1
|
Shao D, Huang L, Wang Y, Cui X, Li Y, Wang Y, Ma Q, Du W, Cui J. HBFP: a new repository for human body fluid proteome. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6395039. [PMID: 34642750 PMCID: PMC8516408 DOI: 10.1093/database/baab065] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/15/2022]
Abstract
Body fluid proteome has been intensively studied as a primary source for disease
biomarker discovery. Using advanced proteomics technologies, early research
success has resulted in increasingly accumulated proteins detected in different
body fluids, among which many are promising biomarkers. However, despite a
handful of small-scale and specific data resources, current research is clearly
lacking effort compiling published body fluid proteins into a centralized and
sustainable repository that can provide users with systematic analytic tools. In
this study, we developed a new database of human body fluid proteome (HBFP) that
focuses on experimentally validated proteome in 17 types of human body fluids.
The current database archives 11 827 unique proteins reported by 164
scientific publications, with a maximal false discovery rate of 0.01 on both the
peptide and protein levels since 2001, and enables users to query, analyze and
download protein entries with respect to each body fluid. Three unique features
of this new system include the following: (i) the protein annotation page
includes detailed abundance information based on relative qualitative measures
of peptides reported in the original references, (ii) a new score is calculated
on each reported protein to indicate the discovery confidence and (iii) HBFP
catalogs 7354 proteins with at least two non-nested uniquely mapping peptides of
nine amino acids according to the Human Proteome Project Data Interpretation
Guidelines, while the remaining 4473 proteins have more than two unique peptides
without given sequence information. As an important resource for human protein
secretome, we anticipate that this new HBFP database can be a powerful tool that
facilitates research in clinical proteomics and biomarker discovery. Database URL:https://bmbl.bmi.osumc.edu/HBFP/
Collapse
Affiliation(s)
- Dan Shao
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, 122E Avery Hall, 1144 T St., Lincoln, NE 68588, USA.,Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China.,Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Lan Huang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Yan Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Xueteng Cui
- Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Yufei Li
- Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Yao Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 310G Lincoln tower, 1800 cannon drive, Columbus, OH 43210, USA
| | - Wei Du
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Juan Cui
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, 122E Avery Hall, 1144 T St., Lincoln, NE 68588, USA
| |
Collapse
|
2
|
Voukali E, Veetil NK, Němec P, Stopka P, Vinkler M. Comparison of plasma and cerebrospinal fluid proteomes identifies gene products guiding adult neurogenesis and neural differentiation in birds. Sci Rep 2021; 11:5312. [PMID: 33674647 PMCID: PMC7935914 DOI: 10.1038/s41598-021-84274-x] [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: 12/30/2020] [Accepted: 02/10/2021] [Indexed: 11/27/2022] Open
Abstract
Cerebrospinal fluid (CSF) proteins regulate neurogenesis, brain homeostasis and participate in signalling during neuroinflammation. Even though birds represent valuable models for constitutive adult neurogenesis, current proteomic studies of the avian CSF are limited to chicken embryos. Here we use liquid chromatography-tandem mass spectrometry (nLC-MS/MS) to explore the proteomic composition of CSF and plasma in adult chickens (Gallus gallus) and evolutionarily derived parrots: budgerigar (Melopsittacus undulatus) and cockatiel (Nymphicus hollandicus). Because cockatiel lacks a complete genome information, we compared the cross-species protein identifications using the reference proteomes of three model avian species: chicken, budgerigar and zebra finch (Taeniopygia guttata) and found the highest identification rates when mapping against the phylogenetically closest species, the budgerigar. In total, we identified 483, 641 and 458 unique proteins consistently represented in the CSF and plasma of all chicken, budgerigar and cockatiel conspecifics, respectively. Comparative pathways analyses of CSF and blood plasma then indicated clusters of proteins involved in neurogenesis, neural development and neural differentiation overrepresented in CSF in each species. This study provides the first insight into the proteomics of adult avian CSF and plasma and brings novel evidence supporting the adult neurogenesis in birds.
Collapse
Affiliation(s)
- Eleni Voukali
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.
| | - Nithya Kuttiyarthu Veetil
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Pavel Němec
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Pavel Stopka
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.
| |
Collapse
|
3
|
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: 8] [Impact Index Per Article: 2.7] [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.
Collapse
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.
| |
Collapse
|
4
|
Huang L, Shao D, Wang Y, Cui X, Li Y, Chen Q, Cui J. Human body-fluid proteome: quantitative profiling and computational prediction. Brief Bioinform 2021; 22:315-333. [PMID: 32020158 PMCID: PMC7820883 DOI: 10.1093/bib/bbz160] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/22/2019] [Accepted: 10/18/2019] [Indexed: 12/15/2022] Open
Abstract
Empowered by the advancement of high-throughput bio technologies, recent research on body-fluid proteomes has led to the discoveries of numerous novel disease biomarkers and therapeutic drugs. In the meantime, a tremendous progress in disclosing the body-fluid proteomes was made, resulting in a collection of over 15 000 different proteins detected in major human body fluids. However, common challenges remain with current proteomics technologies about how to effectively handle the large variety of protein modifications in those fluids. To this end, computational effort utilizing statistical and machine-learning approaches has shown early successes in identifying biomarker proteins in specific human diseases. In this article, we first summarized the experimental progresses using a combination of conventional and high-throughput technologies, along with the major discoveries, and focused on current research status of 16 types of body-fluid proteins. Next, the emerging computational work on protein prediction based on support vector machine, ranking algorithm, and protein-protein interaction network were also surveyed, followed by algorithm and application discussion. At last, we discuss additional critical concerns about these topics and close the review by providing future perspectives especially toward the realization of clinical disease biomarker discovery.
Collapse
Affiliation(s)
- Lan Huang
- College of Computer Science and Technology in the Jilin University
| | - Dan Shao
- College of Computer Science and Technology in the Jilin University
- College of Computer Science and Technology in Changchun University
| | - Yan Wang
- College of Computer Science and Technology in the Jilin University
| | - Xueteng Cui
- College of Computer Science and Technology in the Changchun University
| | - Yufei Li
- College of Computer Science and Technology in the Changchun University
| | - Qian Chen
- College of Computer Science and Technology in the Jilin University
| | - Juan Cui
- Department of Computer Science and Engineering in the University of Nebraska-Lincoln
| |
Collapse
|
5
|
Bueno D, Parvas M, Nabiuni M, Miyan J. Embryonic cerebrospinal fluid formation and regulation. Semin Cell Dev Biol 2019; 102:3-12. [PMID: 31615690 DOI: 10.1016/j.semcdb.2019.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/10/2019] [Accepted: 09/12/2019] [Indexed: 01/01/2023]
Abstract
The vertebrate brain is organized, from its embryonic origin and throughout adult life, around a dynamic and complex fluid, the cerebrospinal fluid (CSF). There is growing interest in the composition, dynamics and function of the CSF in brain development research. It has been demonstrated in higher vertebrates that CSF has key functions in delivering diffusible signals and nutrients to the developing brain, contributing to the proliferation, differentiation and survival of neural progenitor cells, and to the patterning of the brain. It has also been shown that the composition and the homeostasis of CSF are tightly regulated following the closure of the anterior neuropore, just before the initiation of primary neurogenesis in the neural tissue surrounding brain cavities, before the formation of functional choroid plexus. In this review we draw together existing literature about the composition and formation of embryonic cerebrospinal fluid in birds and mammals, from the closure of the anterior neuropore to the formation of functional fetal choroid plexus, including mechanisms regulating its composition and homeostasis. The significance of CSF regulation within embryonic brain is also discussed from an evolutionary perspective.
Collapse
Affiliation(s)
- David Bueno
- Section of Biomedical, Evolutionary and Developmental Genetics, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643. Barcelona 08028, Catalonia Spain.
| | - Maryam Parvas
- Section of Biomedical, Evolutionary and Developmental Genetics, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 643. Barcelona 08028, Catalonia Spain
| | - Mohammad Nabiuni
- Division of Neuroscience & Experimental Psychology, Faculty of Biology, Medicine & Health, The University of Manchester, Stopford Building, Oxford Road. Manchester M13 9PT, UK
| | - Jaleel Miyan
- Division of Neuroscience & Experimental Psychology, Faculty of Biology, Medicine & Health, The University of Manchester, Stopford Building, Oxford Road. Manchester M13 9PT, UK
| |
Collapse
|
6
|
Identification of Potential Cerebrospinal Fluid Biomarkers To Discriminate between Infection and Sterile Inflammation in a Rat Model of Staphylococcus epidermidis Catheter Infection. Infect Immun 2019; 87:IAI.00311-19. [PMID: 31262978 PMCID: PMC6704599 DOI: 10.1128/iai.00311-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus epidermidis cerebrospinal fluid (CSF) shunt infection is a common complication of hydrocephalus treatment, creating grave neurological consequences for patients, especially when diagnosis is delayed. The current method of diagnosis relies on microbiological culture; however, awaiting culture results may cause treatment delays, or culture may fail to identify infection altogether, so newer methods are needed. Staphylococcus epidermidis cerebrospinal fluid (CSF) shunt infection is a common complication of hydrocephalus treatment, creating grave neurological consequences for patients, especially when diagnosis is delayed. The current method of diagnosis relies on microbiological culture; however, awaiting culture results may cause treatment delays, or culture may fail to identify infection altogether, so newer methods are needed. To investigate potential CSF biomarkers of S. epidermidis shunt infection, we developed a rat model allowing for serial CSF sampling. We found elevated levels of interleukin-10 (IL-10), IL-1β, chemokine ligand 2 (CCL2), and CCL3 in the CSF of animals implanted with S. epidermidis-infected catheters compared to sterile controls at day 1 postinfection. Along with increased chemokine and cytokine expression early in infection, neutrophil influx was significantly increased in the CSF of animals with infected catheters, suggesting that coupling leukocyte counts with inflammatory mediators may differentiate infection from sterile inflammation. Mass spectrometry analysis revealed that the CSF proteome in sterile animals was similar to that in infected animals at day 1; however, by day 5 postinfection, there was an increase in the number of differently expressed proteins in the CSF of infected compared to sterile groups. The expansion of the proteome at day 5 postinfection was interesting, as bacterial burdens began to decline by this point, yet the CSF proteome data indicated that the host response remained active, especially with regard to the complement cascade. Collectively, these results provide potential biomarkers to distinguish S. epidermidis infection from sterile postoperative inflammation.
Collapse
|
7
|
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.
Collapse
|
8
|
Lachén-Montes M, González-Morales A, Fernández-Irigoyen J, Santamaría E. Deployment of Label-Free Quantitative Olfactory Proteomics to Detect Cerebrospinal Fluid Biomarker Candidates in Synucleinopathies. Methods Mol Biol 2019; 2044:273-289. [PMID: 31432419 DOI: 10.1007/978-1-4939-9706-0_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nowadays, diagnosis of neurodegenerative disorders is mainly based on neuroimaging and clinical symptoms, although postmortem neuropathological confirmation remains the gold standard diagnostic technique. Therefore, cerebrospinal fluid (CSF) proteome is considered a valuable molecular repository for diagnosing and targeting the neurodegenerative process. It is well known that olfactory dysfunction is among the earliest features of synucleinopathies such as Parkinson's disease (PD). Consequently, we consider that the application of tissue proteomics in primary olfactory structures is an ideal approach to explore early pathophysiological changes, detecting olfactory proteins that might be tested in CSF as potential biomarkers. Data mining of mass spectrometry-generated datasets has revealed that 30% of the olfactory bulb (OB) proteome is also localized in CSF. In this chapter, we describe a method that utilizes label-free quantitative proteomics and computational analysis to characterize human OB proteomes and potential cerebrospinal fluid (CSF) biomarkers associated with neurodegenerative syndromes. For that, we applied peptide fractionation methods, followed by tandem mass spectrometry (nanoLC-MS/MS), in silico analysis, and semi-quantitative orthogonal techniques in OB derived from PD subjects. After obtaining the differential OB proteome across Lewy-type alpha-synucleinopathy (LTS) stages and further validating the method, this workflow was applied to probe changes in NEGR1 (neuronal growth regulator 1) and GNPDA2 (glucosamine-6-phosphate deaminase 2) protein levels in CSF derived from parkinsonian subjects with respect to controls, observing an inverse correlation between both proteins and α-synuclein, the principal component analysis of Lewy pathology.
Collapse
Affiliation(s)
- Mercedes Lachén-Montes
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Andrea González-Morales
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain
| | - Enrique Santamaría
- Proteomics Unit, Clinical Neuroproteomics Laboratory, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Proteored-ISCIII, Pamplona, Spain.
| |
Collapse
|
9
|
Kushnir MM, Peterson LK, Strathmann FG. Parathyroid hormone related protein concentration in human serum and CSF correlates with age. Clin Biochem 2017; 52:56-60. [PMID: 29122643 DOI: 10.1016/j.clinbiochem.2017.10.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 02/02/2023]
Abstract
BACKGROUND Parathyroid Hormone-Related Protein (PTHrP) is involved in intracellular calcium (Ca) regulation, and has been demonstrated to participate in regulation of Ca in brain cells, activation of neurons, and modulation of pain. However, there are conflicting reports regarding the presence of PTHrP in CSF. DESIGN AND METHODS PTHrP and Ca were quantified in paired CSF and serum samples using mass spectrometry-based methods. Associations between PTHrP and Ca concentrations with age, sex and concentrations of nine CSF diagnostic markers in a set of 140 paired serum and CSF patient samples were evaluated. RESULTS The observed median PTHrP concentration in CSF was 51 times higher than in serum; the median concentration of Ca in CSF was 1.8 times lower than in serum. We observed positive correlation between concentrations of PTHrP in CSF and serum (p=0.013). Distribution of PTHrP concentrations in serum was associated with age (p=0.0068) and the concentrations were higher in women. In samples with serum calcium concentrations within the reference intervals (n=118), central 95% distribution of concentrations for Ca-CSF, PTHrP-serum and PTHrP-CSF were 5.4 (4.5-6.1) mg/dL, 1.2 (0.5-2.5) pmol/L, 62 (22-125) pmol/L, respectively. CONCLUSIONS Our data demonstrate that PTHrP is a normal constituent of human CSF with median concentrations 51 fold higher than in serum. Elevated serum PTHrP concentrations were positively correlated with age and significantly higher in women. Our data suggest that CSF could be a significant source of circulating PTHrP.
Collapse
Affiliation(s)
- Mark M Kushnir
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States; Department of Pathology, University of Utah, Salt Lake City, UT, United States.
| | - Lisa K Peterson
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States; Department of Pathology, University of Utah, Salt Lake City, UT, United States
| | | |
Collapse
|
10
|
Pampalakis G, Sykioti VS, Ximerakis M, Stefanakou-Kalakou I, Melki R, Vekrellis K, Sotiropoulou G. KLK6 proteolysis is implicated in the turnover and uptake of extracellular alpha-synuclein species. Oncotarget 2017; 8:14502-14515. [PMID: 27845893 PMCID: PMC5362421 DOI: 10.18632/oncotarget.13264] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/28/2016] [Indexed: 01/08/2023] Open
Abstract
KLK6 is a serine protease highly expressed in the nervous system. In synucleinopathies, including Parkinson disease, the levels of KLK6 inversely correlate with α-synuclein in CSF. Recently, we suggested that recombinant KLK6 mediates the degradation of extracellular α-synuclein directly and via a proteolytic cascade that involves unidentified metalloproteinase(s). Here, we show that recombinant and naturally secreted KLK6 can readily cleave α-synuclein fibrils that have the potential for cell-to-cell propagation in “a prion-like mechanism”. Importantly, KLK6-deficient primary cortical neurons have increased ability for α-synuclein fibril uptake. We also demonstrate that KLK6 activates proMMP2, which in turn can cleave α-synuclein. The repertoire of proteases activated by KLK6 in a neuronal environment was analyzed by degradomic profiling, which also identified ADAMTS19 and showed that KLK6 has a limited number of substrates indicating specific biological functions such as the regulation of α-synuclein turnover. We generated adenoviral vectors for KLK6 delivery and demonstrated that the levels of extracellular α-synuclein can be reduced by neuronally secreted KLK6. Our findings open the possibility to exploit KLK6 as a novel therapeutic target for Parkinson disease and other synucleinopathies.
Collapse
Affiliation(s)
- Georgios Pampalakis
- Department of Pharmacy, School of Health Sciences, University of Patras, Rion-Patras, Athens, Greece
| | - Vasia-Samantha Sykioti
- Center for Neurosciences, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Methodios Ximerakis
- Center for Neurosciences, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Ioanna Stefanakou-Kalakou
- Department of Pharmacy, School of Health Sciences, University of Patras, Rion-Patras, Athens, Greece
| | - Ronald Melki
- Paris-Saclay Institute of Neuroscience, Centre National de la Recherche Scientifique, Gif-Sur-Yvette, France
| | - Kostas Vekrellis
- Center for Neurosciences, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Georgia Sotiropoulou
- Department of Pharmacy, School of Health Sciences, University of Patras, Rion-Patras, Athens, Greece.,Center for Neurosciences, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| |
Collapse
|
11
|
Galicia N, Dégano R, Díez P, González-González M, Góngora R, Ibarrola N, Fuentes M. CSF analysis for protein biomarker identification in patients with leptomeningeal metastases from CNS lymphoma. Expert Rev Proteomics 2017; 14:363-372. [DOI: 10.1080/14789450.2017.1307106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- N. Galicia
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - R. Dégano
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - P. Díez
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
- Department of Medicine and General Service of Cytometry, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - M. González-González
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
- Department of Medicine and General Service of Cytometry, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - R. Góngora
- Department of Medicine and General Service of Cytometry, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - N. Ibarrola
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - M. Fuentes
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
- Department of Medicine and General Service of Cytometry, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| |
Collapse
|
12
|
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.
Collapse
|
13
|
Quanico J, Franck J, Wisztorski M, Salzet M, Fournier I. Combined MALDI Mass Spectrometry Imaging and Parafilm-Assisted Microdissection-Based LC-MS/MS Workflows in the Study of the Brain. Methods Mol Biol 2017; 1598:269-283. [PMID: 28508367 DOI: 10.1007/978-1-4939-6952-4_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Proteins and other biomolecules such as lipids are significant players in the central nervous system and are implicated in various neurological disorders. Their identification, quantification, and distribution are thus important not only in understanding the disease but also in developing treatments. A combined workflow allowing the localized microextraction of discrete regions identified by a matrix-assisted laser desorption/ionization mass spectrometry (MSI) imaging experiment for proteomics analysis by liquid chromatography/tandem mass spectrometry (LC MS/MS) is described in this chapter. MSI was initially used to map lipid distributions allowing for the identification of regions of interest (ROIs) that are then subjected to microextraction in a consecutive tissue section. Mounting of consecutive tissue on parafilm allows microdissection of the ROIs, where proteins can then be recovered for processing and LC MS/MS analysis. The PAM method provides a fast and cheap means to perform further downstream analysis after an MSI experiment.
Collapse
Affiliation(s)
- Jusal Quanico
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Julien Franck
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Maxence Wisztorski
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Michel Salzet
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France
| | - Isabelle Fournier
- Université de Lille 1, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000, Lille, France.
| |
Collapse
|
14
|
Abstract
Traumatic brain injury (TBI) is an injury to the brain caused by an external mechanical force, affecting millions of people worldwide. The disease course and prognosis are often unpredictable, and it can be challenging to determine an early diagnosis in case of mild injury as well as to accurately phenotype the injury. There is currently no cure for TBI-drugs having failed repeatedly in clinical trials-but an intense effort has been put to identify effective neuroprotective treatment. The detection of novel biomarkers, to understand more of the disease mechanism, facilitates early diagnosis, predicts disease progression, and develops molecularly targeted therapies that would be of high clinical interest. Over the last decade, there has been an increasing effort and initiative toward finding TBI-specific biomarker candidates. One promising strategy has been to use state-of-the-art neuroproteomics approaches to assess clinical biofluids and compare the cerebrospinal fluid (CSF) and blood proteome between TBI and control patients or between different subgroups of TBI. In this chapter, we summarize and discuss the status of biofluid proteomics in TBI, with a particular focus on the latest findings.
Collapse
|
15
|
Wang J, Cunningham R, Zetterberg H, Asthana S, Carlsson C, Okonkwo O, Li L. Label-free quantitative comparison of cerebrospinal fluid glycoproteins and endogenous peptides in subjects with Alzheimer's disease, mild cognitive impairment, and healthy individuals. Proteomics Clin Appl 2016; 10:1225-1241. [DOI: 10.1002/prca.201600009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 10/18/2016] [Accepted: 11/08/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Jingxin Wang
- Neuroscience Training Program; University of Wisconsin-Madison; Madison WI USA
| | | | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory; Sahlgrenska University Hospital; Mölndal Sweden
- Department of Psychiatry and Neurochemistry; Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg; Mölndal Sweden
- Department of Molecular Neuroscience; UCL Institute of Neurology; Queen Square London UK
| | - Sanjay Asthana
- Wisconsin Alzheimer's Disease Research Center; University of Wisconsin School of Medicine and Public Health; Madison WI USA
- Geriatric Research Education and Clinical Center; Wm. S. Middleton Veterans Hospital; Madison WI USA
- Wisconsin Alzheimer's Institute; University of Wisconsin School of Medicine and Public Health; Madison WI USA
| | - Cynthia Carlsson
- Wisconsin Alzheimer's Disease Research Center; University of Wisconsin School of Medicine and Public Health; Madison WI USA
- Geriatric Research Education and Clinical Center; Wm. S. Middleton Veterans Hospital; Madison WI USA
- Wisconsin Alzheimer's Institute; University of Wisconsin School of Medicine and Public Health; Madison WI USA
| | - Ozioma Okonkwo
- Neuroscience Training Program; University of Wisconsin-Madison; Madison WI USA
- Wisconsin Alzheimer's Disease Research Center; University of Wisconsin School of Medicine and Public Health; Madison WI USA
- Geriatric Research Education and Clinical Center; Wm. S. Middleton Veterans Hospital; Madison WI USA
- Wisconsin Alzheimer's Institute; University of Wisconsin School of Medicine and Public Health; Madison WI USA
| | - Lingjun Li
- Neuroscience Training Program; University of Wisconsin-Madison; Madison WI USA
- School of Pharmacy; University of Wisconsin-Madison; Madison WI USA
- Department of Chemistry; University of Wisconsin-Madison; Madison WI USA
- School of Life Sciences; Tianjin University; Tianjin China
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Remnestål J, Just D, Mitsios N, Fredolini C, Mulder J, Schwenk JM, Uhlén M, Kultima K, Ingelsson M, Kilander L, Lannfelt L, Svenningsson P, Nellgård B, Zetterberg H, Blennow K, Nilsson P, Häggmark-Månberg A. CSF profiling of the human brain enriched proteome reveals associations of neuromodulin and neurogranin to Alzheimer's disease. Proteomics Clin Appl 2016; 10:1242-1253. [PMID: 27604409 PMCID: PMC5157753 DOI: 10.1002/prca.201500150] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/25/2016] [Accepted: 09/02/2016] [Indexed: 01/08/2023]
Abstract
Purpose This study is part of a larger effort aiming to expand the knowledge of brain‐enriched proteins in human cerebrospinal fluid (CSF) and to provide novel insight into the relation between such proteins and different neurodegenerative diseases. Experimental design Here 280 brain‐enriched proteins in CSF from patients with Alzheimer's disease (AD), Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are profiled. In total, 441 human samples of ventricular CSF collected post mortem and lumbar CSF collected ante mortem are analyzed using 376 antibodies in a suspension bead array setup, utilizing a direct labelling approach. Results Among several proteins displaying differentiated profiles between sample groups, we focus here on two synaptic proteins, neuromodulin (GAP43) and neurogranin (NRGN). They are both found at elevated levels in CSF from AD patients in two independent cohorts, providing disease‐associated profiles in addition to verifying and strengthening previously observed patterns. Increased levels are also observed for patients for whom the AD diagnosis was not established at the time of sampling. Conclusions and clinical relevance These findings indicate that analyzing the brain‐enriched proteins in CSF is of particular interest to increase the understanding of the CSF proteome and its relation to neurodegenerative disorders. In addition, this study lends support to the notion that measurements of these synaptic proteins could potentially be of great relevance in future diagnostic tests for AD.
Collapse
Affiliation(s)
- Julia Remnestål
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - David Just
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Nicholas Mitsios
- SciLifeLab, Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Claudia Fredolini
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Jan Mulder
- SciLifeLab, Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kim Kultima
- Department of Medical Sciences, Cancer Pharmacology and Computational Medicine, Uppsala University, Uppsala, Sweden
| | - Martin Ingelsson
- Department of Public Health/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Lena Kilander
- Department of Public Health/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Lars Lannfelt
- Department of Public Health/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Per Svenningsson
- Translational Neuropharmacology, Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Bengt Nellgård
- Department of Anaesthesiology and Intensive Care, Institute of Clinical Sciences, The Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Anna Häggmark-Månberg
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Stockholm, Sweden
| |
Collapse
|
18
|
Proteomic Analysis of Non-depleted Serum Proteins from Bottlenose Dolphins Uncovers a High Vanin-1 Phenotype. Sci Rep 2016; 6:33879. [PMID: 27667588 PMCID: PMC5036180 DOI: 10.1038/srep33879] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/05/2016] [Indexed: 12/22/2022] Open
Abstract
Targeted approaches have been widely used to help explain physiological adaptations, but few studies have used non-targeted omics approaches to explore differences between diving marine mammals and terrestrial mammals. A rank comparison of undepleted serum proteins from common bottlenose dolphins (Tursiops truncatus) and pooled normal human serum led to the discovery of 11 proteins that appeared exclusive to dolphin serum. Compared to the comprehensive human plasma proteome, 5 of 11 serum proteins had a differential rank greater than 200. One of these proteins, Vanin-1, was quantified using parallel reaction monitoring in dolphins under human care and free-ranging dolphins. Dolphin serum Vanin-1 ranged between 31–106 μg/ml, which is 20–1000 times higher than concentrations reported for healthy humans. Serum Vanin-1 was also higher in dolphins under human care compared to free-ranging dolphins (64 ± 16 vs. 47 ± 12 μg/ml P < 0.05). Vanin-1 levels positively correlated with liver enzymes AST and ALT, and negatively correlated with white blood cell counts and fibrinogen in free-ranging dolphins. Major differences exist in the circulating blood proteome of the bottlenose dolphin compared to terrestrial mammals and exploration of these differences in bottlenose dolphins and other marine mammals may identify veiled protective strategies to counter physiological stress.
Collapse
|
19
|
Zheng Q, Chen H. Development and Applications of Liquid Sample Desorption Electrospray Ionization Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:411-448. [PMID: 27145689 DOI: 10.1146/annurev-anchem-071015-041620] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Desorption electrospray ionization mass spectrometry (DESI-MS) is a recent advance in the field of analytical chemistry. This review surveys the development of liquid sample DESI-MS (LS-DESI-MS), a variant form of DESI-MS that focuses on fast analysis of liquid samples, and its novel analy-tical applications in bioanalysis, proteomics, and reaction kinetics. Due to the capability of directly ionizing liquid samples, liquid sample DESI (LS-DESI) has been successfully used to couple MS with various analytical techniques, such as microfluidics, microextraction, electrochemistry, and chromatography. This review also covers these hyphenated techniques. In addition, several closely related ionization methods, including transmission mode DESI, thermally assisted DESI, and continuous flow-extractive DESI, are briefly discussed. The capabilities of LS-DESI extend and/or complement the utilities of traditional DESI and electrospray ionization and will find extensive and valuable analytical application in the future.
Collapse
Affiliation(s)
- Qiuling Zheng
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, and Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701;
| | - Hao Chen
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, and Edison Biotechnology Institute, Ohio University, Athens, Ohio 45701;
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Richens JL, Spencer HL, Butler M, Cantlay F, Vere KA, Bajaj N, Morgan K, O'Shea P. Rationalising the role of Keratin 9 as a biomarker for Alzheimer's disease. Sci Rep 2016; 6:22962. [PMID: 26973255 PMCID: PMC4789650 DOI: 10.1038/srep22962] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/19/2016] [Indexed: 02/07/2023] Open
Abstract
Keratin 9 was recently identified as an important component of a biomarker panel which demonstrated a high diagnostic accuracy (87%) for Alzheimer's disease (AD). Understanding how a protein which is predominantly expressed in palmoplantar epidermis is implicated in AD may shed new light on the mechanisms underlying the disease. Here we use immunoassays to examine blood plasma expression patterns of Keratin 9 and its relationship to other AD-associated proteins. We correlate this with the use of an in silico analysis tool VisANT to elucidate possible pathways through which the involvement of Keratin 9 may take place. We identify possible links with Dickkopf-1, a negative regulator of the wnt pathway, and propose that the abnormal expression of Keratin 9 in AD blood and cerebrospinal fluid may be a result of blood brain barrier dysregulation and disruption of the ubiquitin proteasome system. Our findings suggest that dysregulated Keratin 9 expression is a consequence of AD pathology but, as it interacts with a broad range of proteins, it may have other, as yet uncharacterized, downstream effects which could contribute to AD onset and progression.
Collapse
Affiliation(s)
- Joanna L Richens
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Hannah L Spencer
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Molly Butler
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Fiona Cantlay
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Kelly-Ann Vere
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Nin Bajaj
- Department of Neurology, Nottingham University Hospitals NHS Trust, Queen's Medical Centre, Nottingham, United Kingdom
| | - Kevin Morgan
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Paul O'Shea
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| |
Collapse
|
22
|
A Multiplex Protein Panel Applied to Cerebrospinal Fluid Reveals Three New Biomarker Candidates in ALS but None in Neuropathic Pain Patients. PLoS One 2016; 11:e0149821. [PMID: 26914813 PMCID: PMC4767403 DOI: 10.1371/journal.pone.0149821] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 02/04/2016] [Indexed: 12/13/2022] Open
Abstract
The objective of this study was to develop and apply a novel multiplex panel of solid-phase proximity ligation assays (SP-PLA) requiring only 20 μL of samples, as a tool for discovering protein biomarkers for neurological disease and treatment thereof in cerebrospinal fluid (CSF). We applied the SP-PLA to samples from two sets of patients with poorly understood nervous system pathologies amyotrophic lateral sclerosis (ALS) and neuropathic pain, where patients were treated with spinal cord stimulation (SCS). Forty-seven inflammatory and neurotrophic proteins were measured in samples from 20 ALS patients and 15 neuropathic pain patients, and compared to normal concentrations in CSF from control individuals. Nineteen of the 47 proteins were detectable in more than 95% of the 72 controls. None of the 21 proteins detectable in CSF from neuropathic pain patients were significantly altered by SCS. The levels of the three proteins, follistatin, interleukin-1 alpha, and kallikrein-5 were all significantly reduced in the ALS group compared to age-matched controls. These results demonstrate the utility of purpose designed multiplex SP-PLA panels in CSF biomarker research for understanding neuropathological and neurotherapeutic mechanisms. The protein changes found in the CSF of ALS patients may be of diagnostic interest.
Collapse
|
23
|
Häggmark A, Schwenk JM, Nilsson P. Neuroproteomic profiling of human body fluids. Proteomics Clin Appl 2015; 10:485-502. [PMID: 26286680 DOI: 10.1002/prca.201500065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/17/2015] [Accepted: 08/12/2015] [Indexed: 12/11/2022]
Abstract
Analysis of protein expression and abundance provides a possibility to extend the current knowledge on disease-associated processes and pathways. The human brain is a complex organ and dysfunction or damage can give rise to a variety of neurological diseases. Although many proteins potentially reflecting disease progress are originating from brain, the scarce availability of human tissue material has lead to utilization of body fluids such as cerebrospinal fluid and blood in disease-related research. Within the most common neurological disorders, much effort has been spent on studying the role of a few hallmark proteins in disease pathogenesis but despite extensive investigation, the signatures they provide seem insufficient to fully understand and predict disease progress. In order to expand the view the field of neuroproteomics has lately emerged alongside developing technologies, such as affinity proteomics and mass spectrometry, for multiplexed and high-throughput protein profiling. Here, we provide an overview of how such technologies have been applied to study neurological disease and we also discuss some important considerations concerning discovery of disease-associated profiles.
Collapse
Affiliation(s)
- Anna Häggmark
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| |
Collapse
|
24
|
Sundberg M, Bergquist J, Ramström M. High-abundant protein depletion strategies applied on dog cerebrospinal fluid and evaluated by high-resolution mass spectrometry. Biochem Biophys Rep 2015; 3:68-75. [PMID: 30338299 PMCID: PMC6189695 DOI: 10.1016/j.bbrep.2015.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/18/2015] [Accepted: 07/22/2015] [Indexed: 12/27/2022] Open
Abstract
As the number of fully sequenced animal genomes and the performance of advanced mass spectrometry-based proteomics techniques are continuously improving, there is now a great opportunity to increase the knowledge of various animal proteomes. This research area is further stimulated by a growing interest from veterinary medicine and the pharmaceutical industry. Cerebrospinal fluid (CSF) is a good source for better understanding of diseases related to the central nervous system, both in humans and other animals. In this study, four high-abundant protein depletion columns, developed for human or rat serum, were evaluated for dog CSF. For the analysis, a shotgun proteomics approach, based on nanoLC-LTQ Orbitrap MS/MS, was applied. All the selected approaches were shown to deplete dog CSF with different success. It was demonstrated that the columns significantly improved the coverage of the detected dog CSF proteome. An antibody-based column showed the best performance, in terms of efficiency, repeatability and the number of proteins detected in the sample. In total 983 proteins were detected. Of those, 801 proteins were stated as uncharacterized in the UniProt database. To the best of our knowledge, this is the so far largest number of proteins reported for dog CSF in one single study. We evaluated four high-abundant protein depletion kits on dog CSF. High abundant depletion kit developed for humans/rats can be used for dog CSF. Protein depletion of dog CSF gives extended coverage of the CSF proteome. In total, 983 dog proteins were identified in this study.
Collapse
Affiliation(s)
- Mårten Sundberg
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Box 599, 751 24 Uppsala, Sweden
| | - Jonas Bergquist
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Box 599, 751 24 Uppsala, Sweden
| | - Margareta Ramström
- Department of Chemistry - BMC, Analytical Chemistry and Science for Life Laboratory, Uppsala University, Box 599, 751 24 Uppsala, Sweden
| |
Collapse
|
25
|
Fernández-Irigoyen J, Zelaya MV, Perez-Valderrama E, Santamaría E. New insights into the human brain proteome: Protein expression profiling of deep brain stimulation target areas. J Proteomics 2015; 127:395-405. [PMID: 25845585 DOI: 10.1016/j.jprot.2015.03.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/09/2015] [Accepted: 03/19/2015] [Indexed: 12/30/2022]
Abstract
UNLABELLED Deep brain stimulation (DBS) is a neurosurgical procedure that provides therapeutic benefits for movement and affective disorders. The nucleus basalis of Meynert (NBM) and substantia nigra (SN) are considered target areas to apply DBS. Even though the degeneration of NBM and SN underlies the cognitive decline observed in neurological diseases, the protein knowledge derived from both areas is scarce. We have characterized the proteome present in both subcortical brain areas using the Triple TOF 5600 mass spectrometer, identifying 2775 and 3469 proteoforms in NBM and SN respectively. Data mining of MS-generated proteomic data have revealed that: i) 675 proteins tend to localize to synaptic ending, ii) 61% of the global dataset is also present in human CSF and/or plasma, and iii) 894 proteins have not been previously identified in healthy brain by MS. The correlation of NBM and SN proteomic expression profiles with human brain transcriptome data available at Allen Brain Atlas has revealed protein evidence for 250 genes considered with brain-wide expression and 112 genes with region-specific expression in human brain. In addition, protein datasets have been classified according to their chromosomal origin, increasing the current proteome coverage in healthy human brain. BIOLOGICAL SIGNIFICANCE The nucleus basalis of Meynert and substantia nigra are brain areas of clinical interest to apply the deep brain stimulation (DBS) technology in neurosurgery. Our proteomic characterization has revealed 675 proteins involved in the regulation of synaptic transmission, electrical machinery, and neurotransmitter release in both DBS target areas. Moreover, 2599 identified proteins present capacity to be secreted to the CSF and plasma. Our data contribute to a further step towards the characterization of the anatomical atlas of the human brain proteome, detecting 652 proteins that are common between different basal ganglia structures. This article is part of a Special Issue entitled: HUPO 2014.
Collapse
Affiliation(s)
- Joaquín Fernández-Irigoyen
- ProteoRed-ISCIII, Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Fundación Miguel Servet, Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain
| | - María Victoria Zelaya
- ProteoRed-ISCIII, Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Fundación Miguel Servet, Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain; Neurological Tissue Bank, Navarrabiomed, Fundación Miguel Servet, 31008 Pamplona, Spain
| | - Estela Perez-Valderrama
- ProteoRed-ISCIII, Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Fundación Miguel Servet, Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain
| | - Enrique Santamaría
- ProteoRed-ISCIII, Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Fundación Miguel Servet, Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain.
| |
Collapse
|
26
|
Fernandez-Irigoyen J, Labarga A, Zabaleta A, de Morentin XM, Perez-Valderrama E, Zelaya MV, Santamaria E. Toward defining the anatomo-proteomic puzzle of the human brain: An integrative analysis. Proteomics Clin Appl 2015; 9:796-807. [PMID: 25418211 DOI: 10.1002/prca.201400127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 10/17/2014] [Accepted: 11/18/2014] [Indexed: 01/18/2023]
Abstract
The human brain is exceedingly complex, constituted by billions of neurons and trillions of synaptic connections that, in turn, define ∼900 neuroanatomical subdivisions in the adult brain (Hawrylycz et al. An anatomically comprehensive atlas of the human brain transcriptome. Nature 2012, 489, 391-399). The human brain transcriptome has revealed specific regional transcriptional signatures that are regulated in a spatiotemporal manner, increasing the complexity of the structural and molecular organization of this organ (Kang et al. Spatio-temporal transcriptome of the human brain. Nature 2011, 478, 483-489). During the last decade, neuroproteomics has emerged as a powerful approach to profile neural proteomes using shotgun-based MS, providing complementary information about protein content and function at a global level. Here, we revise recent proteome profiling studies performed in human brain, with special emphasis on proteome mapping of anatomical macrostructures, specific subcellular compartments, and cerebrospinal fluid. Moreover, we have performed an integrative functional analysis of the protein compilation derived from these large-scale human brain proteomic studies in order to obtain a comprehensive view of human brain biology. Finally, we also discuss the potential contribution of our meta-analysis to the Chromosome-centric Human Proteome Project initiative.
Collapse
Affiliation(s)
- Joaquín Fernandez-Irigoyen
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | - Alberto Labarga
- Bioinformatics Unit, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | - Aintzane Zabaleta
- Biofunctional Nanomaterials Laboratory, CIC Biomagune, San Sebastian, Spain
| | - Xabier Martínez de Morentin
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | - Estela Perez-Valderrama
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| | | | - Enrique Santamaria
- Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Pamplona, Spain
| |
Collapse
|
27
|
Fernández-Irigoyen J, Zelaya MV, Tuñon T, Santamaría E. Anatomo-proteomic characterization of human basal ganglia: focus on striatum and globus pallidus. Mol Brain 2014; 7:83. [PMID: 25406675 PMCID: PMC4236423 DOI: 10.1186/s13041-014-0083-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 11/04/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The basal ganglia (BG) are a complex network of subcortical nuclei involved in the coordination and integration of the motor activity. Although these independent anatomical structures are functionally related, the proteome present in each isolated nucleus remains largely unexplored. In order to analyse the BG proteome in a large-scale format, we used a multi-dimensional fractionation approach which combines isolation of anatomically-defined nuclei, and protein/peptide chromatographic fractionation strategies coupled to mass spectrometry. RESULTS Using this workflow, we have obtained a proteomic expression profile across striatum and globus pallidus structures among which 1681 proteins were located in caudate nucleus (CN), 1329 in putamen, 1419 in medial globus pallidus (GPi), and 1480 in lateral globus pallidus (GPe), establishing a BG reference proteome to a depth of 2979 unique proteins. Protein interactome mapping highlighted significant clustering of common proteins in striatal and pallidal structures, contributing to oxidative phosphorylation, protein degradation and neurotrophin signalling pathways. In silico analyses emphasized specific pathways represented in striatal and pallidal structures highlighting 5-hydroxytryptamine degradation, synaptic vesicle trafficking, and dopamine, metabotropic glutamate and muscarinic acetylcholine receptor pathways. Additional bioinformatic analyses also revealed that: i) nearly 4% of identified proteins have been previously associated to neurodegenerative syndromes, ii) 11% of protein set tends to localize to synaptic terminal, and iii) 20% of identified proteins were also localized in cerebrospinal fluid (CSF). CONCLUSIONS Overall, the anatomo-proteomic profiling of BG complements the anatomical atlas of the human brain transcriptome, increasing our knowledge about the molecular basis of the BG and the etiology of the movement disorders.
Collapse
Affiliation(s)
- Joaquín Fernández-Irigoyen
- />Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Irunlarrea Street, 31008 Pamplona, Spain
| | - María Victoria Zelaya
- />Neurological Tissue Bank, Navarrabiomed, Fundación Miguel Servet, 31008 Pamplona, Spain
| | - Teresa Tuñon
- />Pathological Anatomy Department, Navarra Hospital Complex, Pamplona, Spain
| | - Enrique Santamaría
- />Clinical Neuroproteomics Group, Proteomics Unit, Proteored-ISCIII, Navarrabiomed, Fundación Miguel Servet, Irunlarrea Street, 31008 Pamplona, Spain
| |
Collapse
|
28
|
Kotrcova E, Jarkovska K, Valekova I, Zizkova M, Motlik J, Gadher SJ, Kovarova H. Challenges of Huntington's disease and quest for therapeutic biomarkers. Proteomics Clin Appl 2014; 9:147-58. [PMID: 25290828 DOI: 10.1002/prca.201400073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 08/29/2014] [Accepted: 10/01/2014] [Indexed: 11/10/2022]
Abstract
Huntington's disease (HD) is the most common inherited neurodegenerative disorder among polyglutamine (polyQ) diseases caused by cytosine-adenine-guanine repeat expansion in exon 1 of the huntingtin gene whose translation results in polyQ stretch in the N-terminus of the huntingtin protein (HD protein). This mutation significantly affects huntingtin conformation, proteolysis, PTMs, as well as its ability to bind interacting proteins. As a consequence, a variety of cellular mechanisms such as transcription, mitochondrial energy metabolism, axonal transport, neuronal vulnerability to oxidative stress, neurotransmission, and immune response are altered and involved in the pathogenesis of HD. Promising candidate molecular biomarkers of HD have emerged from proteomic studies. Recent analyses focused on HD protein itself, its PTM, and interacting proteins, which are of great importance for disease course. Furthermore, brain, body fluids, and immune system are intensively studied in order to search for additional proteins with a view to their use as a biomarker(s) or set of biomarkers in clinical trials in HD translational research.
Collapse
Affiliation(s)
- Eva Kotrcova
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Libechov, Czech Republic; Research Center PIGMOD, Libechov, Czech Republic
| | | | | | | | | | | | | |
Collapse
|
29
|
Hyung SW, Piehowski PD, Moore RJ, Orton DJ, Schepmoes AA, Clauss TR, Chu RK, Fillmore TL, Brewer H, Liu T, Zhao R, Smith RD. Microscale depletion of high abundance proteins in human biofluids using IgY14 immunoaffinity resin: analysis of human plasma and cerebrospinal fluid. Anal Bioanal Chem 2014; 406:7117-25. [PMID: 25192788 DOI: 10.1007/s00216-014-8058-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/09/2014] [Accepted: 07/22/2014] [Indexed: 12/30/2022]
Abstract
Removal of highly abundant proteins in plasma is often carried out using immunoaffinity depletion to extend the dynamic range of measurements to lower abundance species. While commercial depletion columns are available for this purpose, they generally are not applicable to limited sample quantities (<20 μL) due to low yields stemming from losses caused by nonspecific binding to the column matrix and concentration of large eluent volumes. Additionally, the cost of the depletion media can be prohibitive for larger-scale studies. Modern LC-MS instrumentation provides the sensitivity necessary to scale-down depletion methods with minimal sacrifice to proteome coverage, which makes smaller volume depletion columns desirable for maximizing sample recovery when samples are limited, as well as for reducing the expense of large-scale studies. We characterized the performance of a 346 μL column volume microscale depletion system, using four different flow rates to determine the most effective depletion conditions for ∼6-μL injections of human plasma proteins and then evaluated depletion reproducibility at the optimum flow rate condition. Depletion of plasma using a commercial 10-mL depletion column served as the control. Results showed depletion efficiency of the microscale column increased as flow rate decreased, and that our microdepletion was reproducible. In an initial application, a 600-μL sample of human cerebrospinal fluid (CSF) pooled from multiple sclerosis patients was depleted and then analyzed using reversed phase liquid chromatography-mass spectrometry to demonstrate the utility of the system for this important biofluid where sample quantities are more commonly limited.
Collapse
Affiliation(s)
- Seok-Won Hyung
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA,
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Technological advances for deciphering the complexity of psychiatric disorders: merging proteomics with cell biology. Int J Neuropsychopharmacol 2014; 17:1327-41. [PMID: 24524332 DOI: 10.1017/s146114571400008x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Proteomic studies have increased our understanding of the molecular pathways affected in psychiatric disorders. Mass spectrometry and two-dimensional gel electrophoresis analyses of post-mortem brain samples from psychiatric patients have revealed effects on synaptic, cytoskeletal, antioxidant and mitochondrial protein networks. Multiplex immunoassay profiling studies have found alterations in hormones, growth factors, transport and inflammation-related proteins in serum and plasma from living first-onset patients. Despite these advances, there are still difficulties in translating these findings into platforms for improved treatment of patients and for discovery of new drugs with better efficacy and side effect profiles. This review describes how the next phase of proteomic investigations in psychiatry should include stringent replication studies for validation of biomarker candidates and functional follow-up studies which can be used to test the impact on physiological function. All biomarker candidates should now be tested in series with traditional and emerging cell biological approaches. This should include investigations of the effects of post-translational modifications, protein dynamics and network analyses using targeted proteomic approaches. Most importantly, there is still an urgent need for development of disease-relevant cellular models for improved translation of proteomic findings into a means of developing novel drug treatments for patients with these life-altering disorders.
Collapse
|
31
|
Guldbrandsen A, Vethe H, Farag Y, Oveland E, Garberg H, Berle M, Myhr KM, Opsahl JA, Barsnes H, Berven FS. In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR). Mol Cell Proteomics 2014; 13:3152-63. [PMID: 25038066 PMCID: PMC4223498 DOI: 10.1074/mcp.m114.038554] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this study, the human cerebrospinal fluid (CSF) proteome was mapped using three different strategies prior to Orbitrap LC-MS/MS analysis: SDS-PAGE and mixed mode reversed phase-anion exchange for mapping the global CSF proteome, and hydrazide-based glycopeptide capture for mapping glycopeptides. A maximal protein set of 3081 proteins (28,811 peptide sequences) was identified, of which 520 were identified as glycoproteins from the glycopeptide enrichment strategy, including 1121 glycopeptides and their glycosylation sites. To our knowledge, this is the largest number of identified proteins and glycopeptides reported for CSF, including 417 glycosylation sites not previously reported. From parallel plasma samples, we identified 1050 proteins (9739 peptide sequences). An overlap of 877 proteins was found between the two body fluids, whereas 2204 proteins were identified only in CSF and 173 only in plasma. All mapping results are freely available via the new CSF Proteome Resource (http://probe.uib.no/csf-pr), which can be used to navigate the CSF proteome and help guide the selection of signature peptides in targeted quantitative proteomics.
Collapse
Affiliation(s)
- Astrid Guldbrandsen
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Heidrun Vethe
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Yehia Farag
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; ¶Department of Informatics, University of Bergen, Bergen, Norway
| | - Eystein Oveland
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway; ‖Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hilde Garberg
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Magnus Berle
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; **Surgical Clinic, Haukeland University Hospital, Bergen, Norway
| | - Kjell-Morten Myhr
- §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway; ‡‡Norwegian Multiple Sclerosis Registry and Biobank, Haukeland University Hospital, Bergen, Norway
| | - Jill A Opsahl
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Harald Barsnes
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- From the ‡Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway; §KG Jebsen Centre for Multiple Sclerosis Research, Department of Clinical Medicine, University of Bergen, Bergen, Norway; §§Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway.
| |
Collapse
|
32
|
Percy AJ, Yang J, Chambers AG, Simon R, Hardie DB, Borchers CH. Multiplexed MRM with Internal Standards for Cerebrospinal Fluid Candidate Protein Biomarker Quantitation. J Proteome Res 2014; 13:3733-3747. [DOI: 10.1021/pr500317d] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew J. Percy
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Juncong Yang
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Andrew G. Chambers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Romain Simon
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Darryl B. Hardie
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Christoph H. Borchers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
- Department
of Biochemistry and Microbiology, University of Victoria, Petch Building
Room 207, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
| |
Collapse
|
33
|
Cerebrospinal fluid analysis in Alzheimer's disease: technical issues and future developments. J Neurol 2014; 261:1234-43. [PMID: 24807087 DOI: 10.1007/s00415-014-7366-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 04/28/2014] [Accepted: 04/28/2014] [Indexed: 12/11/2022]
Abstract
Alzheimer's disease (AD) is a leading cause of morbidity, mortality, and a major epidemic worldwide. Although clinical assessment continues to remain the keystone for patient management and clinical trials, such evaluation has important limitations. In this context, cerebrospinal fluid (CSF) biomarkers are important tools to better identify high-risk individuals, to diagnose AD promptly and accurately, especially at the prodromal mild cognitive impairment stage of the disease, and to effectively prognosticate and treat AD patients. Recent advances in functional genomics, proteomics, metabolomics, and bioinformatics will hopefully revolutionize unbiased inquiries into several putative CSF markers of cerebral pathology that may be concisely informative with regard to the various stages of AD progression through years and decades. Moreover, the identification of efficient drug targets and development of optimal therapeutic strategies for AD will increasingly rely on a better understanding and integration of the systems biology paradigm, which will allow predicting the series of events and resulting responses of the biological network triggered by the introduction of new therapeutic compounds. In this scenario, unbiased systems biology-based diagnostic and prognostic models in AD will consist of relevant comprehensive panels of molecules and key branches of the disease-affected cellular neuronal network. Such characteristic and unbiased biomarkers will more accurately and comprehensively reflect pathophysiology from the early asymptomatic and presymptomatic to the final prodromal and symptomatic clinical stages in individual patients (and their individual genetic disease predisposition), ultimately increasing the chances of success of future disease modifying and preventive treatments.
Collapse
|
34
|
Fernández-Irigoyen J, Zelaya MV, Santamaría E. Applying mass spectrometry-based qualitative proteomics to human amygdaloid complex. Front Cell Neurosci 2014; 8:80. [PMID: 24688456 PMCID: PMC3960493 DOI: 10.3389/fncel.2014.00080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 02/27/2014] [Indexed: 11/13/2022] Open
Abstract
The amygdaloid complex is a key brain structure involved in the expression of behaviors and emotions such as learning, fear, and anxiety. Brain diseases including depression, epilepsy, autism, schizophrenia, and Alzheimer's disease, have been associated with amygdala dysfunction. For several decades, neuroanatomical, neurophysiological, volumetric, and cognitive approaches have been the gold standard techniques employed to characterize the amygdala functionality. However, little attention has been focused specifically on the molecular composition of the human amygdala from the perspective of proteomics. We have performed a global proteome analysis employing protein and peptide fractionation methods followed by nano-liquid chromatography tandem mass spectrometry (nanoLC-MS/MS), detecting expression of at least 1820 protein species in human amygdala, corresponding to 1814 proteins which represent a nine-fold increase in proteome coverage with respect to previous proteomic profiling of the rat amygdala. Gene ontology analysis were used to determine biological process represented in human amygdala highlighting molecule transport, nucleotide binding, and oxidoreductase and GTPase activities. Bioinformatic analyses have revealed that nearly 4% of identified proteins have been previously associated to neurodegenerative syndromes, and 26% of amygdaloid proteins were also found to be present in cerebrospinal fluid (CSF). In particular, a subset of amygdaloid proteins was mainly involved in axon guidance, synaptic vesicle release, L1CAM interactome, and signaling pathways transduced by NGF and NCAM1. Taken together, our data contributes to the repertoire of the human brain proteome, serving as a reference library to provide basic information for understanding the neurobiology of the human amygdala.
Collapse
Affiliation(s)
| | - María V Zelaya
- Neurological Tissue Bank, Navarrabiomed, Fundación Miguel Servet Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Group, Proteomics Unit, Navarrabiomed, Fundación Miguel Servet Pamplona, Spain
| |
Collapse
|
35
|
van Gool AJ, Hendrickson RC. The proteomic toolbox for studying cerebrospinal fluid. Expert Rev Proteomics 2014; 9:165-79. [DOI: 10.1586/epr.12.6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
|
36
|
Gao M, Qi D, Zhang P, Deng C, Zhang X. Development of multidimensional liquid chromatography and application in proteomic analysis. Expert Rev Proteomics 2014; 7:665-78. [DOI: 10.1586/epr.10.49] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
37
|
Martínez-Morillo E, García Hernández P, Begcevic I, Kosanam H, Prieto García B, Alvarez Menéndez FV, Diamandis EP. Identification of novel biomarkers of brain damage in patients with hemorrhagic stroke by integrating bioinformatics and mass spectrometry-based proteomics. J Proteome Res 2013; 13:969-81. [PMID: 24295473 DOI: 10.1021/pr401111h] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hemorrhagic stroke (HS) is a significant cause of mortality that requires rapid diagnosis and prompt medical attention. A time-efficient diagnostic test to assist in the early classification of patients with stroke would be of great value. The aims here were to (a) select "brain-specific" proteins using a bioinformatics approach, (b) develop selected reaction monitoring (SRM) assays for candidate proteins, and (c) quantify these proteins in cerebrospinal fluid (CSF). "The Human Protein Atlas" and the "Peptide Atlas" were used to select proteins specifically and abundantly expressed in brain tissue, excluding high-abundance plasma proteins. Protein extracts from brain tissue were used for SRM assay development of proteins of interest. The levels of 68 "brain-specific" proteins were measured by SRM in 36 age-matched patients, including individuals with HS (n = 15), ischemic stroke (n = 11), and controls (n = 10). Additionally, S100B was measured using an electrochemoluminometric immunoassay. CSF levels of S100B and eight of the "brain-specific" proteins (NSE, GFAP, α-Inx, MBP, MT3, NFM, β-Syn, and γ-Syn) were increased in a subset of samples from HS patients, especially in those individuals with intraventricular hemorrhage and poor outcome. Seven of these proteins (S100B, NSE, GFAP, α-Inx, MBP, NFM, and β-Syn) showed significant differences between patients with and without brain hemorrhage. Novel biomarkers of brain injury (α-Inx, NFM, and β-Syn) were identified in the CSF of patients with HS. Investigating the role of these proteins in blood with more sensitive methods is warranted.
Collapse
Affiliation(s)
- Eduardo Martínez-Morillo
- Lunenfeld-Tanenbaum Research Institute, Joseph and Wolf Lebovic Health Complex, Mount Sinai Hospital , Toronto, Ontario M5T 1A8, Canada
| | | | | | | | | | | | | |
Collapse
|
38
|
Jha MK, Kim JH, Suk K. Proteome of brain glia: the molecular basis of diverse glial phenotypes. Proteomics 2013; 14:378-98. [PMID: 24124134 DOI: 10.1002/pmic.201300236] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/16/2013] [Accepted: 07/30/2013] [Indexed: 12/11/2022]
Abstract
Several different types of nonneuronal glial cells with diverse phenotypes are present in the CNS, and all have distinct indispensible functions. Although glial cells primarily provide neurons with metabolic and structural support in the healthy brain, they may switch phenotype from a "resting" to a "reactive" state in response to pathological insults. Furthermore, this reactive gliosis is an invariant feature of the pathogeneses of CNS maladies. The glial proteome serves as a signature of glial phenotype, and not only executes physiological functions, but also acts as a molecular mediator of the reactive glial phenotype. The glial proteome is also involved in intra- and intercellular communications as exemplified by glia-glia and neuron-glia interactions. The utilization of authoritative proteomic tools and the bioinformatic analyses have helped to profile the brain glial proteome and explore the molecular mechanisms of diverse glial phenotypes. Furthermore, technologic innovations have equipped the field of "glioproteomics" with refined tools for studies of the expression, interaction, and function of glial proteins in the healthy and in the diseased CNS. Glioproteomics is expected to contribute to the elucidation of the molecular mechanisms of CNS pathophysiology and to the discovery of biomarkers and theragnostic targets in CNS disorders.
Collapse
Affiliation(s)
- Mithilesh Kumar Jha
- Department of Pharmacology, Brain Science & Engineering Institute, Kyungpook National University School of Medicine, Daegu, South Korea
| | | | | |
Collapse
|
39
|
Adult neural stem cells and their niche: a dynamic duo during homeostasis, regeneration, and aging. Curr Opin Neurobiol 2013; 23:935-42. [PMID: 24090877 DOI: 10.1016/j.conb.2013.09.004] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 09/03/2013] [Indexed: 12/27/2022]
Abstract
Stem cells persist in specialized niches in the adult mammalian brain. Emerging findings highlight the complexity and heterogeneity of different compartments in the niche, as well as the presence of local signaling microdomains. Stem cell quiescence and activation are regulated not only by anchorage to the niche and diffusible signals, but also by biophysical properties, including fluid dynamics. Importantly, the adult neural stem cell niche integrates both local and systemic changes, reflecting the physiological state of the organism. Moreover niche signaling is bidirectional, with stem cells and their progeny and niche cells dynamically interacting with each other during homeostasis, regeneration and aging.
Collapse
|
40
|
Kadakkuzha BM, Puthanveettil SV. Genomics and proteomics in solving brain complexity. MOLECULAR BIOSYSTEMS 2013; 9:1807-21. [PMID: 23615871 PMCID: PMC6425491 DOI: 10.1039/c3mb25391k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The human brain is extraordinarily complex, composed of billions of neurons and trillions of synaptic connections. Neurons are organized into circuit assemblies that are modulated by specific interneurons and non-neuronal cells, such as glia and astrocytes. Data on human genome sequences predicts that each of these cells in the human brain has the potential of expressing ∼20 000 protein coding genes and tens of thousands of noncoding RNAs. A major challenge in neuroscience is to determine (1) how individual neurons and circuitry utilize this potential during development and maturation of the nervous system, and for higher brain functions such as cognition, and (2) how this potential is altered in neurological and psychiatric disorders. In this review, we will discuss how recent advances in next generation sequencing, proteomics and bioinformatics have transformed our understanding of gene expression and the functions of neural circuitry, memory storage, and disorders of cognition.
Collapse
Affiliation(s)
- Beena M Kadakkuzha
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida 130 Scripps Way, Jupiter, FL 33458, USA
| | | |
Collapse
|
41
|
Kim JH, Lee SK, Yoo YC, Park NH, Park DB, Yoo JS, An HJ, Park YM, Cho KG. Proteome analysis of human cerebrospinal fluid as a diagnostic biomarker in patients with meningioma. Med Sci Monit 2013; 18:BR450-60. [PMID: 23111736 PMCID: PMC3560610 DOI: 10.12659/msm.883538] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND To identify meningioma-specific proteins, cerebrospinal fluid (CSF) from 4 patients with a meningioma and 4 patients with a non-brain tumorous lesion were analyzed. MATERIAL/METHODS Two-dimensional electrophoresis and electrospray quadrupole time-of-flight tandem mass spectrometry analyses revealed 10 unique spots, containing 11 independent proteins (spot #2 and #4 each contained 2 proteins and spot #3 was not identified) were evident in CSF associated with human meningioma: serum albumin precursor (3 different isoforms), Apolipoprotein E (Apo E), Apolipoprotein J precursor (Apo J), Transthyretin precursor (TTR), Prostaglandin D2 synthase 21 kDa (PTGDS), proapolipoprotein, Chain D hemoglobin Ypsilanti, alpha-1-antitrypsin (AAT), and beta-2-microglobulin precursor (β2M). RESULTS The contents of Apo E, Apo J and AAT were increased, while PTGDS, TTR and β2M were decreased. CONCLUSIONS The results observed by 2-dimensional electrophoresis were verified by Western blot analysis. The unique proteins may represent possible candidate biomarkers of meningioma.
Collapse
Affiliation(s)
- Jae Ho Kim
- Mass Spectrometry Research Center, Korea Basic Science Institute, Ochang, Republic of Korea
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Lista S, Faltraco F, Prvulovic D, Hampel H. Blood and plasma-based proteomic biomarker research in Alzheimer's disease. Prog Neurobiol 2013; 101-102:1-17. [DOI: 10.1016/j.pneurobio.2012.06.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 03/28/2012] [Accepted: 06/18/2012] [Indexed: 12/14/2022]
|
43
|
Thouvenot E, Urbach S, Vigy O, Séveno M, Galéotti N, Nguyen G, Bockaert J, Marin P. Quantitative proteomic analysis reveals protein expression changes in the murine neuronal secretome during apoptosis. J Proteomics 2012; 77:394-405. [DOI: 10.1016/j.jprot.2012.09.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 08/24/2012] [Accepted: 09/12/2012] [Indexed: 01/08/2023]
|
44
|
Mollenhauer B, Zhang J. Biochemical premotor biomarkers for Parkinson's disease. Mov Disord 2012; 27:644-50. [PMID: 22508282 DOI: 10.1002/mds.24956] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A biomarker is a biological characteristic that is objectively measured and evaluated as an indicator of normal biological or pathologic processes or of pharmacologic responses to a therapeutic intervention. We reviewed the current status of target protein biomarkers (eg, total/oligomeric α-synuclein and DJ-1) in cerebrospinal fluid, as well as on unbiased processes that can be used to discover novel biomarkers. We have also provide details about strategies toward potential populations/models and technologies, including the need for standardized sampling techniques, to pursue the identification of new biochemical markers in the premotor stage of Parkinson's disease in the future.
Collapse
Affiliation(s)
- Brit Mollenhauer
- Paracelsus-Elena-Klinik and Georg August University Goettingen, Kassel, Germany.
| | | |
Collapse
|
45
|
Hölttä M, Zetterberg H, Mirgorodskaya E, Mattsson N, Blennow K, Gobom J. Peptidome analysis of cerebrospinal fluid by LC-MALDI MS. PLoS One 2012; 7:e42555. [PMID: 22880031 PMCID: PMC3412831 DOI: 10.1371/journal.pone.0042555] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 07/10/2012] [Indexed: 12/18/2022] Open
Abstract
We report on the analysis of endogenous peptides in cerebrospinal fluid (CSF) by mass spectrometry. A method was developed for preparation of peptide extracts from CSF. Analysis of the extracts by offline LC-MALDI MS resulted in the detection of 3,000–4,000 peptide-like features. Out of these, 730 peptides were identified by MS/MS. The majority of these peptides have not been previously reported in CSF. The identified peptides were found to originate from 104 proteins, of which several have been reported to be involved in different disorders of the central nervous system. These results support the notion that CSF peptidomics may be viable complement to proteomics in the search of biomarkers of CNS disorders.
Collapse
Affiliation(s)
- Mikko Hölttä
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Ekaterina Mirgorodskaya
- Department of Occupational and Environmental Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Niklas Mattsson
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Johan Gobom
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- * E-mail:
| |
Collapse
|
46
|
Lista S, Faltraco F, Hampel H. Biological and methodical challenges of blood-based proteomics in the field of neurological research. Prog Neurobiol 2012; 101-102:18-34. [PMID: 22743551 DOI: 10.1016/j.pneurobio.2012.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 03/28/2012] [Accepted: 06/18/2012] [Indexed: 12/17/2022]
Abstract
Biomarker discovery is an application of major importance in today's proteomic research. There is an urgent need for suitable biomarkers to improve diagnostic tools and treatment in various neurological diseases, such as neurodegenerative disorders. Recent years have witnessed an enormous interest in proteomics, which is currently seen as an invaluable tool to shed more light on complex interacting signalling pathways and molecular networks involved in several neuropathological conditions. However, while first results of proteomic research studies have sparked much public attention, the momentum of further proteomic biomarker research in neurological disorders may suffer by its very complex methodology which is sensitive to various sources of artefacts. A major source of variability is proteome perturbation caused by sample handling/preservation (preanalytical phase) and processing/measurement (analytical phase). The aim of the present review is to summarize the current literature focusing on the crucial role played by preanalytical and analytical factors that affect the quality of samples and the reliability of the data produced in blood-based proteomic biomarker research in neurology, which may apply to Alzheimer's disease (AD) as well as other neurological disorders. Procedures for sample preparation and protocols for the analysis of serum and plasma samples will be delineated. Finally, the potential usefulness of bioinformatics--allowing for the assembly, store, and processing of data--as well as its contribution to the execution of proteomic studies will be critically discussed.
Collapse
Affiliation(s)
- Simone Lista
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Goethe-University of Frankfurt, Frankfurt am Main, Germany.
| | | | | |
Collapse
|
47
|
Characterization of the glycated human cerebrospinal fluid proteome. J Proteomics 2012; 75:4766-82. [PMID: 22300578 DOI: 10.1016/j.jprot.2012.01.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 12/28/2011] [Accepted: 01/12/2012] [Indexed: 12/12/2022]
Abstract
Protein glycation is a nonenzymatic modification that involves pathological functions in neurological diseases. Despite the high number of studies showing accumulation of advanced end glycation products (AGEs) at clinical stage, there is a lack of knowledge about which proteins are modified, where those modifications occur, and to what extent. The goal of this study was to achieve a comprehensive characterization of proteins modified by early glycation in human cerebrospinal fluid (CSF). Approaches based on glucose diferential labeling and mass spectrometry have been applied to evaluate the glycated CSF proteome at two physiological conditions: native glucose level and in vitro high glucose content. For both purposes, detection of glycated proteins was carried out by HCD-MS2 and CID-MS3 modes after endoproteinase Glu-C digestion and boronate affinity chromatography. The abundance of glycation was assessed by protein labeling with (13)C(6)-glucose incubation. The analysis of native glycated CSF identified 111 glycation sites corresponding to 48 glycated proteins. Additionally, the in vitro high glucose level approach detected 265 glycation sites and 101 glycated proteins. The comparison of glycation levels under native and 15 mM glucose conditions showed relative concentration increases up to ten folds for some glycated proteins. This report revealed for the first time a number of key glycated CSF proteins known to be involved in neuroinflammation and neurodegenerative disorders. Altogether, the present study contains valuable and unique information, which should further help to clarify the pathological role of glycation in central nervous system pathologies. This article is part of a Special Issue entitled: Translational Proteomics.
Collapse
|
48
|
Borg J, Campos A, Diema C, Omeñaca N, de Oliveira E, Guinovart J, Vilaseca M. Spectral counting assessment of protein dynamic range in cerebrospinal fluid following depletion with plasma-designed immunoaffinity columns. Clin Proteomics 2011; 8:6. [PMID: 21906361 PMCID: PMC3167203 DOI: 10.1186/1559-0275-8-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 06/03/2011] [Indexed: 01/25/2023] Open
Abstract
Background In cerebrospinal fluid (CSF), which is a rich source of biomarkers for neurological diseases, identification of biomarkers requires methods that allow reproducible detection of low abundance proteins. It is therefore crucial to decrease dynamic range and improve assessment of protein abundance. Results We applied LC-MS/MS to compare the performance of two CSF enrichment techniques that immunodeplete either albumin alone (IgYHSA) or 14 high-abundance proteins (IgY14). In order to estimate dynamic range of proteins identified, we measured protein abundance with APEX spectral counting method. Both immunodepletion methods improved the number of low-abundance proteins detected (3-fold for IgYHSA, 4-fold for IgY14). The 10 most abundant proteins following immunodepletion accounted for 41% (IgY14) and 46% (IgYHSA) of CSF protein content, whereas they accounted for 64% in non-depleted samples, thus demonstrating significant enrichment of low-abundance proteins. Defined proteomics experiment metrics showed overall good reproducibility of the two immunodepletion methods and MS analysis. Moreover, offline peptide fractionation in IgYHSA sample allowed a 4-fold increase of proteins identified (520 vs. 131 without fractionation), without hindering reproducibility. Conclusions The novelty of this study was to show the advantages and drawbacks of these methods side-to-side. Taking into account the improved detection and potential loss of non-target proteins following extensive immunodepletion, it is concluded that both depletion methods combined with spectral counting may be of interest before further fractionation, when searching for CSF biomarkers. According to the reliable identification and quantitation obtained with APEX algorithm, it may be considered as a cheap and quick alternative to study sample proteomic content.
Collapse
Affiliation(s)
- Jacques Borg
- Laboratoire de Neurobiochimie, Université Jean Monnet, Saint-Etienne, France.
| | | | | | | | | | | | | |
Collapse
|
49
|
Kroksveen A, Opsahl J, Aye T, Ulvik R, Berven F. Proteomics of human cerebrospinal fluid: Discovery and verification of biomarker candidates in neurodegenerative diseases using quantitative proteomics. J Proteomics 2011; 74:371-88. [DOI: 10.1016/j.jprot.2010.11.010] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Revised: 11/16/2010] [Accepted: 11/16/2010] [Indexed: 01/01/2023]
|
50
|
Ahmed SSSJ, Ahameethunisa AR, Santosh W, Chakravarthy S, Kumar S. Systems biological approach on neurological disorders: a novel molecular connectivity to aging and psychiatric diseases. BMC SYSTEMS BIOLOGY 2011; 5:6. [PMID: 21226925 PMCID: PMC3033822 DOI: 10.1186/1752-0509-5-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 01/12/2011] [Indexed: 11/26/2022]
Abstract
Background Systems biological approach of molecular connectivity map has reached to a great interest to understand the gene functional similarities between the diseases. In this study, we developed a computational framework to build molecular connectivity maps by integrating mutated and differentially expressed genes of neurological and psychiatric diseases to determine its relationship with aging. Results The systematic large-scale analyses of 124 human diseases create three classes of molecular connectivity maps. First, molecular interaction of disease protein network generates 3632 proteins with 6172 interactions, which determines the common genes/proteins between diseases. Second, Disease-disease network includes 4845 positively scored disease-disease relationships. The comparison of these disease-disease pairs with Medical Subject Headings (MeSH) classification tree suggests 25% of the disease-disease pairs were in same disease area. The remaining can be a novel disease-disease relationship based on gene/protein similarity. Inclusion of aging genes set showed 79 neurological and 20 psychiatric diseases have the strong association with aging. Third and lastly, a curated disease biomarker network was created by relating the proteins/genes in specific disease contexts, such analysis showed 73 markers for 24 diseases. Further, the overall quality of the results was achieved by a series of statistical methods, to avoid insignificant data in biological networks. Conclusions This study improves the understanding of the complex interactions that occur between neurological and psychiatric diseases with aging, which lead to determine the diagnostic markers. Also, the disease-disease association results could be helpful to determine the symptom relationships between neurological and psychiatric diseases. Together, our study presents many research opportunities in post-genomic biomarkers development.
Collapse
Affiliation(s)
- Shiek S S J Ahmed
- Department of Biotechnology, School of Bioengineering, SRM University, Kattankulathur, Tamil Nadu, India
| | | | | | | | | |
Collapse
|