ulnar compound motor action potential amplitude and single motor unit potential amplitude changes may depict therapeutic response in this population. CONCLUSION This systematic review explored for the first-time biomarkers used to monitor therapeutic efficacy in SMA adolescents and adults treated with DMTs. Research in this area is in its early stages, and our systematic review can facilitate selection of quantitative therapeutic biomarkers that may be used as surrogate measures of treatment efficacy in future trials. PROTOCOL REGISTRATION PROSPERO CRD42021245516.
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Affiliation(s)
- Maria Gavriilaki
- 1st Department of Neurology, School of Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, S. Kyriakidi Str. 1, 546 36, Thessaloniki, Greece.
| | - Vasileios Papaliagkas
- Department of Biomedical Sciences, School of Health Sciences, International Hellenic University, Thessaloniki, Greece
| | - Alexandra Stamperna
- 2nd Department of Pediatrics, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Moschou
- 1st Department of Neurology, School of Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, S. Kyriakidi Str. 1, 546 36, Thessaloniki, Greece
| | - Konstantinos Notas
- Laboratory of Clinical Neurophysiology, School of Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sotirios Papagiannopoulos
- 3rd Department of Neurology, School of Medicine, G. Papanicolaou Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Marianthi Arnaoutoglou
- Laboratory of Clinical Neurophysiology, School of Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Vasilios K Kimiskidis
- 1st Department of Neurology, School of Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, S. Kyriakidi Str. 1, 546 36, Thessaloniki, Greece
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Afridi R, Lee WH, Kim JH, Suk K. Utilizing databases for astrocyte secretome research. Expert Rev Proteomics 2023; 20:371-379. [PMID: 37978891 DOI: 10.1080/14789450.2023.2285311] [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: 06/26/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
INTRODUCTION Astrocytes are the most abundant cell type in the central nervous system (CNS). They play a pivotal role in supporting neuronal function and maintaining homeostasis by releasing a variety of bioactive proteins, collectively known as the astrocyte secretome. Investigating secretome provides insights into the molecular mechanisms underlying astrocyte function and dysfunction, as well as novel strategies to prevent and treat diseases affecting the CNS. AREAS COVERED Proteomics databases are a valuable resource for studying the role of astrocytes in healthy and diseased brain function, as they provide information about gene expression, protein expression, and cellular function. In this review, we discuss existing databases that are useful for astrocyte secretome research. EXPERT OPINION Astrocyte secretomics is a field that is rapidly progressing, yet the availability of dedicated databases is currently limited. To meet the increasing demand for comprehensive omics data in glia research, developing databases specifically focused on astrocyte secretome is crucial. Such databases would allow researchers to investigate the intricate molecular landscape of astrocytes and comprehend their involvement in diverse physiological and pathological processes. Expanding resources through the development of databases dedicated to the astrocyte secretome may facilitate further advancements in this field.
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Affiliation(s)
- Ruqayya Afridi
- Department of Pharmacology, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Won-Ha Lee
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Jong-Heon Kim
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Kyoungho Suk
- Department of Pharmacology, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
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5
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Dayon L, Cominetti O, Affolter M. Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications. Expert Rev Proteomics 2022; 19:131-151. [PMID: 35466824 DOI: 10.1080/14789450.2022.2070477] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids. AREAS COVERED We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics. EXPERT OPINION While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.
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Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
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6
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Klarić TS, Lauc G. The dynamic brain N-glycome. Glycoconj J 2022; 39:443-471. [PMID: 35334027 DOI: 10.1007/s10719-022-10055-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/27/2022] [Accepted: 03/09/2022] [Indexed: 01/17/2023]
Abstract
The attachment of carbohydrates to other macromolecules, such as proteins or lipids, is an important regulatory mechanism termed glycosylation. One subtype of protein glycosylation is asparagine-linked glycosylation (N-glycosylation) which plays a key role in the development and normal functioning of the vertebrate brain. To better understand the role of N-glycans in neurobiology, it's imperative we analyse not only the functional roles of individual structures, but also the collective impact of large-scale changes in the brain N-glycome. The systematic study of the brain N-glycome is still in its infancy and data are relatively scarce. Nevertheless, the prevailing view has been that the neuroglycome is inherently restricted with limited capacity for variation. The development of improved methods for N-glycomics analysis of brain tissue has facilitated comprehensive characterisation of the complete brain N-glycome under various experimental conditions on a larger scale. Consequently, accumulating data suggest that it's more dynamic than previously recognised and that, within a general framework, it has a given capacity to change in response to both intrinsic and extrinsic stimuli. Here, we provide an overview of the many factors that can alter the brain N-glycome, including neurodevelopment, ageing, diet, stress, neuroinflammation, injury, and disease. Given this emerging evidence, we propose that the neuroglycome has a hitherto underappreciated plasticity and we discuss the therapeutic implications of this regarding the possible reversal of pathological changes via interventions. We also briefly review the merits and limitations of N-glycomics as an analytical method before reflecting on some of the outstanding questions in the field.
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Affiliation(s)
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia.,Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
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7
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Wang Y, Liu Y, Chen R, Qiao L. Metabolomic Characterization of Cerebrospinal Fluid from Intracranial Bacterial Infection Pediatric Patients: A Pilot Study. Molecules 2021; 26:molecules26226871. [PMID: 34833963 PMCID: PMC8622478 DOI: 10.3390/molecules26226871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 01/20/2023] Open
Abstract
Intracranial bacterial infection remains a major cause of morbidity and mortality in neurosurgical cases. Metabolomic profiling of cerebrospinal fluid (CSF) holds great promise to gain insights into the pathogenesis of central neural system (CNS) bacterial infections. In this pilot study, we analyzed the metabolites in CSF of CNS infection patients and controls in a pseudo-targeted manner, aiming at elucidating the metabolic dysregulation in response to postoperative intracranial bacterial infection of pediatric cases. Untargeted analysis uncovered 597 metabolites, and screened out 206 differential metabolites in case of infection. Targeted verification and pathway analysis filtered out the glycolysis, amino acids metabolism and purine metabolism pathways as potential pathological pathways. These perturbed pathways are involved in the infection-induced oxidative stress and immune response. Characterization of the infection-induced metabolic changes can provide robust biomarkers of CNS bacterial infection for clinical diagnosis, novel pathways for pathological investigation, and new targets for treatment.
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Affiliation(s)
- Yiwen Wang
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China;
| | - Yu Liu
- Department of Neurosurgery, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai 200062, China;
| | - Ruoping Chen
- Department of Pediatric Neurosurgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
- Correspondence: (R.C.); (L.Q.)
| | - Liang Qiao
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China;
- Correspondence: (R.C.); (L.Q.)
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8
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Greco F, Anastasi F, Pardini LF, Dilillo M, Vannini E, Baroncelli L, Caleo M, McDonnell LA. Longitudinal Bottom-Up Proteomics of Serum, Serum Extracellular Vesicles, and Cerebrospinal Fluid Reveals Candidate Biomarkers for Early Detection of Glioblastoma in a Murine Model. Molecules 2021; 26:5992. [PMID: 34641541 PMCID: PMC8512455 DOI: 10.3390/molecules26195992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/24/2021] [Accepted: 09/30/2021] [Indexed: 12/04/2022] Open
Abstract
Glioblastoma Multiforme (GBM) is a brain tumor with a poor prognosis and low survival rates. GBM is diagnosed at an advanced stage, so little information is available on the early stage of the disease and few improvements have been made for earlier diagnosis. Longitudinal murine models are a promising platform for biomarker discovery as they allow access to the early stages of the disease. Nevertheless, their use in proteomics has been limited owing to the low sample amount that can be collected at each longitudinal time point. Here we used optimized microproteomics workflows to investigate longitudinal changes in the protein profile of serum, serum small extracellular vesicles (sEVs), and cerebrospinal fluid (CSF) in a GBM murine model. Baseline, pre-symptomatic, and symptomatic tumor stages were determined using non-invasive motor tests. Forty-four proteins displayed significant differences in signal intensities during GBM progression. Dysregulated proteins are involved in cell motility, cell growth, and angiogenesis. Most of the dysregulated proteins already exhibited a difference from baseline at the pre-symptomatic stage of the disease, suggesting that early effects of GBM might be detectable before symptom onset.
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Affiliation(s)
- Francesco Greco
- Institute of Life Sciences, Sant’Anna School of Advanced Studies, 56127 Pisa, Italy;
- Fondazione Pisana per la Scienza ONLUS, 56017 San Giuliano Terme, Italy; (F.A.); (L.F.P.); (M.D.)
| | - Federica Anastasi
- Fondazione Pisana per la Scienza ONLUS, 56017 San Giuliano Terme, Italy; (F.A.); (L.F.P.); (M.D.)
- NEST Laboratories, Scuola Normale Superiore, 56127 Pisa, Italy
| | - Luca Fidia Pardini
- Fondazione Pisana per la Scienza ONLUS, 56017 San Giuliano Terme, Italy; (F.A.); (L.F.P.); (M.D.)
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Marialaura Dilillo
- Fondazione Pisana per la Scienza ONLUS, 56017 San Giuliano Terme, Italy; (F.A.); (L.F.P.); (M.D.)
| | - Eleonora Vannini
- CNR, Neuroscience Institute, 56124 Pisa, Italy; (E.V.); (L.B.); (M.C.)
- Fondazione Umberto Veronesi, 20122 Milano, Italy
| | - Laura Baroncelli
- CNR, Neuroscience Institute, 56124 Pisa, Italy; (E.V.); (L.B.); (M.C.)
- IRCCS Fondazione Stella Maris, 56018 Calambrone, Italy
| | - Matteo Caleo
- CNR, Neuroscience Institute, 56124 Pisa, Italy; (E.V.); (L.B.); (M.C.)
- Dipartimento di Scienze Biomediche, Università di Padova, 35131 Padova, Italy
| | - Liam A. McDonnell
- Fondazione Pisana per la Scienza ONLUS, 56017 San Giuliano Terme, Italy; (F.A.); (L.F.P.); (M.D.)
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Schmitt HA, Pich A, Prenzler NK, Lenarz T, Harre J, Staecker H, Durisin M, Warnecke A. Personalized Proteomics for Precision Diagnostics in Hearing Loss: Disease-Specific Analysis of Human Perilymph by Mass Spectrometry. ACS OMEGA 2021; 6:21241-21254. [PMID: 34471729 PMCID: PMC8387986 DOI: 10.1021/acsomega.1c01136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/09/2021] [Indexed: 05/11/2023]
Abstract
Despite a vast amount of data generated by proteomic analysis on cochlear fluid, novel clinically applicable biomarkers of inner ear diseases have not been identified hitherto. The aim of the present study was to analyze the proteome of human perilymph from cochlear implant patients, thereby identifying putative changes of the composition of the cochlear fluid perilymph due to specific diseases. Sampling of human perilymph was performed during cochlear implantation from patients with clinically or radiologically defined inner ear diseases like enlarged vestibular aqueduct (EVA; n = 14), otosclerosis (n = 10), and Ménière's disease (n = 12). Individual proteins were identified by a shotgun proteomics approach and data-dependent acquisition, thereby revealing 895 different proteins in all samples. Based on quantification values, a disease-specific protein distribution in the perilymph was demonstrated. The proteins short-chain dehydrogenase/reductase family 9C member 7 and esterase D were detected in nearly all samples of Ménière's disease patients, but not in samples of patients suffering from EVA and otosclerosis. The presence of both proteins in the inner ear tissue of adult mice and neonatal rats was validated by immunohistochemistry. Whether these proteins have the potential for a biomarker in the perilymph of Ménière's disease patients remains to be elucidated.
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Affiliation(s)
- Heike A. Schmitt
- Department
of Otolaryngology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
- Cluster
of Excellence of the German Research Foundation (DFG; “Deutsche
Forschungsgemeinschaft”) “Hearing4all”, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Andreas Pich
- Core
Facility Proteomics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Nils K. Prenzler
- Department
of Otolaryngology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
- Cluster
of Excellence of the German Research Foundation (DFG; “Deutsche
Forschungsgemeinschaft”) “Hearing4all”, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Thomas Lenarz
- Department
of Otolaryngology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
- Cluster
of Excellence of the German Research Foundation (DFG; “Deutsche
Forschungsgemeinschaft”) “Hearing4all”, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Jennifer Harre
- Department
of Otolaryngology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
- Cluster
of Excellence of the German Research Foundation (DFG; “Deutsche
Forschungsgemeinschaft”) “Hearing4all”, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Hinrich Staecker
- Department
of Otolaryngology, Head and Neck Surgery, University of Kansas School of Medicine, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, United States
| | - Martin Durisin
- Department
of Otolaryngology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
- Cluster
of Excellence of the German Research Foundation (DFG; “Deutsche
Forschungsgemeinschaft”) “Hearing4all”, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Athanasia Warnecke
- Department
of Otolaryngology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
- Cluster
of Excellence of the German Research Foundation (DFG; “Deutsche
Forschungsgemeinschaft”) “Hearing4all”, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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10
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Xu L, Sun H, Zhang Y, Guo Z, Xiao X, Zhou X, Hu K, Sun W, Wang B, Liu W. Proteomic analysis of human frontal and temporal cortex using iTRAQ-based 2D LC-MS/MS. Chin Neurosurg J 2021; 7:27. [PMID: 33952343 PMCID: PMC8101246 DOI: 10.1186/s41016-021-00241-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 03/24/2021] [Indexed: 01/01/2023] Open
Abstract
Background The human brain is the most complex organ in the body, and it is important to have a better understanding of how the protein composition in the brain regions contributes to the pathogenesis of associated neurological disorders. Methods In this study, a comparative analysis of the frontal and temporal cortex proteomes was conducted by isobaric tags of relative and absolute quantification (iTRAQ) labeling and two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS). Brain protein was taken from relatively normal tissue that could not be avoided of damage during emergent surgery of the TBI (traumatic brain injury) patients admitted in Beijing Tiantan Hospital from 2014 to 2017. Eight cases were included. Four frontal lobes and 4 temporal lobes proteome were analyzed and the proteins were quantitated. Gene Ontology (GO), Ingenuity Pathway Analysis (IPA), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were used to analyze the biological function of identified proteins, unchanged proteins, and differentially expressed proteins (DEPs). Results A total number of 2127 protein groups were identified in the frontal and temporal lobe proteomes. A total of 1709 proteins could be quantitated in both the frontal and temporal cortex. Among 90 DEPs, 14 proteins were screened highly expressed in the temporal cortex, including MAPT, SNCG, ATP5IF1, GAP43, HSPE1, STMN1, NDUFS6, LDHB, SNCB, NDUFA7, MRPS36, EPDR1, CISD1, and RALA. In addition, compared to proteins expressed in the frontal cortex, 14 proteins including EDC4, NIT2, VWF, ASTN1, TGM2, SSB, CLU, HBA1, STOM, CRP, LRG1, SAA2, S100A4, and VTN were a low expression in the temporal cortex. The biological process enrichment showed that unchanged proteins between the frontal and temporal cortex mainly take part in regulated exocytosis, axon guidance, and vesicle-mediated transport. The KEGG pathway analysis showed that unchanged proteins between the frontal and temporal cortex mainly take part in oxidative phosphorylation, carbon metabolism, Huntington’s disease, and Parkinson’s disease. Conclusions The majority of proteins are unchanged between the frontal and temporal cortex, and unchanged proteins are closely related to its function. Among DEPs, MATP (tau) is upregulated in the temporal cortex, closely related to Alzheimer’s disease (AD), and is one of the targets for the treatment of AD. CLU is downregulated in the temporal cortex which functions as an extracellular chaperone that prevents aggregation of non-native proteins. It was suggested that the temporal lobe may not be the “functional dumb area” of the traditional view, but could be involved in important neural metabolic circuits. Supplementary Information The online version contains supplementary material available at 10.1186/s41016-021-00241-5.
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Affiliation(s)
- Long Xu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 West Road, South Fourth Ring Road, Beijing, 100070, China.,China National Clinical Research Center for Neurological Diseases (NCRC-ND), Beijing, 100070, China
| | - Haidan Sun
- Core Facility of Instrument, School of Basic Medicine Chinese Academy of Medical Sciences, Institute of Basic Medicine Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, 100005, China
| | - Yang Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 West Road, South Fourth Ring Road, Beijing, 100070, China.,China National Clinical Research Center for Neurological Diseases (NCRC-ND), Beijing, 100070, China
| | - Zhengguang Guo
- Core Facility of Instrument, School of Basic Medicine Chinese Academy of Medical Sciences, Institute of Basic Medicine Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, 100005, China
| | - Xiaoping Xiao
- Core Facility of Instrument, School of Basic Medicine Chinese Academy of Medical Sciences, Institute of Basic Medicine Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, 100005, China
| | - Xin Zhou
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
| | - Kun Hu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
| | - Wei Sun
- Core Facility of Instrument, School of Basic Medicine Chinese Academy of Medical Sciences, Institute of Basic Medicine Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, 100005, China
| | - Bo Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China.
| | - Weiming Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 West Road, South Fourth Ring Road, Beijing, 100070, China. .,China National Clinical Research Center for Neurological Diseases (NCRC-ND), Beijing, 100070, China.
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11
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Schmid D, Warnken U, Latzer P, Hoffmann DC, Roth J, Kutschmann S, Jaschonek H, Rübmann P, Foltyn M, Vollmuth P, Winkler F, Seliger C, Felix M, Sahm F, Haas J, Reuss D, Bendszus M, Wildemann B, von Deimling A, Wick W, Kessler T. Diagnostic biomarkers from proteomic characterization of cerebrospinal fluid in patients with brain malignancies. J Neurochem 2021; 158:522-538. [PMID: 33735443 DOI: 10.1111/jnc.15350] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 12/23/2022]
Abstract
Recent technological advances in molecular diagnostics through liquid biopsies hold the promise to repetitively monitor tumor evolution and treatment response of brain malignancies without the need of invasive surgical tissue accrual. Here, we implemented a mass spectrometry-based protein analysis pipeline which identified hundreds of proteins in 251 cerebrospinal fluid (CSF) samples from patients with four types of brain malignancies (glioblastoma, lymphoma, brain metastasis, and leptomeningeal disease [LMD]) and from healthy individuals with a focus on glioblastoma in a retrospective and confirmatory prospective observational study. CSF proteome deregulation via disruption of the blood brain barrier appeared to be largely conserved across brain tumor entities. CSF analysis of glioblastoma patients identified two proteomic clusters that correlated with tumor size and patient survival. By integrating CSF data with proteomic analyses of matching glioblastoma tumor tissue and primary glioblastoma cells, we identified potential CSF biomarkers for glioblastoma, in particular chitinase-3-like protein 1 (CHI3L1) and glial fibrillary acidic protein (GFAP). Key findings were validated in a prospective cohort consisting of 35 glioma patients. Finally, in LMD patients who frequently undergo repeated CSF work-up, we explored our proteomic pipeline as a mean to profile consecutive CSF samples. Therefore, proteomic analysis of CSF in brain malignancies has the potential to reveal biomarkers for diagnosis and therapy monitoring.
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Affiliation(s)
- Dominic Schmid
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany.,Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Uwe Warnken
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Functional Proteome Analysis, DKFZ, Heidelberg, Germany
| | - Pauline Latzer
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dirk C Hoffmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Judith Roth
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Kutschmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hannah Jaschonek
- Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Petra Rübmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martha Foltyn
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Philipp Vollmuth
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Frank Winkler
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Corinna Seliger
- Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Marius Felix
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jürgen Haas
- Molecular Neuroimmunology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Reuss
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Bendszus
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Brigitte Wildemann
- Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Neuroimmunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Tobias Kessler
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
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12
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Remnestål J, Bergström S, Olofsson J, Sjöstedt E, Uhlén M, Blennow K, Zetterberg H, Zettergren A, Kern S, Skoog I, Nilsson P, Månberg A. Association of CSF proteins with tau and amyloid β levels in asymptomatic 70-year-olds. ALZHEIMERS RESEARCH & THERAPY 2021; 13:54. [PMID: 33653397 PMCID: PMC7923505 DOI: 10.1186/s13195-021-00789-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/11/2021] [Indexed: 12/22/2022]
Abstract
Background Increased knowledge of the evolution of molecular changes in neurodegenerative disorders such as Alzheimer’s disease (AD) is important for the understanding of disease pathophysiology and also crucial to be able to identify and validate disease biomarkers. While several biological changes that occur early in the disease development have already been recognized, the need for further characterization of the pathophysiological mechanisms behind AD still remains. Methods In this study, we investigated cerebrospinal fluid (CSF) levels of 104 proteins in 307 asymptomatic 70-year-olds from the H70 Gothenburg Birth Cohort Studies using a multiplexed antibody- and bead-based technology. Results The protein levels were first correlated with the core AD CSF biomarker concentrations of total tau, phospho-tau and amyloid beta (Aβ42) in all individuals. Sixty-three proteins showed significant correlations to either total tau, phospho-tau or Aβ42. Thereafter, individuals were divided based on CSF Aβ42/Aβ40 ratio and Clinical Dementia Rating (CDR) score to determine if early changes in pathology and cognition had an effect on the correlations. We compared the associations of the analysed proteins with CSF markers between groups and found 33 proteins displaying significantly different associations for amyloid-positive individuals and amyloid-negative individuals, as defined by the CSF Aβ42/Aβ40 ratio. No differences in the associations could be seen for individuals divided by CDR score. Conclusions We identified a series of transmembrane proteins, proteins associated with or anchored to the plasma membrane, and proteins involved in or connected to synaptic vesicle transport to be associated with CSF biomarkers of amyloid and tau pathology in AD. Further studies are needed to explore these proteins’ role in AD pathophysiology. Supplementary Information The online version contains supplementary material available at 10.1186/s13195-021-00789-5.
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Affiliation(s)
- Julia Remnestål
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Tomtebodvägen 23A, Solna, Stockholm, Sweden
| | - Sofia Bergström
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Tomtebodvägen 23A, Solna, Stockholm, Sweden
| | - Jennie Olofsson
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Tomtebodvägen 23A, Solna, Stockholm, Sweden
| | - Evelina Sjöstedt
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Tomtebodvägen 23A, Solna, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Solna, Sweden
| | - Mathias Uhlén
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Tomtebodvägen 23A, Solna, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Solna, Sweden
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Anna Zettergren
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden
| | - Silke Kern
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Psychiatry, Cognition and Old Age Psychiatry Clinic, Gothenburg, Sweden
| | - Ingmar Skoog
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Neuropsychiatric Epidemiology Unit, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, Centre for Ageing and Health (AGECAP) at the University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Psychiatry, Cognition and Old Age Psychiatry Clinic, Gothenburg, Sweden
| | - Peter Nilsson
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Tomtebodvägen 23A, Solna, Stockholm, Sweden
| | - Anna Månberg
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Tomtebodvägen 23A, Solna, Stockholm, Sweden.
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13
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Caminati G, Procacci P. Mounting evidence of FKBP12 implication in neurodegeneration. Neural Regen Res 2020; 15:2195-2202. [PMID: 32594030 PMCID: PMC7749462 DOI: 10.4103/1673-5374.284980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/18/2020] [Accepted: 03/24/2020] [Indexed: 12/25/2022] Open
Abstract
Intrinsically disordered proteins, such as tau or α-synuclein, have long been associated with a dysfunctional role in neurodegenerative diseases. In Alzheimer's and Parkinson's' diseases, these proteins, sharing a common chemical-physical pattern with alternating hydrophobic and hydrophilic domains rich in prolines, abnormally aggregate in tangles in the brain leading to progressive loss of neurons. In this review, we present an overview linking the studies on the implication of the peptidyl-prolyl isomerase domain of immunophilins, and notably FKBP12, to a variety of neurodegenerative diseases, focusing on the molecular origin of such a role. The involvement of FKBP12 dysregulation in the aberrant aggregation of disordered proteins pinpoints this protein as a possible therapeutic target and, at the same time, as a predictive biomarker for early diagnosis in neurodegeneration, calling for the development of reliable, fast and cost-effective detection methods in body fluids for community-based screening campaigns.
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Affiliation(s)
- Gabriella Caminati
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
- Center for Colloid and Surface Science (CSGI), University of Florence, Sesto Fiorentino, Italy
| | - Piero Procacci
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
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14
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An Investigation into Proteomic Constituents of Cerebrospinal Fluid in Patients with Chronic Peripheral Neuropathic Pain Medicated with Opioids- a Pilot Study. J Neuroimmune Pharmacol 2020; 16:634-650. [PMID: 33219474 DOI: 10.1007/s11481-020-09970-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/30/2020] [Indexed: 12/25/2022]
Abstract
The pharmacodynamics of opioids for chronic peripheral neuropathic pain are complex and likely extend beyond classical opioid receptor theory. Preclinical evidence of opioid modulation of central immune signalling has not been identified in vivo in humans. Examining the cerebrospinal fluid (CSF) of patients medicated with opioids is required to identify potential pharmacodynamic mechanisms. We compared CSF samples of chronic peripheral neuropathic pain patients receiving opioids (n = 7) versus chronic peripheral neuropathic pain patients not taking opioids (control group, n = 13). Baseline pain scores with demographics were recorded. Proteome analysis was performed using mass spectrometry and secreted neuropeptides were measured by enzyme-linked immunosorbent assay. Based on Gene Ontology analysis, proteins involved in the positive regulation of nervous system development and myeloid leukocyte activation were increased in patients taking opioids versus the control group. The largest decrease in protein expression in patients taking opioids were related to neutrophil mediated immunity. In addition, notably higher expression levels of neural proteins (85%) and receptors (80%) were detected in the opioid group compared to the control group. This study suggests modulation of CNS homeostasis, possibly attributable to opioids, thus highlighting potential mechanisms for the pharmacodynamics of opioids. We also provide new insights into the immunomodulatory functions of opioids in vivo.
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15
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Zou W, Lv Y, Liu ZI, Xia P, Li H, Jiao J. Loss of Rsph9 causes neonatal hydrocephalus with abnormal development of motile cilia in mice. Sci Rep 2020; 10:12435. [PMID: 32709945 PMCID: PMC7382491 DOI: 10.1038/s41598-020-69447-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 07/13/2020] [Indexed: 12/13/2022] Open
Abstract
Hydrocephalus is a brain disorder triggered by cerebrospinal fluid accumulation in brain cavities. Even though cerebrospinal fluid flow is known to be driven by the orchestrated beating of the bundled motile cilia of ependymal cells, little is known about the mechanism of ciliary motility. RSPH9 is increasingly becoming recognized as a vital component of radial spokes in ciliary "9 + 2" ultrastructure organization. Here, we show that deletion of the Rsph9 gene leads to the development of hydrocephalus in the early postnatal period. However, the neurodevelopment and astrocyte development are normal in embryonic Rsph9-/- mice. The tubular structure of the central aqueduct was comparable in Rsph9-/- mice. Using high-speed video microscopy, we visualized lower beating amplitude and irregular rotation beating pattern of cilia bundles in Rsph9-/- mice compared with that of wild-type mice. And the centriolar patch size was significantly increased in Rsph9-/- cells. TEM results showed that deletion of Rsph9 causes little impact in ciliary axonemal organization but the Rsph9-/- cilia frequently had abnormal ectopic ciliary membrane inclusions. In addition, hydrocephalus in Rsph9-/- mice results in the development of astrogliosis, microgliosis and cerebrovascular abnormalities. Eventually, the ependymal cells sloughed off of the lateral wall. Our results collectively suggested that RSPH9 is essential for ciliary structure and motility of mouse ependymal cilia, and its deletion causes the pathogenesis of hydrocephalus.
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Affiliation(s)
- Wenzheng Zou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuqing Lv
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zux Iang Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Innovation Center of Excellence on Brain Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Pengyan Xia
- State Key Laboratory of Membrane Biology, Institute of Zoology, Beijing, 100101, China
| | - Hong Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China. .,Innovertion Academy for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China. .,Group of Neural Stem Cell and Neurogenesis, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road, Chaoyang District, Beijing, 100101, China.
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16
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Macron C, Núñez Galindo A, Cominetti O, Dayon L. A Versatile Workflow for Cerebrospinal Fluid Proteomic Analysis with Mass Spectrometry: A Matter of Choice between Deep Coverage and Sample Throughput. Methods Mol Biol 2020; 2044:129-154. [PMID: 31432411 DOI: 10.1007/978-1-4939-9706-0_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Human cerebrospinal fluid (CSF) is a sample of choice in the study of brain disorders. This biological fluid circulates in the brain and the spinal cord and contains tissue-specific proteins, indicative of health and disease conditions. Despite its potential as a valid source of biological markers, CSF remains largely understudied as compared to blood, in particular due to its more invasive way of sampling.Challenges remain when performing proteomic analysis in clinical research studies. State-of-the-art mass spectrometry (MS) enables deep characterization of the human proteome. But some technical limitations are cardinal to be addressed, such as the capacity to routinely analyze large cohorts of samples. Importantly, a trade-off still needs to be made between the proteome coverage depth and the number of measured samples. In this context, we developed a scalable automated proteomic pipeline for the analysis of CSF. Because of its versatility, this workflow can be adapted to accommodate proteome coverage and/or sample throughput. It allows us to prepare and quantitatively analyze hundreds to thousands of CSF samples; it can also allow identification of more than 3000 proteins in a CSF sample when coupled with isoelectric focusing fractionation.In this chapter, we describe an end-to-end pipeline for the proteomic analysis of CSF. The main steps of the sample preparation comprise spiking of a standard, protein digestion, isobaric labeling, and purification; these are performed in a 96-well plate format enabling automation. Depending on the targeted depth of the CSF proteome, optional analytical steps can be included, such as the removal of abundant proteins and sample pre-fractionation. Liquid chromatography tandem MS as well as data processing and analysis complete the pipeline.
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Affiliation(s)
- Charlotte Macron
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Loïc Dayon
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland.
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17
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Kessler T, Latzer P, Schmid D, Warnken U, Saffari A, Ziegler A, Kollmer J, Möhlenbruch M, Ulfert C, Herweh C, Wildemann B, Wick W, Weiler M. Cerebrospinal fluid proteomic profiling in nusinersen-treated patients with spinal muscular atrophy. J Neurochem 2020; 153:650-661. [PMID: 31903607 DOI: 10.1111/jnc.14953] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/09/2019] [Accepted: 12/27/2019] [Indexed: 12/13/2022]
Abstract
Promising results from recent clinical trials on the approved antisense oligonucleotide nusinersen in pediatric patients with 5q-linked spinal muscular atrophy (SMA) still have to be confirmed in adult patients but are hindered by a lack of sensitive biomarkers that indicate an early therapeutic response. Changes in the overall neurochemical composition of cerebrospinal fluid (CSF) under therapy may yield additive diagnostic and predictive information. With this prospective proof-of-concept and feasibility study, we evaluated non-targeted CSF proteomic profiles by mass spectrometry along with basic CSF parameters of 10 adult patients with SMA types 2 or 3 before and after 10 months of nusinersen therapy, in comparison with 10 age- and gender-matched controls. These data were analyzed by bioinformatics and correlated with clinical outcomes assessed by the Hammersmith Functional Rating Scale Expanded (HFMSE). CSF proteomic profiles of SMA patients differed from controls. Two groups of SMA patients were identified based on unsupervised clustering. These groups differed in age and expression of proteins related to neurodegeneration and neuroregeneration. Intraindividual CSF differences in response to nusinersen treatment varied between patients who clinically improved and those who did not. Data are available via ProteomeXchange with identifier PXD016757. Comparative CSF proteomic analysis in adult SMA patients before and after treatment with nusinersen-identified subgroups and treatment-related changes and may therefore be suitable for diagnostic and predictive analyses.
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Affiliation(s)
- Tobias Kessler
- Department of Neurology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pauline Latzer
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominic Schmid
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteomic Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Afshin Saffari
- Division of Child Neurology and Metabolic Medicine, Center for Child and Adolescent Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas Ziegler
- Division of Child Neurology and Metabolic Medicine, Center for Child and Adolescent Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Jennifer Kollmer
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus Möhlenbruch
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Ulfert
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Herweh
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Brigitte Wildemann
- Department of Neurology, Heidelberg University Hospital, Heidelberg, Germany
| | - Wolfgang Wick
- Department of Neurology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Markus Weiler
- Department of Neurology, Heidelberg University Hospital, Heidelberg, Germany
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18
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Oeckl P, Weydt P, Thal DR, Weishaupt JH, Ludolph AC, Otto M. Proteomics in cerebrospinal fluid and spinal cord suggests UCHL1, MAP2 and GPNMB as biomarkers and underpins importance of transcriptional pathways in amyotrophic lateral sclerosis. Acta Neuropathol 2020; 139:119-134. [PMID: 31701227 DOI: 10.1007/s00401-019-02093-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/11/2019] [Accepted: 11/01/2019] [Indexed: 01/09/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease and the proteins and pathways involved in the pathophysiology are not fully understood. Even less is known about the preclinical disease phase. To uncover new ALS-related proteins and pathways, we performed a comparative proteomic analysis in cerebrospinal fluid (CSF) of asymptomatic (n = 14) and symptomatic (n = 14) ALS mutation carriers and sporadic ALS patients (n = 12) as well as post-mortem human spinal cord tissue (controls: n = 7, ALS, n = 8). Using a CSF-optimized proteomic workflow, we identified novel (e.g., UCHL1, MAP2, CAPG, GPNMB, HIST1H4A, HIST1H2B) and well-described (e.g., NEFL, NEFH, NEFM, CHIT1, CHI3L1) protein level changes in CSF of sporadic and genetic ALS patients with enrichment of proteins related to transcription, cell cycle and lipoprotein remodeling (total protein IDs: 2303). No significant alteration was observed in asymptomatic ALS mutation carriers representing the prodromal disease phase. We confirmed UCHL1, MAP2, CAPG and GPNMB as novel biomarker candidates for ALS in an independent validation cohort of patients (n = 117) using multiple reaction monitoring. In spinal cord tissue, 292 out of 6810 identified proteins were significantly changed in ALS with enrichment of proteins involved in mRNA splicing and of the neurofilament compartment. In conclusion, our proteomic data in asymptomatic ALS mutation carriers support the hypothesis of a sudden disease onset instead of a long preclinical phase. Both CSF and tissue proteomic data indicate transcriptional pathways to be amongst the most affected. UCHL1, MAP2 and GPNMB are promising ALS biomarker candidates which might provide additional value to the established neurofilaments in patient follow-up and clinical trials.
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Affiliation(s)
- Patrick Oeckl
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany
| | - Patrick Weydt
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, Bonn, Germany
| | - Dietmar R Thal
- Laboratory of Neuropathology, Institute of Pathology, Ulm University, Ulm, Germany
- Department of Imaging and Pathology, KU Leuven and Department of Pathology, UZ Leuven, Louvain, Belgium
| | - Jochen H Weishaupt
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany
| | - Albert C Ludolph
- 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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Mirhosseini M, Shiari R, Esmaeili Motlagh P, Farivar S. Cerebrospinal Fluid and Photobiomodulation Effects on Neural Gene Expression in Dental Pulp Stem Cells. J Lasers Med Sci 2019; 10:S30-S36. [PMID: 32021670 DOI: 10.15171/jlms.2019.s6] [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: 01/20/2023]
Abstract
Introduction: Dental pulp cells, a unique source of ectomesenchymal pluripotent stem cells, are originated from the skull neural crest. They are considered as one ideal source of cells for the regenerative medicine applications. Cerebrospinal fluid (CSF), a transparent fluid found in the brain and spinal cord, is enriched with electrolytes, proteins, and growth factors such as EGF, bFGF, BDNF, GDNF, and neuropeptides and can be utilized as a trigger in order to induce the neural differentiation. On the other hand, photobiomodulation (PBM), with the ability to prevent cell apoptosis, can induce cell proliferation by means of increasing the ATP synthesis in mitochondria and facilitating the secretion of the growth factors. In this research, we first aimed to isolate and culture the dental pulp stem cells (DPSCs) and subsequently to investigate their potential for neural differentiation. Methods: Human dental pulp stem cells (hDPSCs) were isolated from the pulp tissues using an outgrowth method and subsequently cultured. In order to access the cells' differentiation potential, cells were firstly classified into four groups which were treated with CSF, gallium aluminum arsenide diode laser irradiation (808 nm; 30 mW power output) and a combination of both, while the fourth group was considered as the control. MTT assay was then used to examine the viability of cells following the treatments. After 4, 7, and 14 days the cell morphology in the treated groups was evaluated while RT-PCR was used in order to evaluate the Nestin and β-tubulinIII neural gene marker expressions. Results: It was shown that PBM has the ability to elevate the proliferation of DPSCs. Also, the differentiated morphology was obvious in the CSF treated group, especially on day 14 with the formation of three-dimensional (3D) structures. The results of gene expression analysis showed that on the fourth day of post-treatment, Nestin and β-tubulinIII gene expressions were reduced in all groups while a rising trend in their expression was observed subsequently on days 7 and 14. Conclusion: In accordance with previous studies, including functional and protein base researches, it has been demonstrated that CSF has a direct role in neural induction. Although past works have been significant, none of them shows a 3D structure. In this article, we investigated the dual effect of PBM and CSF. Initial results confirmed the upregulation of neural-related transcription factors. The 3D organization of the formed tissue could imply the initiation of organogenesis which has not been reported before. In sum, the dual effect of CSF and PBM has been shown to have the potential for contributing to the initiation of neurogenesis and organogenesis.
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Affiliation(s)
- Malihe Mirhosseini
- Department of Molecular and Cell Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, General Campus, Tehran, Iran
| | - Reza Shiari
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parisa Esmaeili Motlagh
- Department of Molecular and Cell Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, General Campus, Tehran, Iran
| | - Shirin Farivar
- Department of Molecular and Cell Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, General Campus, Tehran, Iran
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20
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Yuan S, Li H, Xie J, Sun X. Quantitative Trait Module-Based Genetic Analysis of Alzheimer's Disease. Int J Mol Sci 2019; 20:E5912. [PMID: 31775305 PMCID: PMC6928939 DOI: 10.3390/ijms20235912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 01/02/2023] Open
Abstract
The pathological features of Alzheimer's Disease (AD) first appear in the medial temporal lobe and then in other brain structures with the development of the disease. In this work, we investigated the association between genetic loci and subcortical structure volumes of AD on 393 samples in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. Brain subcortical structures were clustered into modules using Pearson's correlation coefficient of volumes across all samples. Module volumes were used as quantitative traits to identify not only the main effect loci but also the interactive effect loci for each module. Thirty-five subcortical structures were clustered into five modules, each corresponding to a particular brain structure/area, including the limbic system (module I), the corpus callosum (module II), thalamus-cerebellum-brainstem-pallidum (module III), the basal ganglia neostriatum (module IV), and the ventricular system (module V). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment results indicate that the gene annotations of the five modules were distinct, with few overlaps between different modules. We identified several main effect loci and interactive effect loci for each module. All these loci are related to the function of module structures and basic biological processes such as material transport and signal transduction.
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Affiliation(s)
| | | | | | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (S.Y.)
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21
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Rahman MM, Westermark GT, Zetterberg H, Härd T, Sandgren M. Protofibrillar and Fibrillar Amyloid-β Binding Proteins in Cerebrospinal Fluid. J Alzheimers Dis 2019; 66:1053-1064. [PMID: 30372682 DOI: 10.3233/jad-180596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Aggregation and deposition of misfolded amyloid-β (Aβ) peptide in the brain is central to Alzheimer's disease (AD). Oligomeric, protofibrillar, and fibrillar forms of Aβ are believed to be neurotoxic and cause neurodegeneration in AD, but the toxicity mechanisms are not well understood and may involve Aβ-interacting molecular partners. In a previous study, we identified potential Aβ42 protofibrillar-binding proteins in serum and cerebrospinal fluid (CSF) using an engineered version of Aβ42 (Aβ42CC) that forms protofibrils, but not fibrils. Here we studied binding of proteins to Aβ42 fibrils in AD and non-AD CSF and compared these with protofibrillar Aβ42CC-binding partners. Aβ42 fibrils sequestered 2.4-fold more proteins than Aβ42CC protofibrils. Proteins with selective binding to fibrillar aggregates with low nanomolar affinity were identified. We also found that protofibrillar and fibrillar Aβ-binding proteins represent distinct functional categories. Aβ42CC protofibrils triggered interactions with proteins involved in catalytic activities, like transferases and oxidoreductases, while Aβ42 fibrils were more likely involved in binding to proteoglycans, growth factors and neuron-associated proteins, e.g., neurexin-1, -2, and -3. Interestingly, 10 brain-enriched proteins were identified among the fibril-binding proteins, while protofibril-extracted proteins had more general expression patterns. Both types of Aβ aggregates bound several extracellular proteins. Additionally, we list a set of CSF proteins that might have potential to discriminate between AD and non-AD CSF samples. The results may be of relevance both for biomarker studies and for studies of Aβ-related toxicity mechanisms.
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Affiliation(s)
- M Mahafuzur Rahman
- Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala BioCenter, Uppsala, Sweden
| | | | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Torleif Härd
- Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala BioCenter, Uppsala, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala BioCenter, Uppsala, Sweden
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22
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Thygesen C, Larsen MR, Finsen B. Proteomic signatures of neuroinflammation in Alzheimer’s disease, multiple sclerosis and ischemic stroke. Expert Rev Proteomics 2019; 16:601-611. [DOI: 10.1080/14789450.2019.1633919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Camilla Thygesen
- Institute of Molecular Medicine, Department of Neurobiology, University of Southern Denmark, Odense, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Martin Rössel Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Bente Finsen
- Institute of Molecular Medicine, Department of Neurobiology, University of Southern Denmark, Odense, Denmark
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23
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Development of parallel reaction monitoring assays for cerebrospinal fluid proteins associated with Alzheimer's disease. Clin Chim Acta 2019; 494:79-93. [PMID: 30858094 DOI: 10.1016/j.cca.2019.03.243] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 12/16/2022]
Abstract
Detailed knowledge of protein changes in cerebrospinal fluid (CSF) across healthy and diseased individuals would provide a better understanding of the onset and progression of neurodegenerative disorders. In this study, we selected 20 brain-enriched proteins previously identified in CSF by antibody suspension bead arrays (SBA) to be potentially biomarkers for Alzheimer's disease (AD) and verified these using an orthogonal approach. We examined the same set of 94 CSF samples from patients affected by AD (including preclinical and prodromal), mild cognitive impairment (MCI), non-AD dementia and healthy individuals, which had previously been analyzed by SBA. Twenty-eight parallel reaction monitoring (PRM) assays were developed and 13 of them could be validated for protein quantification. Antibody profiles were verified by PRM. For seven proteins, the antibody profiles were highly correlated with the PRM results (r > 0.7) and GAP43, VCAM1 and PSAP were identified as potential markers of preclinical AD. In conclusion, we demonstrate the usefulness of targeted mass spectrometry as a tool for the orthogonal verification of antibody profiling data, suggesting that these complementary methods can be successfully applied for comprehensive exploration of CSF protein levels in neurodegenerative disorders.
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24
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Lleó A, Núñez-Llaves R, Alcolea D, Chiva C, Balateu-Paños D, Colom-Cadena M, Gomez-Giro G, Muñoz L, Querol-Vilaseca M, Pegueroles J, Rami L, Lladó A, Molinuevo JL, Tainta M, Clarimón J, Spires-Jones T, Blesa R, Fortea J, Martínez-Lage P, Sánchez-Valle R, Sabidó E, Bayés À, Belbin O. Changes in Synaptic Proteins Precede Neurodegeneration Markers in Preclinical Alzheimer's Disease Cerebrospinal Fluid. Mol Cell Proteomics 2019; 18:546-560. [PMID: 30606734 PMCID: PMC6398205 DOI: 10.1074/mcp.ra118.001290] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Indexed: 01/08/2023] Open
Abstract
A biomarker of synapse loss, an early event in Alzheimer's disease (AD) pathophysiology that precedes neuronal death and symptom onset, would be a much-needed prognostic biomarker. With direct access to the brain interstitial fluid, the cerebrospinal fluid (CSF) is a potential source of synapse-derived proteins. In this study, we aimed to identify and validate novel CSF biomarkers of synapse loss in AD. Discovery: Combining shotgun proteomics of the CSF with an exhaustive search of the literature and public databases, we identified 251 synaptic proteins, from which we selected 22 for further study. Verification: Twelve proteins were discarded because of poor detection by Selected Reaction Monitoring (SRM). We confirmed the specific expression of 9 of the remaining proteins (Calsynytenin-1, GluR2, GluR4, Neurexin-2A, Neurexin-3A, Neuroligin-2, Syntaxin-1B, Thy-1, Vamp-2) at the human synapse using Array Tomography microscopy and biochemical fractionation methods. Exploration: Using SRM, we monitored these 9 synaptic proteins (20 peptides) in a cohort of CSF from cognitively normal controls and subjects in the pre-clinical and clinical AD stages (n = 80). Compared with controls, peptides from 8 proteins were elevated 1.3 to 1.6-fold (p < 0.04) in prodromal AD patients. Validation: Elevated levels of a GluR4 peptide at the prodromal stage were replicated (1.3-fold, p = 0.04) in an independent cohort (n = 60). Moreover, 7 proteins were reduced at preclinical stage 1 (0.6 to 0.8-fold, p < 0.04), a finding that was replicated (0.7 to 0.8-fold, p < 0.05) for 6 proteins in a third cohort (n = 38). In a cross-cohort meta-analysis, 6 synaptic proteins (Calsyntenin-1, GluR4, Neurexin-2A, Neurexin-3A, Syntaxin-1B and Thy-1) were reduced 0.8-fold (p < 0.05) in preclinical AD, changes that precede clinical symptoms and CSF markers of neurodegeneration. Therefore, these proteins could have clinical value for assessing disease progression, especially in preclinical stages of AD.
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Affiliation(s)
- Alberto Lleó
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain;
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Raúl Núñez-Llaves
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Daniel Alcolea
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Cristina Chiva
- ‖Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona
- **University Pompeu Fabra, 08003 Barcelona
| | | | - Martí Colom-Cadena
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Gemma Gomez-Giro
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Laia Muñoz
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Marta Querol-Vilaseca
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Jordi Pegueroles
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Lorena Rami
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - Albert Lladó
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - José L Molinuevo
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - Mikel Tainta
- §§Department of Neurology, Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, 20009 San Sebastian, Spain
- ¶¶Servicio de Neurologia, Organización Sanitaria Integrada Goierri-Alto Urola, Osakidetza, Zumárraga, España
| | - Jordi Clarimón
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
| | - Tara Spires-Jones
- ‖‖Centre for Discovery Brain Sciences and UK Dementia Research Institute, University of Edinburgh EH8 9JZ, UK
| | - Rafael Blesa
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Juan Fortea
- From the ‡Memory Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Pablo Martínez-Lage
- §§Department of Neurology, Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, 20009 San Sebastian, Spain
| | - Raquel Sánchez-Valle
- ‡‡Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clínic-Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), 08015 Barcelona, Spain
| | - Eduard Sabidó
- ‖Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona
- **University Pompeu Fabra, 08003 Barcelona
| | - Àlex Bayés
- ***Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025, Barcelona, Spain
- ‡‡‡Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Spain
| | - Olivia Belbin
- §Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain;
- ¶Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025Barcelona, Spain
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25
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Castillo C, Martinez JC, Longart M, García L, Hernández M, Carballo J, Rojas H, Matteo L, Casique L, Escalona JL, Rodríguez Y, Rodriguez J, Hernández D, Balbi D, Villegas R. Extracellular Application of CRMP2 Increases Cytoplasmic Calcium through NMDA Receptors. Neuroscience 2019; 376:204-223. [PMID: 29555037 DOI: 10.1016/j.neuroscience.2018.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 12/27/2022]
Abstract
Collapsin Response Mediator Protein 2 (CRMP2) is an intracellular protein involved in axon and dendrite growth and specification. In this study, CRMP2 was identified in a conditioned media derived from degenerated sciatic nerves (CM). On cultured rat hippocampal neurons, acute extracellular application of CM or partially purified recombinant CRMP2 produced an increase in cytoplasmic calcium. The increase in cytoplasmic calcium was mostly mediated through NMDA receptors, with a minor contribution of N-type VDCC, and it was maintained as long as CM was present. By using live-labeling of CRMP2, Ca2+ channel binding domain 3 (CBD3) peptide derived from CRMP2, and recombinant CRMP2, we demonstrated that that this effect was mediated by an action on the extracellular side of the NMDA receptor. This is the first report of an extracellular action of CRMP2. Prolonged exposure to extracellular CRMP2, may contribute to neuronal calcium dysregulation and neuronal damage.
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Affiliation(s)
- Cecilia Castillo
- Unidad de Neurociencias, Instituto de Estudios Avanzados IDEA, Caracas 1080, Venezuela.
| | - Juan Carlos Martinez
- Unidad de Neurociencias, Instituto de Estudios Avanzados IDEA, Caracas 1080, Venezuela
| | - Marines Longart
- Unidad de Neurociencias, Instituto de Estudios Avanzados IDEA, Caracas 1080, Venezuela
| | - Lisbeth García
- Unidad de Neurociencias, Instituto de Estudios Avanzados IDEA, Caracas 1080, Venezuela
| | - Marianela Hernández
- Unidad de Neurociencias, Instituto de Estudios Avanzados IDEA, Caracas 1080, Venezuela
| | - Jeismar Carballo
- Unidad de Neurociencias, Instituto de Estudios Avanzados IDEA, Caracas 1080, Venezuela
| | - Héctor Rojas
- Instituto de Inmunología, Facultad de Medicina, Universidad Central de Venezuela, Caracas 1051, Venezuela
| | - Lorena Matteo
- Unidad de Neurociencias, Instituto de Estudios Avanzados IDEA, Caracas 1080, Venezuela
| | - Liliana Casique
- Depto. de Biología Celular, Universidad Simón Bolívar, Caracas 1080, Venezuela
| | | | - Yuryanni Rodríguez
- Unidad de Neurociencias, Instituto de Estudios Avanzados IDEA, Caracas 1080, Venezuela
| | - Jessica Rodriguez
- Unidad de Neurociencias, Instituto de Estudios Avanzados IDEA, Caracas 1080, Venezuela
| | - Deyanell Hernández
- Unidad de Neurociencias, Instituto de Estudios Avanzados IDEA, Caracas 1080, Venezuela
| | - Domingo Balbi
- Unidad de Neurociencias, Instituto de Estudios Avanzados IDEA, Caracas 1080, Venezuela
| | - Raimundo Villegas
- Unidad de Neurociencias, Instituto de Estudios Avanzados IDEA, Caracas 1080, Venezuela
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26
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Wei Y, Xiong ZJ, Li J, Zou C, Cairo CW, Klassen JS, Privé GG. Crystal structures of human lysosomal EPDR1 reveal homology with the superfamily of bacterial lipoprotein transporters. Commun Biol 2019; 2:52. [PMID: 30729188 PMCID: PMC6363788 DOI: 10.1038/s42003-018-0262-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/11/2018] [Indexed: 01/01/2023] Open
Abstract
EPDR1, a member of the ependymin-related protein family, is a relatively uncharacterized protein found in the lysosomes and secretomes of most vertebrates. Despite having roles in human disease and health, the molecular functions of EPDR1 remain unknown. Here, we present crystal structures of human EPDR1 and reveal that the protein adopts a fold previously seen only in bacterial proteins related to the LolA lipoprotein transporter. EPDR1 forms a homodimer with an overall shape resembling a half-shell with two non-overlapping hydrophobic grooves on the flat side of the hemisphere. EPDR1 can interact with membranes that contain negatively charged lipids, including BMP and GM1, and we suggest that EPDR1 may function as a lysosomal activator protein or a lipid transporter. A phylogenetic analysis reveals that the fold is more widely distributed than previously suspected, with representatives identified in all branches of cellular life.
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Affiliation(s)
- Yong Wei
- Princess Margaret Cancer Centre, Toronto, M5G 1L7 ON Canada
| | - Zi Jian Xiong
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8 ON Canada
| | - Jun Li
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2 AB Canada
| | - Chunxia Zou
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2 AB Canada
| | - Christopher W. Cairo
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2 AB Canada
| | - John S. Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2 AB Canada
| | - Gilbert G. Privé
- Princess Margaret Cancer Centre, Toronto, M5G 1L7 ON Canada
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8 ON Canada
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7 ON Canada
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27
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Dayon L, Cominetti O, Wojcik J, Galindo AN, Oikonomidi A, Henry H, Migliavacca E, Kussmann M, Bowman GL, Popp J. Proteomes of Paired Human Cerebrospinal Fluid and Plasma: Relation to Blood–Brain Barrier Permeability in Older Adults. J Proteome Res 2019; 18:1162-1174. [DOI: 10.1021/acs.jproteome.8b00809] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Loïc Dayon
- Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | | | | | | | | | - Hugues Henry
- Department of Laboratories, CHUV, 1011 Lausanne, Switzerland
| | | | - Martin Kussmann
- Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Gene L. Bowman
- Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Julius Popp
- Old Age Psychiatry, Department of Psychiatry, CHUV, 1011 Lausanne, Switzerland
- Geriatric Psychiatry, Department of Mental Health and Psychiatry, HUG, 1226 Geneva, Switzerland
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Pkd2l1 is required for mechanoception in cerebrospinal fluid-contacting neurons and maintenance of spine curvature. Nat Commun 2018; 9:3804. [PMID: 30228263 PMCID: PMC6143598 DOI: 10.1038/s41467-018-06225-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 08/20/2018] [Indexed: 02/07/2023] Open
Abstract
Defects in cerebrospinal fluid (CSF) flow may contribute to idiopathic scoliosis. However, the mechanisms underlying detection of CSF flow in the central canal of the spinal cord are unknown. Here we demonstrate that CSF flows bidirectionally along the antero-posterior axis in the central canal of zebrafish embryos. In the cfap298tm304 mutant, reduction of cilia motility slows transport posteriorly down the central canal and abolishes spontaneous activity of CSF-contacting neurons (CSF-cNs). Loss of the sensory Pkd2l1 channel nearly abolishes CSF-cN calcium activity and single channel opening. Recording from isolated CSF-cNs in vitro, we show that CSF-cNs are mechanosensory and require Pkd2l1 to respond to pressure. Additionally, adult pkd2l1 mutant zebrafish develop an exaggerated spine curvature, reminiscent of kyphosis in humans. These results indicate that CSF-cNs are mechanosensory cells whose Pkd2l1-driven spontaneous activity reflects CSF flow in vivo. Furthermore, Pkd2l1 in CSF-cNs contributes to maintenance of natural curvature of the spine. Alteration of cerebrospinal fluid (CSF) flow and cilia defects are clinically associated with idiopathic scoliosis. This study shows that transient receptor potential channel Pkd2l1 is required for mechanosensory function of neurons detecting CSF flow and normal spine curvature development in zebrafish.
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Barkovits K, Linden A, Galozzi S, Schilde L, Pacharra S, Mollenhauer B, Stoepel N, Steinbach S, May C, Uszkoreit J, Eisenacher M, Marcus K. Characterization of Cerebrospinal Fluid via Data-Independent Acquisition Mass Spectrometry. J Proteome Res 2018; 17:3418-3430. [PMID: 30207155 DOI: 10.1021/acs.jproteome.8b00308] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cerebrospinal fluid (CSF) is in direct contact with the brain and serves as a valuable specimen to examine diseases of the central nervous system through analyzing its components. These include the analysis of metabolites, cells as well as proteins. For identifying new suitable diagnostic protein biomarkers bottom-up data-dependent acquisition (DDA) mass spectrometry-based approaches are most popular. Drawbacks of this method are stochastic and irreproducible precursor ion selection. Recently, data-independent acquisition (DIA) emerged as an alternative method. It overcomes several limitations of DDA, since it combines the benefits of DDA and targeted methods like selected reaction monitoring (SRM). We established a DIA method for in-depth proteome analysis of CSF. For this, four spectral libraries were generated with samples from native CSF ( n = 5), CSF fractionation (15 in total) and substantia nigra fractionation (54 in total) and applied to three CSF DIA replicates. The DDA and DIA methods for CSF were conducted with the same nanoLC parameters using a 180 min gradient. Compared to a conventional DDA method, our DIA approach increased the number of identified protein groups from 648 identifications in DDA to 1574 in DIA using a comprehensive spectral library generated with DDA measurements from five native CSF and 54 substantia nigra fractions. We also could show that a sample specific spectral library generated from native CSF only increased the identification reproducibility from three DIA replicates to 90% (77% with a DDA method). Moreover, by utilizing a substantia nigra specific spectral library for CSF DIA, over 60 brain-originated proteins could be identified compared to only 11 with DDA. In conclusion, the here presented optimized DIA method substantially outperforms DDA and could develop into a powerful tool for biomarker discovery in CSF. Data are available via ProteomeXchange with the identifiers PXD010698, PXD010708, PXD010690, PXD010705, and PXD009624.
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Affiliation(s)
- Katalin Barkovits
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Andreas Linden
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Sara Galozzi
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Lukas Schilde
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Sandra Pacharra
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik , Klinikstraße 16 , D-34128 Kassel , Germany
| | - Nadine Stoepel
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Simone Steinbach
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Caroline May
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Julian Uszkoreit
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Martin Eisenacher
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
| | - Katrin Marcus
- Ruhr University Bochum, Medical Faculty , Medizinisches Proteom-Center , Universitaetsstrasse 150 , D-44801 Bochum , Germany
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Macron C, Lane L, Núñez Galindo A, Dayon L. Deep Dive on the Proteome of Human Cerebrospinal Fluid: A Valuable Data Resource for Biomarker Discovery and Missing Protein Identification. J Proteome Res 2018; 17:4113-4126. [PMID: 30124047 DOI: 10.1021/acs.jproteome.8b00300] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cerebrospinal fluid (CSF) is a body fluid of choice for biomarker studies of brain disorders but remains relatively under-studied compared with other biological fluids such as plasma, partly due to the more invasive means of its sample collection. The present study establishes an in-depth CSF proteome through the analysis of a unique CSF sample from a pool of donors. After immunoaffinity depletion, the CSF sample was fractionated using off-gel electrophoresis and analyzed with liquid chromatography tandem mass spectrometry (MS) using the latest generation of hybrid Orbitrap mass spectrometers. The shotgun proteomic analysis allowed the identification of 20 689 peptides mapping on 3379 proteins. To the best of our knowledge, the obtained data set constitutes the largest CSF proteome published so far. Among the CSF proteins identified, 34% correspond to genes whose transcripts are highly expressed in brain according to the Human Protein Atlas. The principal Alzheimer's disease biomarkers (e.g., tau protein, amyloid-β, apolipoprotein E, and neurogranin) were detected. Importantly, our data set significantly contributes to the Chromosome-centric Human Proteome Project (C-HPP), and 12 proteins considered as missing are proposed for validation in accordance with the HPP guidelines. Of these 12 proteins, 8 proteins are based on 2 to 6 uniquely mapping peptides from this CSF analysis, and 4 match a new peptide with a "stranded" single peptide in PeptideAtlas from previous CSF studies. The MS proteomic data are available to the ProteomeXchange Consortium ( http://www.proteomexchange.org/ ) with the data set identifier PXD009646.
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Affiliation(s)
- Charlotte Macron
- Proteomics , Nestlé Institute of Health Sciences , 1015 Lausanne , Switzerland
| | - Lydie Lane
- CALIPHO Group , SIB-Swiss Institute of Bioinformatics , CMU, rue Michel-Servet 1 , 1211 Geneva 4 , Switzerland.,Department of Microbiology and Molecular Medicine, Faculty of Medicine , University of Geneva , rue Michel-Servet 1 , 1211 Geneva 4 , Switzerland
| | | | - Loïc Dayon
- Proteomics , Nestlé Institute of Health Sciences , 1015 Lausanne , Switzerland
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Dayon L, Núñez Galindo A, Wojcik J, Cominetti O, Corthésy J, Oikonomidi A, Henry H, Kussmann M, Migliavacca E, Severin I, Bowman GL, Popp J. Alzheimer disease pathology and the cerebrospinal fluid proteome. Alzheimers Res Ther 2018; 10:66. [PMID: 30021611 PMCID: PMC6052524 DOI: 10.1186/s13195-018-0397-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 06/11/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Altered proteome profiles have been reported in both postmortem brain tissues and body fluids of subjects with Alzheimer disease (AD), but their broad relationships with AD pathology, amyloid pathology, and tau-related neurodegeneration have not yet been fully explored. Using a robust automated MS-based proteomic biomarker discovery workflow, we measured cerebrospinal fluid (CSF) proteomes to explore their association with well-established markers of core AD pathology. METHODS Cross-sectional analysis was performed on CSF collected from 120 older community-dwelling adults with normal (n = 48) or impaired cognition (n = 72). LC-MS quantified hundreds of proteins in the CSF. CSF concentrations of β-amyloid 1-42 (Aβ1-42), tau, and tau phosphorylated at threonine 181 (P-tau181) were determined with immunoassays. First, we explored proteins relevant to biomarker-defined AD. Then, correlation analysis of CSF proteins with CSF markers of amyloid pathology, neuronal injury, and tau hyperphosphorylation (i.e., Aβ1-42, tau, P-tau181) was performed using Pearson's correlation coefficient and Bonferroni correction for multiple comparisons. RESULTS We quantified 790 proteins in CSF samples with MS. Four CSF proteins showed an association with CSF Aβ1-42 levels (p value ≤ 0.05 with correlation coefficient (R) ≥ 0.38). We identified 50 additional CSF proteins associated with CSF tau and 46 proteins associated with CSF P-tau181 (p value ≤ 0.05 with R ≥ 0.37). The majority of those proteins that showed such associations were brain-enriched proteins. Gene Ontology annotation revealed an enrichment for synaptic proteins and proteins originating from reelin-producing cells and the myelin sheath. CONCLUSIONS We used an MS-based proteomic workflow to profile the CSF proteome in relation to cerebral AD pathology. We report strong evidence of previously reported CSF proteins and several novel CSF proteins specifically associated with amyloid pathology or neuronal injury and tau hyperphosphorylation.
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Affiliation(s)
- Loïc Dayon
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | | | | | | | - John Corthésy
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | | | - Hugues Henry
- Department of Laboratories, CHUV, Lausanne, Switzerland
| | - Martin Kussmann
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
- Present address: Liggins Institute, University of Auckland, Auckland, New Zealand
| | | | - India Severin
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Gene L. Bowman
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Julius Popp
- Old Age Psychiatry, Department of Psychiatry, CHUV, Lausanne, Switzerland
- Geriatric Psychiatry, Department of Mental Health and Psychiatry, HUG, Geneva, Switzerland
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32
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Begcevic I, Tsolaki M, Brinc D, Brown M, Martinez-Morillo E, Lazarou I, Kozori M, Tagaraki F, Nenopoulou S, Gkioka M, Lazarou E, Lim B, Batruch I, Diamandis EP. Neuronal pentraxin receptor-1 is a new cerebrospinal fluid biomarker of Alzheimer's disease progression. F1000Res 2018; 7:1012. [PMID: 30191060 PMCID: PMC6081984 DOI: 10.12688/f1000research.15095.1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/22/2018] [Indexed: 12/31/2022] Open
Abstract
Background: Alzheimer's disease (AD) is the most common type of dementia, with progressive onset of clinical symptoms. The main pathological hallmarks are brain deposits of extracellular amyloid beta plaques and intracellular neurofibrillary tangles (NFT). Cerebrospinal fluid reflects pathological changes in the brain; amyloid beta 1-42 is a marker of amyloid plaques, while total and phosphorylated tau are markers of NFT formation. Additional biomarkers associated with disease pathogenesis are needed, for better prognosis, more specific diagnosis, prediction of disease severity and progression and for improved patient classification in clinical trials. The aim of the present study was to evaluate brain-specific proteins as potential biomarkers of progression of AD. Methods: Overall, 30 candidate proteins were quantified in cerebrospinal fluid (CSF) samples from patients with mild cognitive impairment (MCI) and mild, moderate and severe AD dementia (n=101) using mass spectrometry-based selected reaction monitoring assays. ELISA was used for neuronal pentraxin receptor-1 (NPTXR) confirmation. Results: The best discrimination between MCI and more advanced AD stages (moderate and severe dementia) was observed for protein NPTXR (area under the curve, AUC=0.799). A statistically different abundance of this protein was observed between the two groups, with severe AD patients having progressively lower levels (p<0.05). ELISA confirmed lower levels in AD, in a separate cohort that included controls, MCI and AD patients. Conclusions: We conclude that NPTXR protein in CSF is a novel potential biomarker of AD progression and could have important utility in assessing treatment success in clinical trials.
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Affiliation(s)
- Ilijana Begcevic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Magda Tsolaki
- 1st Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Davor Brinc
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Marshall Brown
- Department of Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Eduardo Martinez-Morillo
- Laboratory of Medicine, Department of Clinical Biochemistry, Hospital Universitario Central, Oviedo, Spain
| | - Ioulietta Lazarou
- 1st Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mahi Kozori
- 1st Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Fani Tagaraki
- 1st Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Stella Nenopoulou
- 1st Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mara Gkioka
- 1st Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eutichia Lazarou
- 1st Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Bryant Lim
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Ihor Batruch
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Eleftherios P. Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Canada
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33
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Zhao M, Yang Y, Guo Z, Shao C, Sun H, Zhang Y, Sun Y, Liu Y, Song Y, Zhang L, Li Q, Liu J, Li M, Gao Y, Sun W. A Comparative Proteomics Analysis of Five Body Fluids: Plasma, Urine, Cerebrospinal Fluid, Amniotic Fluid, and Saliva. Proteomics Clin Appl 2018; 12:e1800008. [PMID: 29781159 DOI: 10.1002/prca.201800008] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 05/05/2018] [Indexed: 01/05/2023]
Abstract
PURPOSE Body fluid is considered a rich source of disease biomarkers. Proteins in many body fluids have potential clinical applications for disease diagnostic and prognostic predictions. EXPERIMENTAL DESIGN To determine differences in the protein components and functional features of body fluids, a proteomic comparison of five body fluids (plasma, urine, cerebrospinal fluid, saliva, and amniotic fluid) was conducted by high-resolution mass spectrometry. RESULTS A total of 4717 nonredundant proteins were identified, and the concentrations of 3433 proteins were estimated by an intensity-based algorithm quantitation method. Among them, 564 proteins were shared among the five body fluids, with common functions in the coagulation/prothrombin system and inflammatory response. A total of 36.7% of the proteins were detected in only one body fluid and were closely related to their adjacent tissues by function. The functional analysis of the remaining 2986 proteins showed that similar functions might be shared among different body fluids, which highlighted intimate connection in the body. CONCLUSIONS AND CLINICAL RELEVANCE The quantitative comparative functional analysis indicated that body fluids might reflect the diverse functions of the whole body rather than the characteristics of their adjacent tissues. The above data might indicate the potential application of body fluids for biomarker discovery.
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Affiliation(s)
- Mindi Zhao
- Department of Pathology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.,Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Beijing, 100730, China
| | - Yehong Yang
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Zhengguang Guo
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Chen Shao
- Center for Bioinformatics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Haidan Sun
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Yang Zhang
- Department of Neurosurgery, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China
| | - Ying Sun
- Department of Nephrology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yaoran Liu
- Department of Stomatology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yijun Song
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Liwei Zhang
- Department of Neurosurgery, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China
| | - Qian Li
- Department of Stomatology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Juntao Liu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Mingxi Li
- Department of Nephrology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, Gene Engineering and Biotechnology Beijing Key Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Wei Sun
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
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Proteomic approach to profiling immune complex antigens in cerebrospinal fluid samples from patients with central nervous system autoimmune diseases. Clin Chim Acta 2018; 484:26-31. [PMID: 29775619 DOI: 10.1016/j.cca.2018.05.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/23/2018] [Accepted: 05/11/2018] [Indexed: 01/01/2023]
Abstract
BACKGROUND Immune complexes (ICs) may clearly reflect immunological abnormalities caused by disease, especially for autoimmune diseases. Although ICs have been detected in cerebrospinal fluid (CSF) from patients with CNS autoimmune diseases, identities of antigens in such ICs have not been comprehensively determined. METHODS We used immune complexome analysis, in which nano-liquid chromatography-tandem mass spectrometry is employed to comprehensively identify antigens incorporated into ICs in biological fluids, to characterize ICs in CSF samples from patients with CNS autoimmune diseases, and to find disease-specific IC antigen to a certain CNS autoimmune disease. Also, we compared the IC antigens we identified with the reported CSF proteome or with the published plasma proteome to examine if the method is distinguished from the conventional CSF proteome analysis. RESULTS We identified 176 antigens in 78 CSF samples. We then assessed the overlaps among these antigens, the CSF proteome, and the plasma proteome; 140 of the 176 antigens were found to be exclusively detected by our method. Notably, IC-associated suprabasin in CSF was 100% specific to neuropsychiatric systemic lupus erythematosus (NPSLE). CONCLUSIONS This report is the first to comprehensively identify the antigens incorporated into ICs in CSF. There was limited overlap between the antigens we identified and the CSF proteome or the plasma proteome; therefore, our method can be distinguished from the conventional CSF proteome analysis. Although the sensitivity of disease-specific IC-antigens detected in immune complexome analysis screening, the sensitivity may be improved by developing an ELISA method specifically for detecting the ICs. Immune complexome analysis of CSF may be a new and promising path to biomarker discovery for diagnosis and study for CNS autoimmune diseases.
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A comprehensive profile and inter-individual variations analysis of the human normal amniotic fluid proteome. J Proteomics 2018; 192:1-9. [PMID: 29684686 DOI: 10.1016/j.jprot.2018.04.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/23/2018] [Accepted: 04/14/2018] [Indexed: 11/21/2022]
Abstract
Amniotic fluid contains large amounts of proteins produced by amnion epithelial cells, fetal tissues, fetal excretions and placental tissues; thus, it is an important potential source of biomarkers for identifying fetal pathologies. In this study, a pooled AF sample from 7 healthy volunteers was used to provide a comprehensive profile of normal human AF proteome using immunoaffinity depletion of 14 high-abundance proteins. Each individual AF sample was used to analyze inter-individual variations with iTRAQ method. As a result, a total of 2881 non-redundant proteins were identified, and 1624 proteins were quantified based on the peak intensity-based semi-quantification (iBAQ) method. Gene Ontology (GO) analysis showed that the AF proteome was enriched in extracellular region and extracellular matrix. Further function annotation showed that the top canonical pathway was axonal guidance signaling. The inter-individual variation analysis of 7 individual AF samples showed that the median inter-individual CV (Coefficient of variation) was 0.22. iBAQ quantification analysis revealed that the inter-individual variations were not correlated with protein abundance. GO analysis indicated that intracellular proteins tended to have higher CVs, and extracellular proteins tended to have lower CVs. These data will contribute to a better understanding of amniotic fluid proteomic analysis and biomarker discovery. SIGNIFICANCE: Amniotic fluid is an important potential source of biomarkers for identifying fetal pathologies. This study provided a large database for the normal human amniotic fluid proteome and analysis of inter-individual variations in amniotic fluid proteomes, which will offer a baseline reference for further AF proteomic analysis and pregnancy-related disease biomarker discovery.
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36
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Begcevic I, Brinc D, Brown M, Martinez-Morillo E, Goldhardt O, Grimmer T, Magdolen V, Batruch I, Diamandis EP. Brain-related proteins as potential CSF biomarkers of Alzheimer's disease: A targeted mass spectrometry approach. J Proteomics 2018; 182:12-20. [PMID: 29684683 DOI: 10.1016/j.jprot.2018.04.027] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/15/2018] [Accepted: 04/17/2018] [Indexed: 12/30/2022]
Abstract
Alzheimer's disease (AD) is the most common cause of dementia, characterized by progressive cognitive decline. The main disease hallmarks include amyloid beta aggregates and neurofibrillary tangles. Brain pathology is reflected in cerebrospinal fluid (CSF); the core biomarkers amyloid beta 1-42, total and phosphorylated tau protein levels are changed, relative to cognitively normal elderly. Still, there is a need for additional biomarkers which could identify disease more accurately and at an earlier stage, predict severity and be used in research settings. Here we evaluated 30 brain-related proteins as candidate biomarkers of AD. Proteins were quantified in CSF samples from cognitively healthy individuals (n = 23) and patients with mild cognitive impairment (MCI) due to AD (n = 20) or dementia due to AD (n = 10) using selected reaction monitoring mass spectrometry assays. APLP1 protein was increased in MCI relative to control (p < 0.001). The best discrimination between MCI vs. controls was observed with a model combining APLP1 and SPP1 proteins (area under the curve, AUC = 0.84). The strongest associations between protein abundance and disease severity were found for APLP1, CNTN2 and SPP1 proteins, which had a significant correlation with MMSE and CDR tests (p < 0.05). This study identifies new proteins with biomarker potential at various stages of AD severity. SIGNIFICANCE The current study evaluated 30 brain-related, highly specific proteins as candidate biomarkers of AD diagnosis. Protein APLP1 showed promise as early AD biomarker; protein panel APLP1 and SPP1 had the best diagnostic potential in discriminating MCI from control group, while proteins APLP1, SPP1 and CNTN2 may be indicators of disease progression, demonstrating weak to moderate correlation with cognitive tests. This study therefore identifies new proteins with biomarker potential at early AD stage. If the performance of proposed biomarkers is further confirmed, these proteins may add value in the clinic or clinical trial settings as diagnostic biomarkers (alone or in combination with the existing biomarkers) of the prodromal AD stage, and in monitoring disease progression.
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Affiliation(s)
- Ilijana Begcevic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Davor Brinc
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Marshall Brown
- Department of Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Eduardo Martinez-Morillo
- Laboratory of Medicine, Department of Clinical Biochemistry, Hospital Universitario Central, Oviedo, Spain
| | - Oliver Goldhardt
- Department of Psychiatry and Psychotherapy, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Timo Grimmer
- Department of Psychiatry and Psychotherapy, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Viktor Magdolen
- Department of Obstetrics and Gynecology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Ihor Batruch
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada.
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Waldera-Lupa DM, Etemad-Parishanzadeh O, Brocksieper M, Kirchgaessler N, Seidel S, Kowalski T, Montesinos-Rongen M, Deckert M, Schlegel U, Stühler K. Proteomic changes in cerebrospinal fluid from primary central nervous system lymphoma patients are associated with protein ectodomain shedding. Oncotarget 2017; 8:110118-110132. [PMID: 29299134 PMCID: PMC5746369 DOI: 10.18632/oncotarget.22654] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/27/2017] [Indexed: 01/01/2023] Open
Abstract
Primary central nervous system lymphomas (PCNSLs) are mature B-cell lymphomas confined to the central nervous system (CNS). Blood-brain barrier (BBB) dysfunction drastically alters the cerebrospinal fluid (CSF) proteome in PCNSL patients. To reveal the interaction of PCNSL tumors with CNS structures and the vasculature, we conducted a whole-proteome analysis of CSF from PCNSL patients (n = 17 at initial diagnosis) and tumor-free controls (n = 10) using label-free quantitative mass spectrometry. We identified 601 proteins in the CSF proteome using a one-step approach without further prefractionation, and quantified 438 proteins in detail using the Hi-N method. An immunoassay revealed that 70% of the patients in our unselected PCNSL patient cohort had BBB dysfunction. Correlation analysis indicated that 127 (30%) of the quantified proteins were likely increased in PCSNL patients due to BBB dysfunction. After the exclusion of these proteins, 66 were found to differ in abundance (fold-change > 2.0, p < 0.05) between PCNSL and control CSF proteomes, and most of those were associated with the CNS. These data also provide the first evidence that proteomic changes in CSF from PCNSL patients are mainly associated with protein ectodomain shedding, and that shedding of human leukocyte antigen class 2 proteins is a mechanism of tumor-cell immune evasion.
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Affiliation(s)
- Daniel Michael Waldera-Lupa
- Molecular Proteomics Laboratory, Institute of Molecular Medicine, Universitaetsklinikum Düsseldorf, Düsseldorf, Germany
| | - Omid Etemad-Parishanzadeh
- Molecular Proteomics Laboratory, Institute of Molecular Medicine, Universitaetsklinikum Düsseldorf, Düsseldorf, Germany
| | - Mareike Brocksieper
- Molecular Proteomics Laboratory, Institute of Molecular Medicine, Universitaetsklinikum Düsseldorf, Düsseldorf, Germany
| | - Nina Kirchgaessler
- Molecular Proteomics Laboratory, Institute of Molecular Medicine, Universitaetsklinikum Düsseldorf, Düsseldorf, Germany
| | - Sabine Seidel
- Department of Neurology, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Thomas Kowalski
- Department of Neurology, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | | | - Martina Deckert
- Institute of Neuropathology, University of Cologne, Cologne, Germany
| | - Uwe Schlegel
- Department of Neurology, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Institute of Molecular Medicine, Universitaetsklinikum Düsseldorf, Düsseldorf, Germany.,Biologisch-Medizinisches Forschungszentrum, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
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38
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Lewandowska AE, Macur K, Czaplewska P, Liss J, Łukaszuk K, Ołdziej S. Qualitative and Quantitative Analysis of Proteome and Peptidome of Human Follicular Fluid Using Multiple Samples from Single Donor with LC-MS and SWATH Methodology. J Proteome Res 2017; 16:3053-3067. [PMID: 28658951 DOI: 10.1021/acs.jproteome.7b00366] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Human follicular fluid (hFF) is a natural environment of oocyte maturation, and some components of hFF could be used to judge oocyte capability for fertilization and further development. In our pilot small-scale study three samples from four donors (12 samples in total) were analyzed to determine which hFF proteins/peptides could be used to differentiate individual oocytes and which are patient-specific. Ultrafiltration was used to fractionate hFF to high-molecular-weight (HMW) proteome (>10 kDa) and low-molecular-weight (LMW) peptidome (<10 kDa) fractions. HMW and LMW compositions were analyzed using LC-MS in SWATH data acquisition and processing methodology. In total we were able to identify 158 proteins, from which 59 were never reported before as hFF components. 55 (45 not reported before) proteins were found by analyzing LMW fraction, 67 (14 not reported before) were found by analyzing HMW fraction, and 36 were identified in both fractions of hFF. We were able to perform quantitative analysis for 72 proteins from HMW fraction of hFF. We found that concentrations of 11 proteins varied substantially among hFF samples from single donors, and those proteins are promising targets to identify biomarkers useful in oocyte quality assessment.
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Affiliation(s)
- Aleksandra E Lewandowska
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk , Abrahama 58, 80-307 Gdańsk, Gdańsk, Poland
| | - Katarzyna Macur
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk , Abrahama 58, 80-307 Gdańsk, Gdańsk, Poland
| | - Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk , Abrahama 58, 80-307 Gdańsk, Gdańsk, Poland
| | - Joanna Liss
- INVICTA Fertility and Reproductive Center , Trzy Lipy 3, 80-172 Gdańsk, Gdańsk, Poland
| | - Krzysztof Łukaszuk
- INVICTA Fertility and Reproductive Center , Trzy Lipy 3, 80-172 Gdańsk, Gdańsk, Poland.,Department of Obstetrics and Gynecological Nursing, Faculty of Health Sciences, Medical University of Gdańsk , Dębinki 7, 80-211 Gdańsk, Gdańsk, Poland
| | - Stanisław Ołdziej
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk , Abrahama 58, 80-307 Gdańsk, Gdańsk, Poland
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39
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Metzger F, Mischek D, Stoffers F. The Connected Steady State Model and the Interdependence of the CSF Proteome and CSF Flow Characteristics. Front Neurosci 2017; 11:241. [PMID: 28579938 PMCID: PMC5437178 DOI: 10.3389/fnins.2017.00241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 04/12/2017] [Indexed: 11/14/2022] Open
Abstract
Here we show that the hydrodynamic radii-dependent entry of blood proteins into cerebrospinal fluid (CSF) can best be modeled with a diffusional system of consecutive interdependent steady states between barrier-restricted molecular flux and bulk flow of CSF. The connected steady state model fits precisely to experimental results and provides the theoretical backbone to calculate the in-vivo hydrodynamic radii of blood-derived proteins as well as individual barrier characteristics. As the experimental reference set we used a previously published large-scale patient cohort of CSF to serum quotient ratios of immunoglobulins in relation to the respective albumin quotients. We related the inter-individual variances of these quotient relationships to the individual CSF flow time and barrier characteristics. We claim that this new concept allows the diagnosis of inflammatory processes with Reibergrams derived from population-based thresholds to be shifted to individualized judgment, thereby improving diagnostic sensitivity. We further use the source-dependent gradient patterns of proteins in CSF as intrinsic tracers for CSF flow characteristics. We assume that the rostrocaudal gradient of blood-derived proteins is a consequence of CSF bulk flow, whereas the slope of the gradient is a consequence of the unidirectional bulk flow and bidirectional pulsatile flow of CSF. Unlike blood-derived proteins, the influence of CSF flow characteristics on brain-derived proteins in CSF has been insufficiently discussed to date. By critically reviewing existing experimental data and by reassessing their conformity to CSF flow assumptions we conclude that the biomarker potential of brain-derived proteins in CSF can be improved by considering individual subproteomic dynamics of the CSF system.
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Affiliation(s)
- Fabian Metzger
- Department of Neurology, Ulm University HospitalUlm, Germany
| | | | - Frédéric Stoffers
- Fakultät für Mathematik und Wirtschaftswissenschaften, Institute of Analysis, Universität UlmUlm, Germany
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40
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Yang L, Stewart T, Shi M, Pottiez G, Dator R, Wu R, Aro P, Schuster RJ, Ginghina C, Pan C, Gao Y, Qian W, Zabetian CP, Hu SC, Quinn JF, Zhang J. An alpha-synuclein MRM assay with diagnostic potential for Parkinson's disease and monitoring disease progression. Proteomics Clin Appl 2017; 11. [PMID: 28319654 DOI: 10.1002/prca.201700045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 03/10/2017] [Accepted: 03/15/2017] [Indexed: 12/12/2022]
Abstract
AIM The alpha-synuclein (α-syn) level in human cerebrospinal fluid (CSF), as measured by immunoassays, is promising as a Parkinson's disease (PD) biomarker. However, the levels of total α-syn are inconsistent among studies with large cohorts and different measurement platforms. Total α-syn level also does not correlate with disease severity or progression. Here, the authors developed a highly sensitive MRM method to measure absolute CSF α-syn peptide concentrations without prior enrichment or fractionation, aiming to discover new candidate biomarkers. RESULTS Six peptides covering 73% of protein sequence were reliably identified, and two were consistently quantified in cross-sectional and longitudinal cohorts. Absolute concentration of α-syn in human CSF was determined to be 2.1 ng/mL. A unique α-syn peptide, TVEGAGSIAAATGFVK (81-96), displayed excellent correlation with previous immunoassay results in two independent PD cohorts (p < 0.001), correlated with disease severity, and its changes significantly tracked the disease progression longitudinally. CONCLUSIONS An MRM assay to quantify human CSF α-syn was developed and optimized. Sixty clinical samples from cross-sectional and longitudinal PD cohorts were analyzed with this approach. Although further larger scale validation is needed, the results suggest that α-syn peptide could serve as a promising biomarker in PD diagnosis and progression.
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Affiliation(s)
- Li Yang
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Min Shi
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Gwenael Pottiez
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Romel Dator
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Rui Wu
- Department of Pathology, University of Washington, Seattle, WA, USA.,Department of Pathology, No. 3 Hospital of Beijing University, Beijing, China
| | - Patrick Aro
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Carmen Ginghina
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Catherine Pan
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Yuqian Gao
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Weijun Qian
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Cyrus P Zabetian
- Parkinson's Disease Research and Geriatric Research, Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA.,Department of Neurology, University of Washington School of Medicine, Seattle, WA, USA
| | - Shu-Ching Hu
- Department of Neurology, University of Washington School of Medicine, Seattle, WA, USA
| | - Joseph F Quinn
- Department of Neurology, Oregon Health and Science University, Portland, OR, USA
| | - Jing Zhang
- Department of Pathology, University of Washington, Seattle, WA, USA.,Department of Pathology, Peking University Health Science Centre and Third Hospital, Beijing, 100083, China
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41
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Proteomic Biomarker Identification in Cerebrospinal Fluid for Leptomeningeal Metastases with Neurological Complications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 974:85-96. [PMID: 28353226 DOI: 10.1007/978-3-319-52479-5_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Leptomeningeal metastases (LM) from solid tumours, lymphoma and leukaemia are characterized by multifocal neurological deficits with a high mortality rate. Early diagnosis and initiation of treatment are essential to kerb neurological deterioration. However, this is not always possible as 25% of cerebrospinal fluid samples produce false-negative results at first cytological examination. The identification of biomarkers that allow stratification of individuals according to risk for developing LM would be a major benefit. Proteomic-based approaches are now in increasing use for this purpose, and these are reviewed in this chapter with a focus on cerebrospinal fluid (CSF) analyses. The construction of a CSF proteome disease database would also facilitate analysis of other neurological disorders.
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42
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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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43
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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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44
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Faubel R, Westendorf C, Bodenschatz E, Eichele G. Cilia-based flow network in the brain ventricles. Science 2016; 353:176-8. [PMID: 27387952 DOI: 10.1126/science.aae0450] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 06/10/2016] [Indexed: 12/24/2022]
Abstract
Cerebrospinal fluid conveys many physiologically important signaling factors through the ventricular cavities of the brain. We investigated the transport of cerebrospinal fluid in the third ventricle of the mouse brain and discovered a highly organized pattern of cilia modules, which collectively give rise to a network of fluid flows that allows for precise transport within this ventricle. We also discovered a cilia-based switch that reliably and periodically alters the flow pattern so as to create a dynamic subdivision that may control substance distribution in the third ventricle. Complex flow patterns were also present in the third ventricles of rats and pigs. Our work suggests that ciliated epithelia can generate and maintain complex, spatiotemporally regulated flow networks.
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Affiliation(s)
- Regina Faubel
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Westendorf
- Max Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, 37077 Göttingen, Germany
| | - Eberhard Bodenschatz
- Max Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, 37077 Göttingen, Germany
| | - Gregor Eichele
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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45
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Begcevic I, Brinc D, Drabovich AP, Batruch I, Diamandis EP. Identification of brain-enriched proteins in the cerebrospinal fluid proteome by LC-MS/MS profiling and mining of the Human Protein Atlas. Clin Proteomics 2016; 13:11. [PMID: 27186164 PMCID: PMC4868024 DOI: 10.1186/s12014-016-9111-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/19/2016] [Indexed: 12/21/2022] Open
Abstract
Background Cerebrospinal fluid (CSF) is a proximal fluid which communicates closely with brain tissue, contains numerous brain-derived proteins and thus represents a promising fluid for discovery of biomarkers of central nervous system (CNS) diseases. The main purpose of this study was to generate an extensive CSF proteome and define brain-related proteins identified in CSF, suitable for development of diagnostic assays. Methods Six non-pathological CSF samples from three female and three male individuals were selected for CSF analysis. Samples were first subjected to strong cation exchange chromatography, followed by LC-MS/MS analysis. Secreted and membrane-bound proteins enriched in the brain tissues were retrieved from the Human Protein Atlas. Results In total, 2615 proteins were identified in the CSF. The number of proteins identified per individual sample ranged from 1109 to 1421, with inter-individual variability between six samples of 21 %. Based on the Human Protein Atlas, 78 brain-specific proteins found in CSF samples were proposed as a signature of brain-enriched proteins in CSF. Conclusion A combination of Human Protein Atlas database and experimental search of proteins in specific body fluid can be applied as an initial step in search for disease biomarkers specific for a particular tissue. This signature may be of significant interest for development of novel diagnostics of CNS diseases and identification of drug targets. Electronic supplementary material The online version of this article (doi:10.1186/s12014-016-9111-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ilijana Begcevic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada ; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON Canada
| | - Davor Brinc
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada ; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON Canada ; Department of Clinical Biochemistry, University Health Network, Toronto, ON Canada
| | - Andrei P Drabovich
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada ; Department of Clinical Biochemistry, University Health Network, Toronto, ON Canada
| | - Ihor Batruch
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada ; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON Canada ; Department of Clinical Biochemistry, University Health Network, Toronto, ON Canada
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46
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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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47
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Kazemizadeh Gol MA, Lund TC, Levine SC, Adams ME. Quantitative Proteomics of Vestibular Schwannoma Cerebrospinal Fluid. Otolaryngol Head Neck Surg 2016; 154:902-6. [DOI: 10.1177/0194599816630544] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/13/2016] [Indexed: 12/15/2022]
Abstract
This pilot study aimed to identify candidate proteins for future study that are differentially expressed in vestibular schwannoma (VS) cerebrospinal fluid (CSF) and to compare such proteins with those previously identified in perilymph and specimen secretions. CSF was collected intraoperatively prior to removal of untreated sporadic VS (3 translabyrinthine, 3 middle cranial fossa approaches) and compared with reference CSF samples. After proteolytic digestion and iTRAQ labeling, tandem mass spectrometry with ProteinPilot was used to identify candidate proteins. Of the 237 proteins detected, 13 were dysregulated in ≥3 of the 6 VS patients versus controls, and 13 were dysregulated (12 up, 1 down) in samples from patients with class D versus class B hearing. Four perilymph proteins of interest were dysregulated in ≥1 VS CSF samples. Thus, 26 candidate VS CSF biomarkers were identified that should be considered in future VS biomarker and tumor pathophysiology investigations.
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Affiliation(s)
| | - Troy C. Lund
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Samuel C. Levine
- Department of Otolaryngology/Head and Neck Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Meredith E. Adams
- Department of Otolaryngology/Head and Neck Surgery, University of Minnesota, Minneapolis, Minnesota, USA
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48
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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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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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Lehmann S, Vialaret J, Combe GG, Bauchet L, Hanon O, Girard M, Gabelle A, Hirtz C. Stable Isotope Labeling by Amino acid in Vivo (SILAV): a new method to explore protein metabolism. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1917-1925. [PMID: 26411513 DOI: 10.1002/rcm.7289] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/21/2015] [Accepted: 07/24/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Intravenous administration of stable isotope labeled amino acid ((13)C6-leucine) to humans recently made it possible to study the metabolism of specific biomarkers in cerebrospinal fluid (CSF) using targeted mass spectrometry (MS). This labeling approach could be of great interest for monitoring many leucine-containing peptides in parallel, using high-resolution MS. This will make it possible to quantify the rates of synthesis and clearance of a large range of proteins in humans with a view to obtaining new insights into protein metabolism processes and the pathophysiology of diseases such as Alzheimer's disease. METHODS Proteins from human lumbar and ventricular CSF samples collected at different times after intravenous (13)C6-leucine infusion were digested enzymatically with LysC/trypsin after being denatured, reduced and alkylated. Desalted tryptic peptides were fractionated using Strong Cation eXchange chromatography (SCX) and analyzed using nanoflow liquid chromatography (nano-LC) coupled to a QTOF Impact II (Bruker Daltonics) mass spectrometer. Data-dependent acquisition (DDA) mode was used to identify and quantify light and heavy (13)C6-leucine peptides. The ratios of (13)C6-leucine incorporation were calculated using the Skyline software program in order to determine the rates of appearance and clearance of proteins in the CSF. RESULTS After SCX fractionation and quadrupole time-of-flight (QTOF) analysis, 4528 peptides containing leucine were identified in five fractions prepared from 40 μL of CSF. Upon analyzing one of these fractions, 66 peptides (2.7%) corresponding to 61 individual proteins had significant and reproducible rate of (13)C6-leucine incorporation at various time points. The plots of the light-to-heavy peptide ratios showed the existence of proteins with different patterns of appearance and clearance in the CSF. CONCLUSIONS The Stable Isotope Labeling Amino acid in Vivo (SILAV) method presented here, which yields unprecedented information about protein metabolism in humans, constitutes a promising new approach which certainly holds great potential in the field of clinical proteomics.
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Affiliation(s)
- Sylvain Lehmann
- CHRU de Montpellier, Université de Montpellier and INSERM U1183, IRMB, Laboratoire de Biochimie Protéomique Clinique, Montpellier, France
| | - Jérôme Vialaret
- CHRU de Montpellier, Université de Montpellier and INSERM U1183, IRMB, Laboratoire de Biochimie Protéomique Clinique, Montpellier, France
| | - Guillaume Gras Combe
- Service de Neurochirurgie, CHRU de Montpellier, hôpital Gui de Chauliac, Montpellier, INSERM U 1051 and Université de Montpellier, Montpellier, France
| | - Luc Bauchet
- Service de Neurochirurgie, CHRU de Montpellier, hôpital Gui de Chauliac, Montpellier, INSERM U 1051 and Université de Montpellier, Montpellier, France
| | - Olivier Hanon
- AP-HP, Hôpital Broca, Service de Gériatrie, Paris, France, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Marine Girard
- CHRU de Montpellier, Université de Montpellier and INSERM U1183, IRMB, Laboratoire de Biochimie Protéomique Clinique, Montpellier, France
| | - Audrey Gabelle
- CHRU de Montpellier, Université de Montpellier and INSERM U1183, IRMB, Laboratoire de Biochimie Protéomique Clinique, Montpellier, France
- Centre Mémoire de Ressources et de Recherche Languedoc-Roussillon, Département de Neurologie, CHRU de Montpellier, hôpital Gui de Chauliac, Montpellier, and Université de Montpellier, Montpellier, France
| | - Christophe Hirtz
- CHRU de Montpellier, Université de Montpellier and INSERM U1183, IRMB, Laboratoire de Biochimie Protéomique Clinique, Montpellier, France
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