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Ruiz-Sanmartín A, Ribas V, Suñol D, Chiscano-Camón L, Palmada C, Bajaña I, Larrosa N, González JJ, Canela N, Ferrer R, Ruiz-Rodríguez JC. Characterization of a proteomic profile associated with organ dysfunction and mortality of sepsis and septic shock. PLoS One 2022; 17:e0278708. [PMID: 36459524 PMCID: PMC9718383 DOI: 10.1371/journal.pone.0278708] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022] Open
Abstract
INTRODUCTION The search for new biomarkers that allow an early diagnosis in sepsis and predict its evolution has become a necessity in medicine. The objective of this study is to identify, through omics techniques, potential protein biomarkers that are expressed in patients with sepsis and their relationship with organ dysfunction and mortality. METHODS Prospective, observational and single-center study that included adult patients (≥ 18 years) who were admitted to a tertiary hospital and who met the criteria for sepsis. A mass spectrometry-based approach was used to analyze the plasma proteins in the enrolled subjects. Subsequently, using recursive feature elimination classification and cross-validation with a vector classifier, an association of these proteins with mortality and organ dysfunction was established. The protein-protein interaction network was analyzed with String software. RESULTS 141 patients were enrolled in this study. Mass spectrometry identified 177 proteins. Of all of them, and by recursive feature elimination, nine proteins (GPX3, APOB, ORM1, SERPINF1, LYZ, C8A, CD14, APOC3 and C1QC) were associated with organ dysfunction (SOFA > 6) with an accuracy of 0.82 ± 0.06, precision of 0.85 ± 0.093, sensitivity 0.81 ± 0.10, specificity 0.84 ± 0.10 and AUC 0.82 ± 0.06. Twenty-two proteins (CLU, LUM, APOL1, SAA1, CLEBC3B, C8A, ITIH4, KNG1, AGT, C7, SAA2, APOH, HRG, AFM, APOE, APOC1, C1S, SERPINC1, IGFALS, KLKB1, CFB and BTD) were associated with mortality with an accuracy of 0.86 ± 0.05, a precision of 0.91 ± 0.05, a sensitivity of 0.91 ± 0.05, a specificity of 0.72 ± 0.17, and an area under the curve (AUC) of 0.81 ± 0.08 with a confidence interval of 95%. CONCLUSION In sepsis there are proteomic patterns associated with organ dysfunction and mortality.
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Affiliation(s)
- Adolfo Ruiz-Sanmartín
- Department of Intensive Care, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d’Hebron Research Institute, Barcelona, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Vicent Ribas
- Eurecat, Centre Tecnològic de Catalunya, Digital Health Unit, Barcelona, Spain
| | - David Suñol
- Eurecat, Centre Tecnològic de Catalunya, Digital Health Unit, Barcelona, Spain
| | - Luis Chiscano-Camón
- Department of Intensive Care, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d’Hebron Research Institute, Barcelona, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Clara Palmada
- Department of Intensive Care, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d’Hebron Research Institute, Barcelona, Spain
| | - Iván Bajaña
- Department of Intensive Care, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d’Hebron Research Institute, Barcelona, Spain
| | - Nieves Larrosa
- Department of Clinical Microbiology, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- CIBERINFEC, ISCIII–CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Juan José González
- Department of Clinical Microbiology, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- CIBERINFEC, ISCIII–CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Núria Canela
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit URV-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Reus, Spain
| | - Ricard Ferrer
- Department of Intensive Care, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d’Hebron Research Institute, Barcelona, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan Carlos Ruiz-Rodríguez
- Department of Intensive Care, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d’Hebron Research Institute, Barcelona, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- * E-mail:
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Pan N, Wang Z, Wang B, Wan J, Wan C. Mapping Microproteins and ncRNA-Encoded Polypeptides in Different Mouse Tissues. Front Cell Dev Biol 2021; 9:687748. [PMID: 34381774 PMCID: PMC8350139 DOI: 10.3389/fcell.2021.687748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/30/2021] [Indexed: 12/30/2022] Open
Abstract
Small open reading frame encoded peptides (SEPs), also called microproteins, play a vital role in biological processes. Plenty of their open reading frames are located within the non-coding RNA (ncRNA) range. Recent research has demonstrated that ncRNA-encoded polypeptides have essential functions and exist ubiquitously in various tissues. To better understand the role of microproteins, especially ncRNA-encoded proteins, expressed in different tissues, we profiled the proteomic characterization of five mouse tissues by mass spectrometry, including bottom-up, top-down, and de novo sequencing strategies. Bottom-up and top-down with database-dependent searches identified 811 microproteins in the OpenProt database. De novo sequencing identified 290 microproteins, including 12 ncRNA-encoded microproteins that were not found in current databases. In this study, we discovered 1,074 microproteins in total, including 270 ncRNA-encoded microproteins. From the annotation of these microproteins, we found that the brain contains the largest number of neuropeptides, while the spleen contains the most immunoassociated microproteins. This suggests that microproteins in different tissues have tissue-specific functions. These unannotated ncRNA-coded microproteins have predicted domains, such as the macrophage migration inhibitory factor domain and the Prefoldin domain. These results expand the mouse proteome and provide insight into the molecular biology of mouse tissues.
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Affiliation(s)
- Ni Pan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Zhiwei Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Bing Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Jian Wan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Cuihong Wan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
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Wang W, Wang F, Liu J, Zhao W, Zhao Q, He M, Qian BJ, Xu Y, Liu R, Liu SJ, Liu W, Liu J, Zhou XF, Wang TH. SNAP25 ameliorates sensory deficit in rats with spinal cord transection. Mol Neurobiol 2014; 50:290-304. [PMID: 24519330 DOI: 10.1007/s12035-014-8642-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 01/03/2014] [Indexed: 02/05/2023]
Abstract
Spinal cord injury causes sensory loss below the level of lesion. Synaptosomal-associated protein 25 (SNAP25) is a t-SNARE protein essential for exocytosis and neurotransmitter release, but its role in sensory functional recovery has not been determined. The aim of the present study is therefore to investigate whether SNAP25 can promote sensory recovery. By 2D proteomics, we found a downregulation of SNAP25 and then constructed two lentiviral vectors, Lv-exSNAP25 and Lv-shSNAP25, which allows efficient and stable RNAi-mediated silencing of endogenous SNAP25. Overexpression of SNAP25 enhanced neurite outgrowth in vitro and behavior response to thermal and mechanical stimuli in vivo, while the silencing of SNAP25 had the opposite effect. These results suggest that SNAP25 plays a crucial role in sensory functional recovery following spinal cord injury (SCI). Our study therefore provides a novel target for the management of SCI for sensory dysfunction.
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Affiliation(s)
- Wei Wang
- Department of Anesthesiology and Institute of Neurological Disease, Translation Neuroscience Center, The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
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Srivastava G, Singh K, Tiwari MN, Singh MP. Proteomics in Parkinson’s disease: current trends, translational snags and future possibilities. Expert Rev Proteomics 2014; 7:127-39. [DOI: 10.1586/epr.09.91] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Tribl F, Meyer HE, Marcus K. Analysis of organelles within the nervous system: impact on brain and organelle functions. Expert Rev Proteomics 2014; 5:333-51. [DOI: 10.1586/14789450.5.2.333] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Schmidt O, Schulenborg T, Meyer HE, Marcus K, Hamacher M. How proteomics reveals potential biomarkers in brain diseases. Expert Rev Proteomics 2014; 2:901-13. [PMID: 16307519 DOI: 10.1586/14789450.2.6.901] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The brain is complex, and so are the proteomics studies of brain tissue and its diseases, including Alzheimer's Disease, Parkinson's Disease and schizophrenia. In this review, general considerations and strategies of proteomics technologies, the advantages and challenges as well as the special needs for brain tissue are described and summarized. In addition, the results of the first studies are presented including a quality evaluation of the candidate proteins for these diseases. A paragraph is dedicated to the efforts of standardization in this field.
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Affiliation(s)
- Oliver Schmidt
- Ruhr-Universitaet Bochum, Medizinisches Proteom-Center, ZKF E.141, Universitaetsstrasse 150, D-44801 Bochum, Germany.
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9
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Gold MS, Kobeissy FH, Wang KKW, Merlo LJ, Bruijnzeel AW, Krasnova IN, Cadet JL. Methamphetamine- and trauma-induced brain injuries: comparative cellular and molecular neurobiological substrates. Biol Psychiatry 2009; 66:118-27. [PMID: 19345341 PMCID: PMC2810951 DOI: 10.1016/j.biopsych.2009.02.021] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 02/19/2009] [Accepted: 02/22/2009] [Indexed: 12/21/2022]
Abstract
The use of methamphetamine (METH) is a growing public health problem, because its abuse is associated with long-term biochemical and structural effects on the human brain. Neurodegeneration is often observed in humans, because of mechanical injuries (e.g., traumatic brain injury [TBI]) and ischemic damage (strokes). In this review, we discuss recent findings documenting the fact that the psychostimulant drug METH can cause neuronal damage in several brain regions. The accumulated evidence from our laboratories and those of other investigators indicates that acute administration of METH leads to activation of calpain and caspase proteolytic systems. These systems are also involved in causing neuronal damage secondary to traumatic and ischemic brain injuries. Protease activation is accompanied by proteolysis of endogenous neuronal structural proteins (alphaII-spectrin protein and microtubule-associated protein-tau), evidenced by the appearance of their breakdown products after these injuries. When taken together, these observations suggest that METH exposure, like TBI, can cause substantial damage to the brain by causing both apoptotic and necrotic cell death in the brains of METH addicts who use large doses of the drug during their lifetimes. Finally, because METH abuse is accompanied by functional and structural changes in the brain similar to those in TBI, METH addicts might experience greater benefit if their treatment involved greater emphasis on rehabilitation in conjunction with potential neuroprotective pharmacological agents such as calpain and caspase inhibitors similar to those used in TBI.
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Affiliation(s)
- Mark S Gold
- Center for Neuroproteomics and Biomarkers Research, McKnight Brain Institute of the University of Florida, Gainesville, Florida 32610, USA
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Singh OV, Yaster M, Xu JT, Guan Y, Guan X, Dharmarajan AM, Raja SN, Zeitlin PL, Tao YX. Proteome of synaptosome-associated proteins in spinal cord dorsal horn after peripheral nerve injury. Proteomics 2009; 9:1241-53. [PMID: 19206110 DOI: 10.1002/pmic.200800636] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Peripheral nerve injury may lead to neuroadaptive changes of cellular signals in spinal cord that are thought to contribute to central mechanisms underlying neuropathic pain. Here we used a 2-DE-based proteomic technique to determine the global expression changes of synaptosome-associated proteins in spinal cord dorsal horn after unilateral fifth spinal nerve injury (SNI). The fifth lumbar dorsal horns ipsilateral to SNI or sham surgery were harvested on day 14 post-surgery, and the total soluble and synaptosomal fractions were isolated. The proteins derived from the synaptosomal fraction were resolved by 2-DE. We identified 27 proteins that displayed different expression levels after SNI, including proteins involved in transmission and modulation of noxious information, cellular metabolism, membrane receptor trafficking, oxidative stress, apoptosis, and degeneration. Six of the 27 proteins were chosen randomly and further validated in the synaptosomal fraction by Western blot analysis. Unexpectedly, Western blot analysis showed that only one protein in the total soluble fraction exhibited a significant expression change after SNI. The data indicate that peripheral nerve injury changes not only protein expression but also protein subcellular distribution in dorsal horn cells. These changes might participate in the central mechanism that underlies the maintenance of neuropathic pain.
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Affiliation(s)
- Om V Singh
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Kobeissy FH, Sadasivan S, Liu J, Gold MS, Wang KKW. Psychiatric research: psychoproteomics, degradomics and systems biology. Expert Rev Proteomics 2008; 5:293-314. [PMID: 18466058 DOI: 10.1586/14789450.5.2.293] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
While proteomics has excelled in several disciplines in biology (cancer, injury and aging), neuroscience and psychiatryproteomic studies are still in their infancy. Several proteomic studies have been conducted in different areas of psychiatric disorders, including drug abuse (morphine, alcohol and methamphetamine) and other psychiatric disorders (depression, schizophrenia and psychosis). However, the exact cellular and molecular mechanisms underlying these conditions have not been fully investigated. Thus, one of the primary objectives of this review is to discuss psychoproteomic application in the area of psychiatric disorders, with special focus on substance- and drug-abuse research. In addition, we illustrate the potential role of degradomic utility in the area of psychiatric research and its application in establishing and identifying biomarkers relevant to neurotoxicity as a consequence of drug abuse. Finally, we will discuss the emerging role of systems biology and its current use in the field of neuroscience and its integral role in establishing a comprehensive understanding of specific brain disorders and brain function in general.
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Affiliation(s)
- Firas H Kobeissy
- McKnight Brain Institute, Department of Psychiatry, University of Florida College of Medicine, Gainesville, FL 32611, USA.
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Wang J, Gu Y, Wang L, Hang X, Gao Y, Wang H, Zhang C. HUPO BPP pilot study: A proteomics analysis of the mouse brain of different developmental stages. Proteomics 2007; 7:4008-15. [DOI: 10.1002/pmic.200700341] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Abstract
In spite of the rapid advances in the development of the new proteomic technologies, there are, to date, relatively fewer studies aiming to explore the neuronal proteome. One of the reasons is the complexity of the brain, which presents high cellular heterogeneity and a unique subcellular compartmentalization. Therefore, tissue fractionation of the brain to enrich proteins of interest will reduce the complexity of the proteomics approach leading to the production of manageable and meaningful results. In this review, general considerations and strategies of proteomics, the advantages and challenges to exploring the neuronal proteome are described and summarized. In addition, this article presents an overview of recent advances of proteomic technologies and shows that proteomics can serve as a valuable tool to globally explore the changes in brain proteome during various disease states. Understanding the molecular basis of brain function will be extremely useful in identifying novel targets for the treatment of brain diseases.
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Affiliation(s)
- Jose A Morón
- Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, New York 10029, USA
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Fröhlich T, Arnold GJ. Proteome research based on modern liquid chromatography – tandem mass spectrometry: separation, identification and quantification. J Neural Transm (Vienna) 2006; 113:973-94. [PMID: 16835695 DOI: 10.1007/s00702-006-0509-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2005] [Accepted: 04/05/2006] [Indexed: 01/31/2023]
Abstract
Recent developments of new generations of mass spectrometers and improvements in the field of chromatography have revolutionized protein analytics. Particularly the combination of liquid chromatography as a separation tool for proteins and peptides with tandem mass spectrometry as an identification tool referred to as LC-MS/MS has generated a powerful and broadly used technique in the field of proteomics. The resolution and sensitivity of state-of-the-art LC-MS/MS systems has reached dimensions allowing not only the analysis of individual proteins but also investigations on the level of complete proteomes. However, the enormous complexity and the extreme concentration range of proteins within typical eukaryotic proteomes are still the major challenge of this technique. This review gives an overview of modern LC-MS/MS based proteomics, describing state-of-the-art chromatography and modern mass spectrometry. Strategies to perform quantitative proteomics will be presented and capabilities as well as current limitations of this innovative methodology will be discussed.
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Affiliation(s)
- T Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians University Munich, Germany
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Hamacher M, Marcus K, van Hall A, Meyer HE, Stephan C. The HUPO Brain Proteome Project – No need to hurry? J Neural Transm (Vienna) 2006; 113:963-71. [PMID: 16835694 DOI: 10.1007/s00702-006-0510-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2005] [Accepted: 04/05/2006] [Indexed: 10/24/2022]
Abstract
The HUPO Brain Proteome Project (HUPO BPP) is dedicated to the analysis of the brain proteome and has initiated two pilot studies in order to elaborate a standardised system for data collection and reprocessing. Samples of mouse brains (different developmental stages) and human brain tissue (biopsy and post-mortem samples) were shipped to different laboratories in Europe, Asia and the US that were invited to identify as many proteins as possible using their own approaches. In addition, a centralised data reprocessing strategy has been elaborated in an iterative way to generate highly reliable lists of identified proteins. This consortium could be a good example for a standardized proteomics workflow.
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Affiliation(s)
- M Hamacher
- Medical Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
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Tribl F, Marcus K, Bringmann G, Meyer HE, Gerlach M, Riederer P. Proteomics of the human brain: sub-proteomes might hold the key to handle brain complexity. J Neural Transm (Vienna) 2006; 113:1041-54. [PMID: 16835691 DOI: 10.1007/s00702-006-0513-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Accepted: 02/24/2006] [Indexed: 10/24/2022]
Abstract
Proteomics is a promising approach, which provides information about the expression of proteins and increasingly finds application in life science and disease research. Meanwhile, proteomics has proven to be applicable even on post mortem human brain tissue and has opened a new area in neuroproteomics. Thereby, neuroproteomics is usually employed to generate large protein profiles of brain tissue, which mostly reflect the expression of highly abundant proteins. As a complementary approach, the focus on sub-proteomes would enhance more specific insight into brain function. Sub-proteomes are accessible via several strategies, including affinity pull-down approaches, immunoprecipitation or subcellular fractionation. The extraordinary potential of subcellular proteomics to reveal even minute differences in the protein constitution of related cellular organelles is exemplified by a recent global description of neuromelanin granules from the human brain, which could be identified as pigmented lysosome-related organelles.
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Affiliation(s)
- F Tribl
- The National Parkinson Foundation (NPF) Research Laboratories, Miami, FL, USA.
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Abstract
Background Neuronal communication is tightly regulated in time and in space. The neuronal transmission takes place in the nerve terminal, at a specialized structure called the synapse. Following neuronal activation, an electrical signal triggers neurotransmitter (NT) release at the active zone. The process starts by the signal reaching the synapse followed by a fusion of the synaptic vesicle and diffusion of the released NT in the synaptic cleft; the NT then binds to the appropriate receptor, and as a result, a potential change at the target cell membrane is induced. The entire process lasts for only a fraction of a millisecond. An essential property of the synapse is its capacity to undergo biochemical and morphological changes, a phenomenon that is referred to as synaptic plasticity. Results In this survey, we consider the mammalian brain synapse as our model. We take a cell biological and a molecular perspective to present fundamental properties of the synapse:(i) the accurate and efficient delivery of organelles and material to and from the synapse; (ii) the coordination of gene expression that underlies a particular NT phenotype; (iii) the induction of local protein expression in a subset of stimulated synapses. We describe the computational facet and the formulation of the problem for each of these topics. Conclusion Predicting the behavior of a synapse under changing conditions must incorporate genomics and proteomics information with new approaches in computational biology.
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Affiliation(s)
- Michal Linial
- Dept of Biological Chemistry, The Hebrew University of Jerusalem, 91904, Israel.
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