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Kandpal M, Varshney N, Rawal KS, Jha HC. Gut dysbiosis and neurological modalities: An engineering approach via proteomic analysis of gut-brain axis. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 140:199-248. [PMID: 38762270 DOI: 10.1016/bs.apcsb.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
The human gut microbiota is a complex and dynamic community of microorganisms, that influence metabolic, neurodevelopmental, and immune pathways. Microbial dysbiosis, characterized by changes in microbial diversity and relative abundances, is implicated in the development of various chronic neurological and neurodegenerative disorders. These disorders are marked by the accumulation of pathological protein aggregates, leading to the progressive loss of neurons and behavioural functions. Dysregulations in protein-protein interaction networks and signalling complexes, critical for normal brain function, are common in neurological disorders but challenging to unravel, particularly at the neuron and synapse-specific levels. To advance therapeutic strategies, a deeper understanding of neuropathogenesis, especially during the progressive disease phase, is needed. Biomarkers play a crucial role in identifying disease pathophysiology and monitoring disease progression. Proteomics, a powerful technology, shows promise in accelerating biomarker discovery and aiding in the development of novel treatments. In this chapter, we provide an in-depth overview of how proteomic techniques, utilizing various biofluid samples from patients with neurological conditions and diverse animal models, have contributed valuable insights into the pathogenesis of numerous neurological disorders. We also discuss the current state of research, potential challenges, and future directions in proteomic approaches to unravel neuro-pathological conditions.
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Affiliation(s)
- Meenakshi Kandpal
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Nidhi Varshney
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Kunal Sameer Rawal
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India; Centre for Rural Development & Technology, IIT Indore, Indore, India.
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Lorefice L, Pitzalis M, Murgia F, Fenu G, Atzori L, Cocco E. Omics approaches to understanding the efficacy and safety of disease-modifying treatments in multiple sclerosis. Front Genet 2023; 14:1076421. [PMID: 36793897 PMCID: PMC9922720 DOI: 10.3389/fgene.2023.1076421] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/09/2023] [Indexed: 02/03/2023] Open
Abstract
From the perspective of precision medicine, the challenge for the future is to improve the accuracy of diagnosis, prognosis, and prediction of therapeutic responses through the identification of biomarkers. In this framework, the omics sciences (genomics, transcriptomics, proteomics, and metabolomics) and their combined use represent innovative approaches for the exploration of the complexity and heterogeneity of multiple sclerosis (MS). This review examines the evidence currently available on the application of omics sciences to MS, analyses the methods, their limitations, the samples used, and their characteristics, with a particular focus on biomarkers associated with the disease state, exposure to disease-modifying treatments (DMTs), and drug efficacies and safety profiles.
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Affiliation(s)
- Lorena Lorefice
- Multiple Sclerosis Center, Binaghi Hospital, ASL Cagliari, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- *Correspondence: Lorena Lorefice,
| | - Maristella Pitzalis
- Institute for Genetic and Biomedical Research, National Research Council, Cagliari, Italy
| | - Federica Murgia
- Dpt of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Giuseppe Fenu
- Department of Neurosciences, ARNAS Brotzu, Cagliari, Italy
| | - Luigi Atzori
- Multiple Sclerosis Center, Binaghi Hospital, ASL Cagliari, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Eleonora Cocco
- Multiple Sclerosis Center, Binaghi Hospital, ASL Cagliari, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
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Proteomics in Multiple Sclerosis: The Perspective of the Clinician. Int J Mol Sci 2022; 23:ijms23095162. [PMID: 35563559 PMCID: PMC9100097 DOI: 10.3390/ijms23095162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 02/08/2023] Open
Abstract
Multiple sclerosis (MS) is the inflammatory demyelinating and neurodegenerative disease of the central nervous system (CNS) that affects approximately 2.8 million people worldwide. In the last decade, a new era was heralded in by a new phenotypic classification, a new diagnostic protocol and the first ever therapeutic guideline, making personalized medicine the aim of MS management. However, despite this great evolution, there are still many aspects of the disease that are unknown and need to be further researched. A hallmark of these research are molecular biomarkers that could help in the diagnosis, differential diagnosis, therapy and prognosis of the disease. Proteomics, a rapidly evolving discipline of molecular biology may fulfill this dire need for the discovery of molecular biomarkers. In this review, we aimed to give a comprehensive summary on the utility of proteomics in the field of MS research. We reviewed the published results of the method in case of the pathogenesis of the disease and for biomarkers of diagnosis, differential diagnosis, conversion of disease courses, disease activity, progression and immunological therapy. We found proteomics to be a highly effective emerging tool that has been providing important findings in the research of MS.
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Smoluch M, Sobczyk J, Szewczyk I, Karaszkiewicz P, Silberring J. Mass spectrometry in art conservation-With focus on paintings. MASS SPECTROMETRY REVIEWS 2021:e21767. [PMID: 34870867 DOI: 10.1002/mas.21767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/02/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Conservation of historic artifacts has been a multidisciplinary field from its very beginning. Traditionally, it has been and still is associated with the history of art. It applies knowledge from technical and basic sciences, adapting their solutions to its goals. At present, however, a new tendency is clearly emerging-scientific research is starting to play an increasingly important role not only as a service, but also by proposing new solutions both in the traditional conservation areas and in new areas of conservation activities. The above trend opens up new perspectives for the field of preservation of our heritage but may also create new threats. Therefore, the conservators' caution in introducing new technologies should always be justified; after all, they are responsible for the effects of any activities on the historic objects. This, quite selective review, discusses application of mass spectrometry techniques for the detection of various components that are important to the conservators of our heritage with particular focus on paintings. The text also contains some basic knowledge of technical details to introduce the methodology to a broader group of professionals.
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Affiliation(s)
- Marek Smoluch
- AGH University of Science and Technology, Mickiewicza, Poland
| | - Joanna Sobczyk
- Department of Museum Prevention, Krakow Division, National Museum, Kraków, Poland
| | - Ireneusz Szewczyk
- Department of Museum Prevention, Krakow Division, National Museum, Kraków, Poland
| | - Pawel Karaszkiewicz
- Department of Museum Prevention, Krakow Division, National Museum, Kraków, Poland
| | - Jerzy Silberring
- AGH University of Science and Technology, Mickiewicza, Poland
- Department of Museum Prevention, Krakow Division, National Museum, Kraków, Poland
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Xu Y, Song X, Wang D, Wang Y, Li P, Li J. Proteomic insights into synaptic signaling in the brain: the past, present and future. Mol Brain 2021; 14:37. [PMID: 33596935 PMCID: PMC7888154 DOI: 10.1186/s13041-021-00750-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/09/2021] [Indexed: 12/29/2022] Open
Abstract
Chemical synapses in the brain connect neurons to form neural circuits, providing the structural and functional bases for neural communication. Disrupted synaptic signaling is closely related to a variety of neurological and psychiatric disorders. In the past two decades, proteomics has blossomed as a versatile tool in biological and biomedical research, rendering a wealth of information toward decoding the molecular machinery of life. There is enormous interest in employing proteomic approaches for the study of synapses, and substantial progress has been made. Here, we review the findings of proteomic studies of chemical synapses in the brain, with special attention paid to the key players in synaptic signaling, i.e., the synaptic protein complexes and their post-translational modifications. Looking toward the future, we discuss the technological advances in proteomics such as data-independent acquisition mass spectrometry (DIA-MS), cross-linking in combination with mass spectrometry (CXMS), and proximity proteomics, along with their potential to untangle the mystery of how the brain functions at the molecular level. Last but not least, we introduce the newly developed synaptomic methods. These methods and their successful applications marked the beginnings of the synaptomics era.
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Affiliation(s)
- Yalan Xu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Xiuyue Song
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Dong Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Jing Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China.
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Mori Y, Oikawa S, Kurimoto S, Kitamura Y, Tada-Oikawa S, Kobayashi H, Yamashima T, Murata M. Proteomic analysis of the monkey hippocampus for elucidating ischemic resistance. J Clin Biochem Nutr 2020; 67:167-173. [PMID: 33041514 PMCID: PMC7533853 DOI: 10.3164/jcbn.19-78] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/13/2020] [Indexed: 01/25/2023] Open
Abstract
It is well-known that the cornu Ammonis 1 (CA1) sector of hippocampus is vulnerable for the ischemic insult, whereas the dentate gyrus (DG) is resistant. Here, to elucidate its underlying mechanism, alternations of protein oxidation and expression of DG in the monkey hippocampus after ischemia-reperfusion by the proteomic analysis were studied by comparing CA1 data. Oxidative damage to proteins such as protein carbonylation interrupt the protein function. Carbonyl modification of molecular chaperone, heat shock 70 kDa protein 1 (Hsp70.1) was increased remarkably in CA1, but slightly in DG. In addition, expression levels of nicotinamide adenine dinucleotide (NAD)-dependent protein deacetylase sirtuin-2 (SIRT2) was significantly increased in DG after ischemia, but decreased in CA1. Accordingly, it is likely that SIRT2 upregulation and negligible changes of carbonylation of Hsp70.1 exert its neuroprotective effect in DG. On the contrary, carbonylation level of dihydropyrimidinase related protein 2 (DRP-2) and l-lactate dehydrogenase B chain (LDHB) were slightly increased in CA1 as shown previously, but remarkably increased in DG after ischemia. It is considered that DRP-2 and LDHB are specific targets of oxidative stress by ischemia insult and high carbonylation levels of DRP-2 may play an important role in modulating ischemic neuronal death.
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Affiliation(s)
- Yurie Mori
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Shinji Oikawa
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Shota Kurimoto
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Yuki Kitamura
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan.,College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Saeko Tada-Oikawa
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan.,Department of Human Nutrition, School of Life Studies, Sugiyama Jogakuen University, 17-3 Hoshigaoka-motomachi, Chikusa-ku, Nagoya, Aichi 464-8662, Japan
| | - Hatasu Kobayashi
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
| | - Tetsumori Yamashima
- Departments of Psychiatry and Neurobiology, Kanazawa University Graduate School of Medical Science, Takakura-machi 13-1, Kanazawa, Ishikawa 920-8641, Japan
| | - Mariko Murata
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Edobashi 2-174, Tsu, Mie 514-8507, Japan
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Ner-Kluza J, Wawrzykowski J, Franczyk M, Siberring J, Kankofer M. Identification of protein patterns in bovine placenta at early-mid pregnancy - Pilot studies. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1084-1090. [PMID: 30912867 DOI: 10.1002/rcm.8444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/26/2019] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Placenta is a crucial tissue for an appropriate development of the fetus and the course of pregnancy. Its composition and structure change dynamically along pregnancy but the full pattern of these changes is not fully described in cows yet. The aim of the present study was to detect qualitative and quantitative protein profiles of bovine placenta during early-mid pregnancy at the time of placental formation. METHODS Placental tissues from healthy cows (n = 3) in early pregnancy (3-5 months) were collected at the slaughterhouse. Maternal and fetal parts were manually divided prior to homogenization. Further analysis was done in triplicates on the maternal and fetal parts separately and subjected to one-dimensional (1D) electrophoretic separation, followed by identification of peptide maps by nanospray liquid chromatography/tandem mass spectrometry (nanoLC/MS/MS). Proteins were identified by use of the MASCOT software with the SwissProt database. RESULTS Proteomic analysis showed more than 4000 differentially expressed proteins in maternal and fetal parts of placenta. Each part expressed around 900 proteins, of which ca. 90 were common. The identified proteins were analyzed in accordance to molecular function and their participation in biological processes. CONCLUSIONS The obtained results provide new insight into the knowledge about biochemical characteristics of placenta (new proteins) and serve for further studies on the possible markers of physiological/pathological pregnancy or function of placenta. Moreover, our data can be a good starting point for further studies on the processes underlying the attachment of placenta.
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Affiliation(s)
- Joanna Ner-Kluza
- Department of Biochemistry and Neurobiology, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, 30-059, Krakow, Mickiewicza 30 ave., Poland
| | - Jacek Wawrzykowski
- Department of Biochemistry, Faculty of Veterinary Medicine, University of Life Science in Lublin, 20-033, Lublin, Akademicka 12, Poland
| | - Monika Franczyk
- Department of Biochemistry, Faculty of Veterinary Medicine, University of Life Science in Lublin, 20-033, Lublin, Akademicka 12, Poland
| | - Jerzy Siberring
- Department of Biochemistry and Neurobiology, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, 30-059, Krakow, Mickiewicza 30 ave., Poland
| | - Marta Kankofer
- Department of Biochemistry, Faculty of Veterinary Medicine, University of Life Science in Lublin, 20-033, Lublin, Akademicka 12, Poland
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Naveed M, Tallat A, Butt A, Khalid M, Shehzadi M, Bashir N, Malik KKU, Tufail S, Nouroz F. Neuroproteomics in Paving the Pathway for Drug Abuse Research. CURR PROTEOMICS 2019. [DOI: 10.2174/1570164616666181127144621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Neuroproteomics, as a sub-discipline of proteomics, has enlightened the pathway for the
study of different complicated diseases and brain disorders. Since four decades, various analytical and
quantitative techniques have been used to cure problems related to brain and memory. Brain has a
complex structure with various cells and cell types, the expressing proteins and suppressing factors too.
Drug addiction is one of the main health concerns as it causes physiological changes in brain and affects
its different parts. Some of these drugs like cocaine, marijuana, nicotine and alcohol not only
affect memory and brain cells but also lead to expression and suppression of unwanted and beneficial
proteins respectively. A variety of techniques involving separation techniques, quantification techniques
and analytical techniques are used along with the combination of bioinformatics and magical
tools for analyzing different aspects of brain parts especially proteome of the brain cells. Moreover,
different animal models preferably those resembling human beings are routinely used in neuroproteomics
to study the effects of different drugs on the brain proteome. Different experiments have already
been performed by the researchers on drug abuse that helped massively in estimating not only the effects
of drug addiction on the brain of highly complex organisms (human beings) but also to propose
different therapeutics.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, University of Central Punjab, Lahore, Pakistan
| | - Attha Tallat
- Department of Biotechnology, University of Gujrat, Sialkot Sub campus, Sialkot, Pakistan
| | - Ayesha Butt
- Department of Biotechnology, University of Gujrat, Sialkot Sub campus, Sialkot, Pakistan
| | - Maria Khalid
- Department of Biotechnology, University of Gujrat, Sialkot Sub campus, Sialkot, Pakistan
| | - Marium Shehzadi
- Department of Biotechnology, University of Gujrat, Sialkot Sub campus, Sialkot, Pakistan
| | - Nida Bashir
- Department of Biotechnology, University of Gujrat, Sialkot Sub campus, Sialkot, Pakistan
| | | | - Shafia Tufail
- Department of Biotechnology, University of Gujrat, Sialkot Sub campus, Sialkot, Pakistan
| | - Faisal Nouroz
- Department of Botany, Hazara University, Mansehra, Pakistan
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Filipović D, Costina V, Perić I, Stanisavljević A, Findeisen P. Chronic fluoxetine treatment directs energy metabolism towards the citric acid cycle and oxidative phosphorylation in rat hippocampal nonsynaptic mitochondria. Brain Res 2017; 1659:41-54. [DOI: 10.1016/j.brainres.2017.01.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/24/2016] [Accepted: 01/12/2017] [Indexed: 01/12/2023]
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10
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Ujcikova H, Vosahlikova M, Roubalova L, Svoboda P. Proteomic analysis of protein composition of rat forebrain cortex exposed to morphine for 10 days; comparison with animals exposed to morphine and subsequently nurtured for 20 days in the absence of this drug. J Proteomics 2016; 145:11-23. [DOI: 10.1016/j.jprot.2016.02.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/18/2016] [Accepted: 02/21/2016] [Indexed: 01/20/2023]
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Giuliano S, Agresta AM, De Palma A, Viglio S, Mauri P, Fumagalli M, Iadarola P, Montalbetti L, Salvini R, Bardoni A. Proteomic analysis of lymphoblastoid cells from Nasu-Hakola patients: a step forward in our understanding of this neurodegenerative disorder. PLoS One 2014; 9:e110073. [PMID: 25470616 PMCID: PMC4254282 DOI: 10.1371/journal.pone.0110073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 09/05/2014] [Indexed: 12/31/2022] Open
Abstract
Nasu-Hakola disease (NHD) is a recessively inherited rare disorder characterized by a combination of neuropsychiatric and bone symptoms which, while being unique to this disease, do not provide a rationale for the unambiguous identification of patients. These individuals, in fact, are likely to go unrecognized either because they are considered to be affected by other kinds of dementia or by fibrous dysplasia of bone. Given that dementia in NHD has much in common with Alzheimer’s disease and other neurodegenerative disorders, it cannot be expected to achieve the differential diagnosis of this disease without performing a genetic analysis. Under this scenario, the availability of protein biomarkers would indeed provide a novel context to facilitate interpretation of symptoms and to make the precise identification of this disease possible. The work here reported was designed to generate, for the first time, protein profiles of lymphoblastoid cells from NHD patients. Two-dimensional electrophoresis (2-DE) and nano liquid chromatography-tandem mass spectrometry (nLC-MS/MS) have been applied to all components of an Italian family (seven subjects) and to five healthy subjects included as controls. Comparative analyses revealed differences in the expression profile of 21 proteins involved in glucose metabolism and information pathways as well as in stress responses.
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Affiliation(s)
- Serena Giuliano
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy; Laboratoire d'excellence-Ion channel science and therapeutics, UMR, CNRS, Nice, France
| | - Anna Maria Agresta
- Institute for Biochemical Technologies, Proteomics and Metabolomics Unit, National Research Council, Segrate (Milano), Italy
| | - Antonella De Palma
- Institute for Biochemical Technologies, Proteomics and Metabolomics Unit, National Research Council, Segrate (Milano), Italy
| | - Simona Viglio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Pierluigi Mauri
- Institute for Biochemical Technologies, Proteomics and Metabolomics Unit, National Research Council, Segrate (Milano), Italy
| | - Marco Fumagalli
- Department of Biology and Biotechnologies, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Paolo Iadarola
- Department of Biology and Biotechnologies, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Lorenza Montalbetti
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Roberta Salvini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Anna Bardoni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
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Ujcikova H, Eckhardt A, Kagan D, Roubalova L, Svoboda P. Proteomic analysis of post-nuclear supernatant fraction and percoll-purified membranes prepared from brain cortex of rats exposed to increasing doses of morphine. Proteome Sci 2014; 12:11. [PMID: 24528483 PMCID: PMC3936806 DOI: 10.1186/1477-5956-12-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 02/03/2014] [Indexed: 11/10/2022] Open
Abstract
Background Proteomic analysis was performed in post-nuclear supernatant (PNS) and Percoll-purified membranes (PM) prepared from fore brain cortex of rats exposed to increasing doses of morphine (10–50 mg/kg) for 10 days. Results In PNS, the 10 up (↑)- or down (↓)-regulated proteins exhibiting the largest morphine-induced change were selected, excised manually from the gel and identified by MALDI-TOF MS/MS: 1-(gi|148747414, Guanine deaminase), ↑2.5×; 2-(gi|17105370, Vacuolar-type proton ATP subunit B, brain isoform), ↑2.6×; 3-(gi|1352384, Protein disulfide-isomerase A3), ↑3.4×; 4-(gi|40254595, Dihydropyrimidinase-related protein 2), ↑3.6×; 5-(gi|149054470, N-ethylmaleimide sensitive fusion protein, isoform CRAa), ↑2.0×; 6-(gi|42476181, Malate dehydrogenase, mitochondrial precursor), ↑1.4×; 7-(gi|62653546, Glyceraldehyde-3-phosphate dehydrogenase), ↑1.6×; 8-(gi|202837, Aldolase A), ↑1.3×; 9-(gi|31542401, Creatine kinase B-type), ↓0.86×; 10-(gi|40538860, Aconitate hydratase, mitochondrial precursor), ↑1.3×. The identified proteins were of cytoplasmic (1, 4, 5, 7, 9), cell membrane (2), endoplasmic reticulum (3) and mitochondrial (6, 8, 10) origin and 9 of them were significantly increased, 1.3-3.6×. The 4 out of 9 up-regulated proteins (4, 6, 7, 10) were described as functionally related to oxidative stress; the 2 proteins participate in genesis of apoptotic cell death. In PM, the 18 up (↑)- or down (↓)-regulated proteins were identified by LC-MS/MS and were of plasma membrane [Brain acid soluble protein, ↓2.1×; trimeric Gβ subunit, ↓2.0x], myelin membrane [MBP, ↓2.5×], cytoplasmic [Internexin, ↑5.2×; DPYL2, ↑4.9×; Ubiquitin hydrolase, ↓2.0×; 60S ribosomal protein, ↑2.7×; KCRB, ↓2.6×; Sirtuin-2, ↑2.5×; Peroxiredoxin-2, ↑2.2×; Septin-11, ↑2.2×; TERA, ↑2.1×; SYUA, ↑2.0×; Coronin-1A, ↓5.4×] and mitochondrial [Glutamate dehydrogenase 1, ↑2.7×; SCOT1, ↑2.2×; Prohibitin, ↑2.2×; Aspartate aminotransferase, ↓2.2×] origin. Surprisingly, the immunoblot analysis of the same PM resolved by 2D-ELFO indicated that the “active”, morphine-induced pool of Gβ subunits represented just a minor fraction of the total signal of Gβ which was decreased 1.2x only. The dominant signal of Gβ was unchanged. Conclusion Brain cortex of rats exposed to increasing doses of morphine is far from being adapted. Significant up-regulation of proteins functionally related to oxidative stress and apoptosis suggests a major change of energy metabolism resulting in the state of severe brain cell “discomfort” or even death.
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Affiliation(s)
| | | | | | | | - Petr Svoboda
- Laboratories of Biochemistry of Membrane Receptors, Institute of Physiology, v,v,i,, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 14220, Czech Republic.
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Gorini G, Adron Harris R, Dayne Mayfield R. Proteomic approaches and identification of novel therapeutic targets for alcoholism. Neuropsychopharmacology 2014; 39:104-30. [PMID: 23900301 PMCID: PMC3857647 DOI: 10.1038/npp.2013.182] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 07/02/2013] [Accepted: 07/04/2013] [Indexed: 01/01/2023]
Abstract
Recent studies have shown that gene regulation is far more complex than previously believed and does not completely explain changes at the protein level. Therefore, the direct study of the proteome, considerably different in both complexity and dynamicity to the genome/transcriptome, has provided unique insights to an increasing number of researchers. During the past decade, extraordinary advances in proteomic techniques have changed the way we can analyze the composition, regulation, and function of protein complexes and pathways underlying altered neurobiological conditions. When combined with complementary approaches, these advances provide the contextual information for decoding large data sets into meaningful biologically adaptive processes. Neuroproteomics offers potential breakthroughs in the field of alcohol research by leading to a deeper understanding of how alcohol globally affects protein structure, function, interactions, and networks. The wealth of information gained from these advances can help pinpoint relevant biomarkers for early diagnosis and improved prognosis of alcoholism and identify future pharmacological targets for the treatment of this addiction.
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Affiliation(s)
- Giorgio Gorini
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, USA
| | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, USA
| | - R Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, USA
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Rubenstein R. Proteomic analysis of prion diseases: creating clarity or causing confusion? Electrophoresis 2012; 33:3631-43. [PMID: 23161058 DOI: 10.1002/elps.201200310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 06/25/2012] [Accepted: 07/04/2012] [Indexed: 11/10/2022]
Abstract
Prion diseases, or transmissible spongiform encephalopathies, are progressive, fatal neurodegenerative diseases. There are both human and animal forms of the disease and all are associated with the conversion of a normal host-coded cellular prion protein (PrP(C) ) into an abnormal protease-resistant isoform (PrP(Sc) ). Although methodologies are sensitive and specific for postmortem disease diagnosis, the use of PrP(Sc) as a preclinical or general biomarker for surveillance is difficult, due to the fact that it is present in extremely small amounts in accessible tissues or body fluids such as blood, urine, saliva, and cerebrospinal fluid. Recently, amplification techniques have been developed, which have enabled increased sensitivity for PrP(Sc) detection. However, it has recently been reported that proteinase K sensitive, pathological isoforms of PrP may have a significant role in the pathogenesis of some prion diseases. Accordingly, the development of new diagnostic tests that do not rely on PrP(Sc) and proteinase K digestion is desirable. The search for biomarkers (other than PrP(Sc) ) as tools for diagnosis of prion diseases has a long history. Ideally biomarkers able to detect all transmissible spongiform encephalopathies, even at preclinical stages of infection are desirable but not yet possible due to the heterogeneity of the disease and lengthy disease progression. Recent advances in neuroproteomics have led to an overwhelming amount of information, which may offer insight on protein-protein interactions. While the amount of data obtained is impressive, the ability to relate it to the disease and validating its usefulness in diagnostic biomarker development remains a formidable challenge.
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Affiliation(s)
- Richard Rubenstein
- Department of Neurology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA.
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16
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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.
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Affiliation(s)
- Simone Lista
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Goethe-University of Frankfurt, Frankfurt am Main, Germany.
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17
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Singh V, Hintzen RQ, Luider TM, Stoop MP. Proteomics technologies for biomarker discovery in multiple sclerosis. J Neuroimmunol 2011; 248:40-7. [PMID: 22129845 DOI: 10.1016/j.jneuroim.2011.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 11/02/2011] [Indexed: 12/17/2022]
Abstract
Multiple sclerosis is a disabling inflammatory and neurodegenerative disorder that predominantly affects young adults. There is a great need for biomarkers, which could elucidate pathology as well as provide prognosis of disease progression and therapy response in multiple sclerosis. Rapidly evolving, technology driven applications such as mass spectrometry based proteomics are currently being developed for this purpose. In this review, we will outline the current status of the field and detail a number of the bottlenecks as well as future prospects of this type of biomarker research.
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Affiliation(s)
- Vaibhav Singh
- Laboratories of Neuro-Oncology/Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
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18
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Juhász G, Földi I, Penke B. Systems biology of Alzheimer's disease: How diverse molecular changes result in memory impairment in AD. Neurochem Int 2011; 58:739-50. [DOI: 10.1016/j.neuint.2011.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 01/19/2011] [Accepted: 02/10/2011] [Indexed: 01/13/2023]
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19
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Vanguilder HD, Freeman WM. The hippocampal neuroproteome with aging and cognitive decline: past progress and future directions. Front Aging Neurosci 2011; 3:8. [PMID: 21647399 PMCID: PMC3102218 DOI: 10.3389/fnagi.2011.00008] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 05/12/2011] [Indexed: 01/12/2023] Open
Abstract
Although steady progress on understanding brain aging has been made over recent decades through standard anatomical, immunohistochemical, and biochemical techniques, the biological basis of non-neurodegenerative cognitive decline with aging remains to be determined. This is due in part to technical limitations of traditional approaches, in which only a small fraction of neurobiologically relevant proteins, mRNAs or metabolites can be assessed at a time. With the development and refinement of proteomic technologies that enable simultaneous quantitative assessment of hundreds to thousands of proteins, neuroproteomic studies of brain aging and cognitive decline are becoming more widespread. This review focuses on the contributions of neuroproteomic investigations to advances in our understanding of age-related deficits of hippocampus-dependent spatial learning and memory. Accumulating neuroproteomic data demonstrate that hippocampal aging involves common themes of dysregulated metabolism, increased oxidative stress, altered protein processing, and decreased synaptic function. Additionally, growing evidence suggests that cognitive decline does not represent a "more aged" phenotype, but rather is associated with specific neuroproteomic changes that occur in addition to age-related alterations. Understanding if and how age-related changes in the hippocampal neuroproteome contribute to cognitive decline and elucidating the pathways and processes that lead to cognitive decline are critical objectives that remain to be achieved. Progress in the field and challenges that remain to be addressed with regard to animal models, behavioral testing, and proteomic reporting are also discussed.
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Affiliation(s)
- Heather D Vanguilder
- Department of Pharmacology, Penn State College of Medicine, Milton S. Hershey Medical Center Hershey, PA, USA
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20
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Shevchenko G, Sjödin MOD, Malmström D, Wetterhall M, Bergquist J. Cloud-Point Extraction and Delipidation of Porcine Brain Proteins in Combination with Bottom-Up Mass Spectrometry Approaches for Proteome Analysis. J Proteome Res 2010; 9:3903-11. [DOI: 10.1021/pr100116k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ganna Shevchenko
- Department of Physical and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Marcus O. D. Sjödin
- Department of Physical and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - David Malmström
- Department of Physical and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Magnus Wetterhall
- Department of Physical and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Jonas Bergquist
- Department of Physical and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
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21
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Li A, Choi YS, Dziema H, Cao R, Cho HY, Jung YJ, Obrietan K. Proteomic profiling of the epileptic dentate gyrus. Brain Pathol 2010; 20:1077-89. [PMID: 20608933 DOI: 10.1111/j.1750-3639.2010.00414.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The development of epilepsy is often associated with marked changes in central nervous system cell structure and function. Along these lines, reactive gliosis and granule cell axonal sprouting within the dentate gyrus of the hippocampus are commonly observed in individuals with temporal lobe epilepsy (TLE). Here we used the pilocarpine model of TLE in mice to screen the proteome and phosphoproteome of the dentate gyrus to identify molecular events that are altered as part of the pathogenic process. Using a two-dimensional gel electrophoresis-based approach, followed by liquid chromatography-tandem mass spectrometry, 24 differentially expressed proteins, including 9 phosphoproteins, were identified. Functionally, these proteins were organized into several classes, including synaptic physiology, cell structure, cell stress, metabolism and energetics. The altered expression of three proteins involved in synaptic physiology, actin, profilin 1 and α-synuclein was validated by secondary methods. Interestingly, marked changes in protein expression were detected in the supragranular cell region, an area where robust mossy fibers sprouting occurs. Together, these data provide new molecular insights into the altered protein profile of the epileptogenic dentate gyrus and point to potential pathophysiologic mechanisms underlying epileptogenesis.
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Affiliation(s)
- Aiqing Li
- Key Lab. for Organ Failure Research, Education Ministry of P.R. China, Southern Medical University, Guangzhou, China
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22
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Liu X, Wen F, Yang J, Chen L, Wei YQ. A review of current applications of mass spectrometry for neuroproteomics in epilepsy. MASS SPECTROMETRY REVIEWS 2010; 29:197-246. [PMID: 19598206 DOI: 10.1002/mas.20243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The brain is unquestionably the most fascinating organ, and the hippocampus is crucial in memory storage and retrieval and plays an important role in stress response. In temporal lobe epilepsy (TLE), the seizure origin typically involves the hippocampal formation. Despite tremendous progress, current knowledge falls short of being able to explain its function. An emerging approach toward an improved understanding of the complex molecular mechanisms that underlie functions of the brain and hippocampus is neuroproteomics. Mass spectrometry has been widely used to analyze biological samples, and has evolved into an indispensable tool for proteomics research. In this review, we present a general overview of the application of mass spectrometry in proteomics, summarize neuroproteomics and systems biology-based discovery of protein biomarkers for epilepsy, discuss the methodology needed to explore the epileptic hippocampus proteome, and also focus on applications of ingenuity pathway analysis (IPA) in disease research. This neuroproteomics survey presents a framework for large-scale protein research in epilepsy that can be applied for immediate epileptic biomarker discovery and the far-reaching systems biology understanding of the protein regulatory networks. Ultimately, knowledge attained through neuroproteomics could lead to clinical diagnostics and therapeutics to lessen the burden of epilepsy on society.
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Affiliation(s)
- Xinyu Liu
- National Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
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23
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Baker ES, Livesay EA, Orton DJ, Moore RJ, Danielson WF, Prior DC, Ibrahim YM, LaMarche BL, Mayampurath AM, Schepmoes AA, Hopkins DF, Tang K, Smith RD, Belov ME. An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies. J Proteome Res 2010; 9:997-1006. [PMID: 20000344 DOI: 10.1021/pr900888b] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A high-throughput approach and platform using 15 min reversed-phase capillary liquid chromatography (RPLC) separations in conjunction with ion mobility spectrometry-mass spectrometry (IMS-MS) measurements was evaluated for the rapid analysis of complex proteomics samples. To test the separation quality of the short LC gradient, a sample was prepared by spiking 20 reference peptides at varying concentrations from 1 ng/mL to 10 microg/mL into a tryptic digest of mouse blood plasma and analyzed with both a LC-Linear Ion Trap Fourier Transform (FT) MS and LC-IMS-TOF MS. The LC-FT MS detected 13 out of the 20 spiked peptides that had concentrations >or=100 ng/mL. In contrast, the drift time selected mass spectra from the LC-IMS-TOF MS analyses yielded identifications for 19 of the 20 peptides with all spiking levels present. The greater dynamic range of the LC-IMS-TOF MS system could be attributed to two factors. First, the LC-IMS-TOF MS system enabled drift time separation of the low concentration spiked peptides from the high concentration mouse peptide matrix components, reducing signal interference and background, and allowing species to be resolved that would otherwise be obscured by other components. Second, the automatic gain control (AGC) in the linear ion trap of the hybrid FT MS instrument limits the number of ions that are accumulated to reduce space charge effects and achieve high measurement accuracy, but in turn limits the achievable dynamic range compared to the IMS-TOF instrument.
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Affiliation(s)
- Erin Shammel Baker
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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24
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Maurer MH. Proteomics of brain extracellular fluid (ECF) and cerebrospinal fluid (CSF). MASS SPECTROMETRY REVIEWS 2010; 29:17-28. [PMID: 19116946 DOI: 10.1002/mas.20213] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Mass spectrometry has become the gold standard for the identification of proteins in proteomics. In this review, I will discuss the available literature on proteomic experiments that analyze human cerebrospinal fluid (CSF) and brain extracellular fluid (ECF), mostly obtained by cerebral microdialysis. Both materials are of high diagnostic value in clinical neurology, for example, in cerebrovascular disorders like stroke, neurodegenerative diseases like Alzheimer's Disease, Parkinson's Disease, amyotrophic lateral sclerosis (ALS), traumatic brain injury and cerebral infectious and inflammatory disease, such as multiple sclerosis. Moreover, there are standard procedures for sampling. In a number of studies in recent years, biomarkers have been proposed in CSF and ECF for improved diagnosis or to control therapy, based on proteomics and mass spectrometry. I will also discuss the needs for a transition of research-based experimental screening with mass spectrometry to fast and reliable diagnostic instrumentation for clinical use.
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Affiliation(s)
- Martin H Maurer
- Department of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany.
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25
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Altelaar AFM, Mohammed S, Brans MAD, Adan RAH, Heck AJR. Improved identification of endogenous peptides from murine nervous tissue by multiplexed peptide extraction methods and multiplexed mass spectrometric analysis. J Proteome Res 2009; 8:870-6. [PMID: 19152261 DOI: 10.1021/pr800449n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In recent years, mass spectrometry (MS) based techniques have made their entrance in the analysis of endogenous peptides extracted from nervous tissue. In this study, we introduce a novel peptide extraction procedure using 8 M urea, next to the more established extraction method that uses acetic acid. The extracted peptide mixtures are analyzed by both high-resolution nanoLC MS/MS using collision induced dissociation (CID) on an LTQ-Orbitrap and nanoLC electron transfer induced dissociation (ETD) on a linear ion trap. The combined use of the two extraction methods significantly increased the yield of identified endogenous neuropeptides. The multiplexed use of high mass accuracy mass spectrometry and the ETD fragmentation technique further increased the yield and confidence of peptide identifications. Furthermore, reduction of disulfide bridges during sample preparation was essential in the identification of several endogenous peptides containing cysteine disulfide bonds. Through this study, we identified in total 142 peptides in extracts of the mouse pituitary tissue, whereby 43 uniquely in the urea extract and 11 uniquely in the acetic acid extract. A large number of detected endogenous peptides were reported previously, but we confidently identified 22 unreported peptides that possess characteristics of endogenous peptides and are thus interesting targets to be explored further.
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Affiliation(s)
- A F Maarten Altelaar
- Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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26
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Measurement of Biological Materials. Clin Transl Sci 2009. [DOI: 10.1016/b978-0-12-373639-0.00005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
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27
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Proteome alteration of U251 human astrocytoma cell after inhibiting retinoic acid synthesis. Mol Cell Biochem 2008; 323:185-93. [PMID: 19089318 DOI: 10.1007/s11010-008-9978-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 11/28/2008] [Indexed: 10/21/2022]
Abstract
Retinoic acid (Ra) is crucial for the patterning and neuronal differentiation in the central nervous system (CNS). Ra deficiency in animals disrupts the motor activities and memory abilities. The molecular mechanisms underlying these behavior abnormalities remain largely unknown. In the current study, we treated the astrocytoma cells with citral, an inhibitor of Ra synthesis. We analyzed the differences in the protein concentrations between the treated and untreated astrocytoma cells by two-dimensional gel electrophoresis (2-DE), Imagemaster software, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). In total, 39 of 46 altered protein spots with significant mascot scores were identified representing 36 proteins, that were involved in significantly altered glutamate metabolism, lipid metabolism, mitochondrial function, and oxidative stress response by Ingenuity Pathway Analysis (IPA). Altered 3-phosphoglycerate dehydrogenase (PHGDH) was also observed in western blot. These data provide some clues for explaining the behavioral changes caused by Ra deficiency, and support the hypothesis that Ra signaling is associated with some symptoms of neurodegenerative disorders and schizophrenia.
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28
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Shi M, Caudle WM, Zhang J. Biomarker discovery in neurodegenerative diseases: a proteomic approach. Neurobiol Dis 2008; 35:157-64. [PMID: 18938247 DOI: 10.1016/j.nbd.2008.09.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 09/04/2008] [Accepted: 09/14/2008] [Indexed: 11/26/2022] Open
Abstract
Biomarkers for neurodegenerative disorders are essential to facilitate disease diagnosis, ideally at early stages, monitor disease progression, and assess response to existing and future treatments. Application of proteomics to the human brain, cerebrospinal fluid and plasma has greatly hastened the unbiased and high-throughput searches for novel biomarkers. There are many steps critical to biomarker discovery, whether for neurodegenerative or other diseases, including sample preparation, protein/peptide separation and identification, as well as independent confirmation and validation. In this review we have summarized current proteomics technologies involved in discovery of biomarkers for neurodegenerative diseases, practical considerations and limitations of several major aspects, as well as the current status of candidate biomarkers revealed by proteomics for Alzheimer and Parkinson diseases.
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Affiliation(s)
- Min Shi
- Department of Pathology, University of Washington School of Medicine, HMC Box 359635, 325 9th Avenue, Seattle, WA 98104, USA
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29
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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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30
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Tyagi P, Chen X, Hayashi Y, Yoshimura N, Chancellor MB, de Miguel F. Proteomic investigation on chronic bladder irritation in the rat. Urology 2008; 71:536-40. [PMID: 18342204 DOI: 10.1016/j.urology.2007.10.069] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 10/03/2007] [Accepted: 10/29/2007] [Indexed: 11/16/2022]
Abstract
OBJECTIVES Interstitial cystitis (IC) is a painful bladder syndrome associated with urinary frequency and urgency. Elusive cause of IC makes its diagnosis only possible by exclusion in many cases. In this study, we used proteomics for identifying disease-associated proteins in a rat model of chronic bladder irritation. METHODS Chronic irritation of the rat bladder was caused by a brief (90 seconds) intravesical instillation of 0.2 mL of 0.4 N HCl. Whole bladders were collected at different time points after treatment, snap frozen, and nuclear and cytosolic protein extracts were obtained. Samples were resolved in standard 2-dimensional (2D) gels stained with an improved Coomasie stain or by differential gel electrophoresis (DIGE). Differentially expressed spots were excised and identified by MALDI-TOF MS/MS. Histologic and Western blot analyses were also performed. RESULTS Bladder morphology and histologic appearance of bladder sections after HCl treatment reflected hemorrhage, edema, epithelial denudation, detrusor mastocytosis, and eosinophilia. Proteomic analysis of irritated rat bladder revealed marked overexpression of 4 nuclear proteins and marked underexpression of 1 nuclear protein compared with normal rat bladders. Among these proteins, inflammation-associated calgranulin A (over) and smooth muscle protein-22/transgelin (under) showed opposed expression patterns after bladder irritation. CONCLUSIONS Presence of mast cells and eosinophils and overexpression of calgranulin A confirm the inflammatory component of HCl-irritated bladder. Altered expression of nuclear proteins is of particular interest because of their possible role as a prognostic marker in inflammatory bladder disorders. However, more studies are needed before clinical application of these findings can be established.
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Affiliation(s)
- Pradeep Tyagi
- Department of Urology, University of Pittsburgh School of Medicine; Pittsburgh, Pennsylvania 15213, USA.
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31
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Espada A, Molina-Martin M, Dage J, Kuo MS. Application of LC/MS and related techniques to high-throughput drug discovery. Drug Discov Today 2008; 13:417-23. [DOI: 10.1016/j.drudis.2008.03.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Revised: 03/06/2008] [Accepted: 03/10/2008] [Indexed: 11/16/2022]
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32
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Ekegren T, Hanrieder J, Bergquist J. Clinical perspectives of high-resolution mass spectrometry-based proteomics in neuroscience: exemplified in amyotrophic lateral sclerosis biomarker discovery research. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:559-571. [PMID: 18416436 DOI: 10.1002/jms.1409] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Biomarker discovery is a central application in today's proteomic research. There is an urgent need for valid biomarkers to improve diagnostic tools and treatment in many disorders, such as the rapidly progressing neurodegenerative disorder amyotrophic lateral sclerosis (ALS) that has a fatal outcome in about 3 years and yet no curative treatment. Screening for clinically relevant biomarkers puts high demands on high-throughput, rapid and precise proteomic techniques. There is a large variety in the methods of choice involving mainly gel-based approaches as well as chromatographic techniques for multi-dimensional protein and peptide separations followed by mass spectrometry (MS) analysis. This special feature article will discuss some important aspects of MS-based clinical proteomics and biomarker discovery in the field of neurodegenerative diseases and ALS research respectively, with the aim to provide a prospective view on current and future research aspects in the field. Furthermore, examples for application of high-resolution MS-based proteomic strategies for ALS biomarker discovery will be demonstrated with two studies previously reported by our group. These studies include among others, utilization of capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR-MS) for advanced protein pattern classification in cerebrospinal fluid (CSF) samples of ALS patients as well as highly sensitive protein identification in minimal amounts of postmortem spinal cord tissue and laser micro-dissected motor neurons using FT-ICR-MS in conjunction with nanoflow LC coupled to matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry (LC-MALDI-TOF-TOF-MS).
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Affiliation(s)
- Titti Ekegren
- Department of Physical and Analytical Chemistry, Uppsala University, Uppsala, Sweden
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33
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Sugita T, Yoshikawa T, Mukai Y, Yamanada N, Imai S, Nagano K, Yoshida Y, Shibata H, Yoshioka Y, Nakagawa S, Kamada H, Tsunoda SI, Tsutsumi Y. Comparative study on transduction and toxicity of protein transduction domains. Br J Pharmacol 2008; 153:1143-52. [PMID: 18223668 DOI: 10.1038/sj.bjp.0707678] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND AND PURPOSE Protein transduction domains (PTDs), such as Tat, antennapedia homeoprotein (Antp), Rev and VP22, have been extensively utilized for intracellular delivery of biologically active macromolecules in vitro and in vivo. There is little known, however, about the relative transduction efficacy, cytotoxicity and internalization mechanism of individual PTDs. EXPERIMENTAL APPROACH We examined the cargo delivery efficacies of four major PTDs (Tat, Antp, Rev and VP22) and evaluated their toxicities and cell internalizing pathways in various cell lines. KEY RESULTS The relative order of the transduction efficacy of these PTDs conjugated to fluorescein was Rev>Antp>Tat>VP22, independent of cell type (HeLa, HaCaT, A431, Jurkat, MOLT-4 and HL60 cells). Antp produced significant toxicity in HeLa and Jurkat cells, and Rev produced significant toxicity in Jurkat cells. Flow cytometric analysis demonstrated that the uptake of PTD-fluorescein conjugate was dose-dependently inhibited by methyl-beta-cyclodextrin, cytochalasin D and amiloride, indicating that all four PTDs were internalized by the macropinocytotic pathway. Accordingly, in cells co-treated with 'Tat-fused' endosome-disruptive HA2 peptides (HA2-Tat) and independent PTD-fluorescent protein conjugates, fluorescence spread throughout the cytosol, indicating that all four PTDs were internalized into the same vesicles as Tat. CONCLUSIONS AND IMPLICATIONS These findings suggest that macropinocytosis-dependent internalization is a crucial step in PTD-mediated molecular transduction. From the viewpoint of developing effective and safe protein transduction technology, although Tat was the most versatile carrier among the peptides studied, PTDs should be selected based on their individual characteristics.
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Affiliation(s)
- T Sugita
- Laboratory of Pharmaceutical Proteomics, National Institute of Biomedical Innovation (NIBIO), Ibaraki, Osaka, Japan
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Bitarte N, Bandrés E, Zárate R, Ramirez N, Garcia-Foncillas J. Moving forward in colorectal cancer research, what proteomics has to tell. World J Gastroenterol 2007; 13:5813-21. [PMID: 17990347 PMCID: PMC4205428 DOI: 10.3748/wjg.v13.i44.5813] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer is the third most common cancer and is highly fatal. During the last several years, research has been primarily based on the study of expression profiles using microarray technology. But now, investigators are putting into practice proteomic analyses of cancer tissues and cells to identify new diagnostic or therapeutic biomarkers for this cancer. Because the proteome reflects the state of a cell, tissue or organism more accurately, much is expected from proteomics to yield better tumor markers for disease diagnosis and therapy monitoring. This review summarizes the most relevant applications of proteomics the biomarker discovery for colorectal cancer.
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Rozek W, Ricardo-Dukelow M, Holloway S, Gendelman HE, Wojna V, Melendez LM, Ciborowski P. Cerebrospinal fluid proteomic profiling of HIV-1-infected patients with cognitive impairment. J Proteome Res 2007; 6:4189-99. [PMID: 17929958 DOI: 10.1021/pr070220c] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Advanced HIV-1 infection is commonly associated with progressive immune suppression and the development of cognitive, motor, and behavior disturbances. In its most severe form, it is diagnosed as HIV-1 associated dementia (HAD) and can progress to profound functional disability and death. Despite prodigious efforts to uncover biomarkers of HAD, none can adequately reflect disease onset or progression. Thus, we developed a proteomics platform for HAD biomarker discovery and used it to perform a pilot study on cerebrospinal fluid (CSF) from HIV-1-infected people with or without HAD. A 2-dimensional electrophoresis (2-DE) map of a HAD CSF proteome was focused on differentially expressed proteins. 2-DE difference gel electrophoresis (2-D DIGE) analysis showed >90 differences in protein spots of which 20 proteins were identified. Differential expression of 6 proteins was validated by Western blot tests and included vitamin D binding protein, clusterin, gelsolin, complement C3, procollagen C-endopeptidase enhancer 1, and cystatin C. We posit that these proteins, alone or together, are potential HAD biomarkers.
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Affiliation(s)
- Wojciech Rozek
- Center for Neurovirology and Neurodegenerative Disorders, Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5800, USA
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