1
|
Yurduseven K, Babal YK, Celik E, Kerman BE, Kurnaz IA. Multiple Sclerosis Biomarker Candidates Revealed by Cell-Type-Specific Interactome Analysis. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:305-317. [PMID: 35483054 DOI: 10.1089/omi.2022.0023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Multiple sclerosis (MS) is a demyelinating disorder that affects multiple regions of the central nervous system such as the brain, spinal cord, and optic nerves. Susceptibility to MS, as well as disease progression rates, displays marked patient-to-patient variability. To date, biomarkers that forecast differences in clinical phenotypes and outcomes have been limited. In this context, cell-type-specific interactome analyses offer important prospects and hope for novel diagnostics and therapeutics. We report here an original study using bioinformatic analysis of MS data sets that revealed interaction profiles as well as specific hub proteins in white matter (WM) and gray matter (GM) that appear critical for disease mechanisms. First, cell-type-specific interactome analyses suggested that while interactions within the WM were focused on oligodendrocytes, interactions within the GM were mostly neuron centric. Second, hub proteins such as APP, EGLN3, PTEN, and LRRK2 were identified to be differentially regulated in MS data sets. Lastly, a comparison of the brain and peripheral blood samples identified biomarker candidates such as NRGN, CRTC1, CDC42, and IFITM3 to be differentially expressed in different types of MS. These findings offer a unique cell-type-specific cell-to-cell interaction network in MS and identify potential biomarkers by comparative analysis of the brain and the blood transcriptomics. From a study design and methodology perspective, we suggest that the cell-type-specific interactome analysis is an important systems science frontier that might offer new insights on other neurodegenerative and brain disorders as well.
Collapse
Affiliation(s)
- Kübra Yurduseven
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
- Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Yigit Koray Babal
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
| | - Esref Celik
- Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Bilal Ersen Kerman
- Regenerative and Restorative Medical Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Işıl Aksan Kurnaz
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
| |
Collapse
|
2
|
Monzón M. Approaches to therapy against prion diseases focused on the individual defence system. AIMS MOLECULAR SCIENCE 2017. [DOI: 10.3934/molsci.2017.3.241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
3
|
Viader A, Ogasawara D, Joslyn CM, Sanchez-Alavez M, Mori S, Nguyen W, Conti B, Cravatt BF. A chemical proteomic atlas of brain serine hydrolases identifies cell type-specific pathways regulating neuroinflammation. eLife 2016; 5:e12345. [PMID: 26779719 PMCID: PMC4737654 DOI: 10.7554/elife.12345] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/13/2015] [Indexed: 12/19/2022] Open
Abstract
Metabolic specialization among major brain cell types is central to nervous system function and determined in large part by the cellular distribution of enzymes. Serine hydrolases are a diverse enzyme class that plays fundamental roles in CNS metabolism and signaling. Here, we perform an activity-based proteomic analysis of primary mouse neurons, astrocytes, and microglia to furnish a global portrait of the cellular anatomy of serine hydrolases in the brain. We uncover compelling evidence for the cellular compartmentalization of key chemical transmission pathways, including the functional segregation of endocannabinoid (eCB) biosynthetic enzymes diacylglycerol lipase-alpha (DAGLα) and –beta (DAGLβ) to neurons and microglia, respectively. Disruption of DAGLβ perturbed eCB-eicosanoid crosstalk specifically in microglia and suppressed neuroinflammatory events in vivo independently of broader effects on eCB content. Mapping the cellular distribution of metabolic enzymes thus identifies pathways for regulating specialized inflammatory responses in the brain while avoiding global alterations in CNS function. DOI:http://dx.doi.org/10.7554/eLife.12345.001 The brain is made up of many types of cells. These include the neurons that transmit messages throughout the nervous system, and microglia, which act as the first line of the brain’s immune defense. The activity of both neurons and microglia can be influenced by molecules called endocannabinoids that bind to proteins on the cells’ surface. For example, endocannabinoids affect how a neuron responds to messages sent to it from a neighbouring neuron, and help microglia to regulate the inflammation of brain tissue. Enzymes called serine hydrolases play important roles in several different signaling processes in the brain, including those involving endocannabinoids. Viader et al. have now studied the activities of these enzymes – including two called DAGLα and DAGLβ – in the mouse brain using a technique called activity-based protein profiling. This revealed that DAGLα plays an important role in controlling how neurons respond to endocannabinoids, while DAGLβ performs the equivalent role in microglia. When Viader et al. shut down DAGLβ activity, this only affected endocannabinoid signaling in microglia. This also had the effect of reducing inflammation in the brain, without affecting how endocannabinoids signal in neurons. These results suggest that inhibitors of DAGLβ could offer a way to suppress inflammation in the brain, which may contribute to neuropsychiatric and neurodegenerative diseases, while preserving the normal pathways that neurons use to communicate with one another. DOI:http://dx.doi.org/10.7554/eLife.12345.002
Collapse
Affiliation(s)
- Andreu Viader
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Daisuke Ogasawara
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Christopher M Joslyn
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Manuel Sanchez-Alavez
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Simone Mori
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - William Nguyen
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Bruno Conti
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States
| | - Benjamin F Cravatt
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, United States.,Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| |
Collapse
|
4
|
de Oliveira Souza VC, de Marco KC, Laure HJ, Rosa JC, Barbosa F. A brain proteome profile in rats exposed to methylmercury or thimerosal (ethylmercury). JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2016; 79:502-512. [PMID: 27294299 DOI: 10.1080/15287394.2016.1182003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Exposure to organomercurials has been associated with harmful effects on the central nervous system (CNS). However, the mechanisms underlying organomercurial-mediated neurotoxic effects need to be elucidated. Exposure to toxic elements may promote cellular modifications such as alterations in protein synthesis in an attempt to protect tissues and organs from damage. In this context, the use of a "proteomic profile" is an important tool to identify potential early biomarkers or targets indicative of neurotoxicity. The aim of this study was to investigate potential modifications in rat cerebral cell proteome following exposure to methylmercury (MeHg) or ethylmercury (EtHg). For MeHg exposure, animals were administered by gavage daily 140 µg/kg/d of Hg (as MeHg) for 60 d and sacrificed 24 h after the last treatment. For EtHg exposure, 800 µg/kg/d of Hg (as EtHg) was given intramuscularly (im) in a single dose and rats were sacrificed after 4 h. Control groups received saline either by gavage or im. After extraction of proteins from whole brain samples and separation by two-dimensional electrophoresis (2-DE), 26 differentially expressed proteins were identified from exposed animals by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF/TOF). Both MeHg and EtHg exposure induced an overexpression of calbindin, a protein that acts as a neuroprotective agent by (1) adjusting the concentration of Ca(2+) within cells and preventing neurodegenerative diseases and (2) decreasing expression of glutamine synthetase, a crucial protein involved in regulation of glutamate concentration in synaptic cleft. In contrast, expression of superoxide dismutase (SOD), a protein involved in antioxidant defense, was elevated in brain of MeHg-exposed animals. Taken together, our data provide new valuable information on the possible molecular mechanisms associated with MeHg- and EtHg-mediated toxicity in cerebral tissue. These observed protein alterations may be considered as biomarkers candidates for biological monitoring of organomercurial poisoning.
Collapse
Affiliation(s)
- Vanessa Cristina de Oliveira Souza
- a Department of Clinical, Bromatological and Toxicological Analysis, Faculty of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , São Paulo , Brazil
| | - Kátia Cristina de Marco
- a Department of Clinical, Bromatological and Toxicological Analysis, Faculty of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , São Paulo , Brazil
| | - Hélen Julie Laure
- b Department of Molecular and Cellular Biology, Faculty of Medicine of Ribeirão Preto , University of São Paulo , São Paulo , Brazil
| | - José Cesar Rosa
- b Department of Molecular and Cellular Biology, Faculty of Medicine of Ribeirão Preto , University of São Paulo , São Paulo , Brazil
| | - Fernando Barbosa
- a Department of Clinical, Bromatological and Toxicological Analysis, Faculty of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , São Paulo , Brazil
| |
Collapse
|
5
|
Decoding neuroproteomics: integrating the genome, translatome and functional anatomy. Nat Neurosci 2014; 17:1491-9. [PMID: 25349915 DOI: 10.1038/nn.3829] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 09/04/2014] [Indexed: 02/07/2023]
Abstract
The immense intercellular and intracellular heterogeneity of the CNS presents major challenges for high-throughput omic analyses. Transcriptional, translational and post-translational regulatory events are localized to specific neuronal cell types or subcellular compartments, resulting in discrete patterns of protein expression and activity. A spatial and quantitative knowledge of the neuroproteome is therefore critical to understanding both normal and pathological aspects of the functional genomics and anatomy of the CNS. Improvements in mass spectrometry allow the profiling of proteins at a sufficient depth to complement results from high-throughput genomic and transcriptomic assays. However, there are challenges in integrating proteomic data with other data modalities and even greater challenges in obtaining comprehensive neuroproteomic data with cell-type specificity. Here we discuss how proteomics should be exploited to enhance high-throughput functional genomic analysis by tighter integration of data analyses. We also discuss experimental strategies to achieve finer cellular and subcellular resolution in transcriptomic and proteomic studies of neural tissues.
Collapse
|
6
|
Haqqani AS, Delaney CE, Tremblay TL, Sodja C, Sandhu JK, Stanimirovic DB. Method for isolation and molecular characterization of extracellular microvesicles released from brain endothelial cells. Fluids Barriers CNS 2013; 10:4. [PMID: 23305214 PMCID: PMC3560214 DOI: 10.1186/2045-8118-10-4] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 12/18/2012] [Indexed: 12/15/2022] Open
Abstract
Background In addition to possessing intracellular vesicles, eukaryotic cells also produce extracellular microvesicles, ranging from 50 to 1000 nm in diameter that are released or shed into the microenvironment under physiological and pathological conditions. These membranous extracellular organelles include both exosomes (originating from internal vesicles of endosomes) and ectosomes (originating from direct budding/shedding of plasma membranes). Extracellular microvesicles contain cell-specific collections of proteins, glycoproteins, lipids, nucleic acids and other molecules. These vesicles play important roles in intercellular communication by acting as carrier for essential cell-specific information to target cells. Endothelial cells in the brain form the blood–brain barrier, a specialized interface between the blood and the brain that tightly controls traffic of nutrients and macromolecules between two compartments and interacts closely with other cells forming the neurovascular unit. Therefore, brain endothelial cell extracellular microvesicles could potentially play important roles in ‘externalizing’ brain-specific biomarkers into the blood stream during pathological conditions, in transcytosis of blood-borne molecules into the brain, and in cell-cell communication within the neurovascular unit. Methods To study cell-specific molecular make-up and functions of brain endothelial cell exosomes, methods for isolation of extracellular microvesicles using mass spectrometry-compatible protocols and the characterization of their signature profiles using mass spectrometry -based proteomics were developed. Results A total of 1179 proteins were identified in the isolated extracellular microvesicles from brain endothelial cells. The microvesicles were validated by identification of almost 60 known markers, including Alix, TSG101 and the tetraspanin proteins CD81 and CD9. The surface proteins on isolated microvesicles could potentially interact with both primary astrocytes and cortical neurons, as cell-cell communication vesicles. Finally, brain endothelial cell extracellular microvesicles were shown to contain several receptors previously shown to carry macromolecules across the blood brain barrier, including transferrin receptor, insulin receptor, LRPs, LDL and TMEM30A. Conclusions The methods described here permit identification of the molecular signatures for brain endothelial cell-specific extracellular microvesicles under various biological conditions. In addition to being a potential source of useful biomarkers, these vesicles contain potentially novel receptors known for delivering molecules across the blood–brain barrier.
Collapse
Affiliation(s)
- Arsalan S Haqqani
- National Research Council of Canada, Human Health Therapeutics Portfolio, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada.
| | | | | | | | | | | |
Collapse
|
7
|
Thouvenot E, Urbach S, Vigy O, Séveno M, Galéotti N, Nguyen G, Bockaert J, Marin P. Quantitative proteomic analysis reveals protein expression changes in the murine neuronal secretome during apoptosis. J Proteomics 2012; 77:394-405. [DOI: 10.1016/j.jprot.2012.09.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 08/24/2012] [Accepted: 09/12/2012] [Indexed: 01/08/2023]
|
8
|
Abstract
AbstractThe science of genetics is undergoing a paradigm shift. Recent discoveries, including the activity of retrotransposons, the extent of copy number variations, somatic and chromosomal mosaicism, and the nature of the epigenome as a regulator of DNA expressivity, are challenging a series of dogmas concerning the nature of the genome and the relationship between genotype and phenotype. According to three widely held dogmas, DNA is the unchanging template of heredity, is identical in all the cells and tissues of the body, and is the sole agent of inheritance. Rather than being an unchanging template, DNA appears subject to a good deal of environmentally induced change. Instead of identical DNA in all the cells of the body, somatic mosaicism appears to be the normal human condition. And DNA can no longer be considered the sole agent of inheritance. We now know that the epigenome, which regulates gene expressivity, can be inherited via the germline. These developments are particularly significant for behavior genetics for at least three reasons: First, epigenetic regulation, DNA variability, and somatic mosaicism appear to be particularly prevalent in the human brain and probably are involved in much of human behavior; second, they have important implications for the validity of heritability and gene association studies, the methodologies that largely define the discipline of behavior genetics; and third, they appear to play a critical role in development during the perinatal period and, in particular, in enabling phenotypic plasticity in offspring. I examine one of the central claims to emerge from the use of heritability studies in the behavioral sciences, the principle of minimal shared maternal effects, in light of the growing awareness that the maternal perinatal environment is a critical venue for the exercise of adaptive phenotypic plasticity. This consideration has important implications for both developmental and evolutionary biology.
Collapse
|
9
|
GlycReSoft: a software package for automated recognition of glycans from LC/MS data. PLoS One 2012; 7:e45474. [PMID: 23049804 PMCID: PMC3458864 DOI: 10.1371/journal.pone.0045474] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/16/2012] [Indexed: 11/19/2022] Open
Abstract
Glycosylation modifies the physicochemical properties and protein binding functions of glycoconjugates. These modifications are biosynthesized in the endoplasmic reticulum and Golgi apparatus by a series of enzymatic transformations that are under complex control. As a result, mature glycans on a given site are heterogeneous mixtures of glycoforms. This gives rise to a spectrum of adhesive properties that strongly influences interactions with binding partners and resultant biological effects. In order to understand the roles glycosylation plays in normal and disease processes, efficient structural analysis tools are necessary. In the field of glycomics, liquid chromatography/mass spectrometry (LC/MS) is used to profile the glycans present in a given sample. This technology enables comparison of glycan compositions and abundances among different biological samples, i.e. normal versus disease, normal versus mutant, etc. Manual analysis of the glycan profiling LC/MS data is extremely time-consuming and efficient software tools are needed to eliminate this bottleneck. In this work, we have developed a tool to computationally model LC/MS data to enable efficient profiling of glycans. Using LC/MS data deconvoluted by Decon2LS/DeconTools, we built a list of unique neutral masses corresponding to candidate glycan compositions summarized over their various charge states, adducts and range of elution times. Our work aims to provide confident identification of true compounds in complex data sets that are not amenable to manual interpretation. This capability is an essential part of glycomics work flows. We demonstrate this tool, GlycReSoft, using an LC/MS dataset on tissue derived heparan sulfate oligosaccharides. The software, code and a test data set are publically archived under an open source license.
Collapse
|
10
|
Guo X, Zhang P, Qi Y, Chen W, Chen X, Zhou Z, Sha J. Proteomic analysis of male 4C germ cell proteins involved in mouse meiosis. Proteomics 2010; 11:298-308. [PMID: 21204256 DOI: 10.1002/pmic.200900726] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 09/30/2010] [Accepted: 10/20/2010] [Indexed: 11/07/2022]
Abstract
Male meiosis is a specialized type of cell division that gives rise to sperm. Errors in this process can result in the generation of aneuploid gametes, which are associated with birth defects and infertility in humans. Until now, there has been a lack of a large-scale identification of proteins involved in male meiosis in mammals. In this study, we report the high-confidence identification of 3625 proteins in mouse male germ cells with 4C DNA content undergoing meiosis I. Of these, 397 were found to be testis specific. Bioinformatics analysis of the proteome led to the identification of 28 proteins known to be essential for male meiosis in mice. We also found 172 proteins that had yeast orthologs known to be essential for meiosis. Chromosome distribution analysis of the proteome showed underrepresentation of the identified proteins on the X chromosome, which may be due to meiotic sex chromosome inactivation. Characterization of the proteome of 4C germ cells from mouse testis provides an inventory of proteins, which is useful for understanding meiosis and the mechanisms of male infertility.
Collapse
Affiliation(s)
- Xuejiang Guo
- Department of Histology and Embryology, Nanjing Medical University, Nanjing, P R China
| | | | | | | | | | | | | |
Collapse
|
11
|
Liu Y, Messadi DV, Wu H, Hu S. Oral lichen planus is a unique disease model for studying chronic inflammation and oral cancer. Med Hypotheses 2010; 75:492-4. [PMID: 20674185 DOI: 10.1016/j.mehy.2010.07.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 07/01/2010] [Indexed: 10/19/2022]
Abstract
Oral lichen planus (OLP) is a chronic inflammatory disease, which has been defined by the World Health Organization as a potential precancerous condition, representing a generalized state associated with a significantly increased risk of oral cancer. We would like to put forward a hypothesis that inflammatory mediators such as cytokines and chemokines released from infiltrating T lymphocytes induce fundamental changes of proteins in oral epithelial cells, leading to the progression of OLP to oral squamous cell carcinoma (OSCC). These altered proteins can act as the key risk factors associated with the local microenvironment and development of OSCC. Identification of these proteins would add to our understanding of the connection between chronic inflammation and OSCC.
Collapse
Affiliation(s)
- Yi Liu
- School of Dentistry and Dental Research Institute, University of California, Los Angeles, CA 90095, USA
| | | | | | | |
Collapse
|
12
|
Zhang P, Ni X, Guo Y, Guo X, Wang Y, Zhou Z, Huo R, Sha J. Proteomic-based identification of maternal proteins in mature mouse oocytes. BMC Genomics 2009; 10:348. [PMID: 19646285 PMCID: PMC2730056 DOI: 10.1186/1471-2164-10-348] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 08/03/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The mature mouse oocyte contains the full complement of maternal proteins required for fertilization, reprogramming, zygotic gene activation (ZGA), and the early stages of embryogenesis. However, due to limitations of traditional proteomics strategies, only a few abundantly expressed proteins have yet been identified. Our laboratory applied a more effective strategy: one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (1D SDS-PAGE) and reverse-phase liquid chromatography tandem mass spectrometry (RP-LC-MS/MS) were employed to analyze the mature oocyte proteome in depth. RESULTS Using this high-performance proteomic approach, we successfully identified 625 different proteins from 2700 mature mouse oocytes lacking zona pellucidae. This is the largest catalog of mature mouse oocyte proteins compiled to date. According to their pattern of expression, we screened 76 maternal proteins with high levels of mRNA expression both in oocytes and fertilized eggs. Many well-known maternal effect proteins were included in this subset, including MATER and NPM2. In addition, our mouse oocyte proteome was compared with a recently published mouse embryonic stem cell (ESC) proteome and 371 overlapping proteins were identified. CONCLUSION This proteomics analysis will be a valuable resource to aid in the characterization of important maternal proteins involved in oogenesis, fertilization, early embryonic development and in revealing their mechanisms of action.
Collapse
Affiliation(s)
- Ping Zhang
- Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, PR China.
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Lu A, Wiśniewski JR, Mann M. Comparative proteomic profiling of membrane proteins in rat cerebellum, spinal cord, and sciatic nerve. J Proteome Res 2009; 8:2418-25. [PMID: 19290618 DOI: 10.1021/pr8010364] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Proteomics is an increasingly powerful technology that can provide in-depth insights into entire proteomes and their variation upon disease. Large-scale proteomics today enables identification and measurement of changes of thousands of proteins from minute amount of tissues. Here, we provide a proteomic profile of three distinct parts of the murine nerve system: cerebellum, spinal cord, and sciatic nerve. We focus on membrane proteins as the key regulators of neural transmission and memory. Rat tissues were homogenized and extracted to remove nonmembrane proteins and the resulting membranes were solubilized with detergents. Proteins were fractionated by size exclusion chromatography, depleted for detergents, digested and analyzed by LC-MS/MS using the LTQ-Orbitrap instrument. With the application of stringent identification criteria, in total, 4124 proteins were identified. Of these proteins, 3528, 3290, and 1649 were mapped to cerebellum, spinal cord, and sciatic nerve, respectively, allowing in-depth mapping of neurotransmitter receptors, ion channels, and transporter proteins. This work is the most in-depth proteomic analysis of nerve tissues to date and provides the first unbiased insights into the proteomes of anatomically and functionally distinct parts of the membrane proteome of the central and peripheral nerve systems. The methods applied here can be directly applied to studying nerve systems and their disorders.
Collapse
Affiliation(s)
- Aiping Lu
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | | | | |
Collapse
|
14
|
Millet C, Yamashita M, Heller M, Yu LR, Veenstra TD, Zhang YE. A negative feedback control of transforming growth factor-beta signaling by glycogen synthase kinase 3-mediated Smad3 linker phosphorylation at Ser-204. J Biol Chem 2009; 284:19808-16. [PMID: 19458083 DOI: 10.1074/jbc.m109.016667] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Through the action of its membrane-bound type I receptor, transforming growth factor-beta (TGF-beta) elicits a wide range of cellular responses that regulate cell proliferation, differentiation, and apo ptosis. Many of these signaling responses are mediated by Smad proteins. As such, controlling Smad activity is crucial for proper signaling by TGF-beta and its related factors. Here, we show that TGF-beta induces phosphorylation at three sites in the Smad3 linker region in addition to the two C-terminal residues, and glycogen synthase kinase 3 is responsible for phosphorylation at one of these sites, namely Ser-204. Alanine substitution at Ser-204 and/or the neighboring Ser-208, the priming site for glycogen synthase kinase 3 in vivo activity, strengthened the affinity of Smad3 to CREB-binding protein, suggesting that linker phosphorylation may be part of a negative feedback loop that modulates Smad3 transcriptional activity. Thus, our findings reveal a novel aspect of the Smad3 signaling mechanism that controls the final amplitude of cellular responses to TGF-beta.
Collapse
Affiliation(s)
- Caroline Millet
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892-4256, USA
| | | | | | | | | | | |
Collapse
|
15
|
Fu YJ, Xiong S, Lovell MA, Lynn BC. Quantitative proteomic analysis of mitochondria in aging PS-1 transgenic mice. Cell Mol Neurobiol 2009; 29:649-64. [PMID: 19241155 DOI: 10.1007/s10571-009-9359-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 02/03/2009] [Indexed: 12/18/2022]
Abstract
Accumulating evidence suggests mitochondrial alterations are intimately associated with the pathogenesis of Alzheimer's disease (AD). In order to determine if mutations of presenilin-1 (PS-1) affect levels of mitochondrial proteins at different ages we enriched mitochondrial fractions from 3-, 6-, 12-month-old knock-in mice expressing the M146V PS-1 mutation and identified, and quantified proteins using cleavable isotope-coded affinity tag labeling and two-dimensional liquid chromatography/tandem mass spectrometry (2D-LC/MS/MS). Using this approach, 165 non-redundant proteins were identified with 80 of them present in all three age groups. Specifically, at young ages (3 and 6 months), Na(+)/K(+) ATPase and several signal transduction proteins exhibited elevated levels, but dropped dramatically at 12 months. In contrast, components of the oxidative phosporylation pathway (OXPHOS), the mitochondrial permeability transition pore (MPTP), and energy metabolism proteins remained unchanged at 3 months but significantly increased with age. We propose that alterations in calcium homeostasis induced by the PS-1 mutation have a major impact in young animals by inhibiting the function of relevant proteins and inducing compensatory changes. However, in older mice combination of the PS-1 mutation and accumulated oxidative damage results in a functional suppression of OXPHOS and MPTP proteins requiring a compensatory increase in expression levels. In contrast, signal transduction proteins showed decreased levels due to a break down in the compensatory mechanisms. The dysfunction of Na(+)/K(+) ATPase and signal transduction proteins may induce impaired cognition and memory before neurodegeneration occurs.
Collapse
Affiliation(s)
- You-Jun Fu
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | | | | | | |
Collapse
|
16
|
Wang G, Wu WW, Zhang Z, Masilamani S, Shen RF. Decoy methods for assessing false positives and false discovery rates in shotgun proteomics. Anal Chem 2009; 81:146-59. [PMID: 19061407 DOI: 10.1021/ac801664q] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The potential of getting a significant number of false positives (FPs) in peptide-spectrum matches (PSMs) obtained by proteomic database search has been well-recognized. Among the attempts to assess FPs, the concomitant use of target and decoy databases is widely practiced. By adjusting filtering criteria, FPs and false discovery rate (FDR) can be controlled at a desired level. Although the target-decoy approach is gaining in popularity, subtle differences in decoy construction (e.g., reversing vs stochastic methods), rate calculation (e.g., total vs unique PSMs), or searching (separate vs composite) do exist among various implementations. In the present study, we evaluated the effects of these differences on FP and FDR estimations using a rat kidney protein sample and the SEQUEST search engine as an example. On the effects of decoy construction, we found that, when a single scoring filter (XCorr) was used, stochastic methods generated a higher estimation of FPs and FDR than sequence reversing methods, likely due to an increase in unique peptides. This higher estimation could largely be attenuated by creating decoy databases similar in effective size but not by a simple normalization with a unique-peptide coefficient. When multiple filters were applied, the differences seen between reversing and stochastic methods significantly diminished, suggesting multiple filterings reduce the dependency on how a decoy is constructed. For a fixed set of filtering criteria, FDR and FPs estimated by using unique PSMs were almost twice those using total PSMs. The higher estimation seemed to be dependent on data acquisition setup. As to the differences between performing separate or composite searches, in general, FDR estimated from the separate search was about three times that from the composite search. The degree of difference gradually decreased as the filtering criteria became more stringent. Paradoxically, the estimated true positives in separate search were higher when multiple filters were used. By analyzing a standard protein mixture, we demonstrated that the higher estimation of FDR and FPs in the separate search likely reflected an overestimation, which could be corrected with a simple merging procedure. Our study illustrates the relative merits of different implementations of the target-decoy strategy, which should be worth contemplating when large-scale proteomic biomarker discovery is to be attempted.
Collapse
Affiliation(s)
- Guanghui Wang
- Proteomics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | | | | | | |
Collapse
|
17
|
Thouvenot E, Urbach S, Dantec C, Poncet J, Séveno M, Demettre E, Jouin P, Touchon J, Bockaert J, Marin P. Enhanced Detection of CNS Cell Secretome in Plasma Protein-Depleted Cerebrospinal Fluid. J Proteome Res 2008; 7:4409-21. [DOI: 10.1021/pr8003858] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Eric Thouvenot
- Centre National de la Recherche Scientifique, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France, Institut National de la Santé et de la Recherche Médicale, U661, Montpellier, F-34094 France, Université Montpellier 1, Montpellier, F-34094 France, Université Montpellier 2, Montpellier, F-34094 France, and Service de Neurologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, F-34295 France
| | - Serge Urbach
- Centre National de la Recherche Scientifique, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France, Institut National de la Santé et de la Recherche Médicale, U661, Montpellier, F-34094 France, Université Montpellier 1, Montpellier, F-34094 France, Université Montpellier 2, Montpellier, F-34094 France, and Service de Neurologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, F-34295 France
| | - Christelle Dantec
- Centre National de la Recherche Scientifique, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France, Institut National de la Santé et de la Recherche Médicale, U661, Montpellier, F-34094 France, Université Montpellier 1, Montpellier, F-34094 France, Université Montpellier 2, Montpellier, F-34094 France, and Service de Neurologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, F-34295 France
| | - Joël Poncet
- Centre National de la Recherche Scientifique, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France, Institut National de la Santé et de la Recherche Médicale, U661, Montpellier, F-34094 France, Université Montpellier 1, Montpellier, F-34094 France, Université Montpellier 2, Montpellier, F-34094 France, and Service de Neurologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, F-34295 France
| | - Martial Séveno
- Centre National de la Recherche Scientifique, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France, Institut National de la Santé et de la Recherche Médicale, U661, Montpellier, F-34094 France, Université Montpellier 1, Montpellier, F-34094 France, Université Montpellier 2, Montpellier, F-34094 France, and Service de Neurologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, F-34295 France
| | - Edith Demettre
- Centre National de la Recherche Scientifique, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France, Institut National de la Santé et de la Recherche Médicale, U661, Montpellier, F-34094 France, Université Montpellier 1, Montpellier, F-34094 France, Université Montpellier 2, Montpellier, F-34094 France, and Service de Neurologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, F-34295 France
| | - Patrick Jouin
- Centre National de la Recherche Scientifique, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France, Institut National de la Santé et de la Recherche Médicale, U661, Montpellier, F-34094 France, Université Montpellier 1, Montpellier, F-34094 France, Université Montpellier 2, Montpellier, F-34094 France, and Service de Neurologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, F-34295 France
| | - Jacques Touchon
- Centre National de la Recherche Scientifique, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France, Institut National de la Santé et de la Recherche Médicale, U661, Montpellier, F-34094 France, Université Montpellier 1, Montpellier, F-34094 France, Université Montpellier 2, Montpellier, F-34094 France, and Service de Neurologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, F-34295 France
| | - Joël Bockaert
- Centre National de la Recherche Scientifique, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France, Institut National de la Santé et de la Recherche Médicale, U661, Montpellier, F-34094 France, Université Montpellier 1, Montpellier, F-34094 France, Université Montpellier 2, Montpellier, F-34094 France, and Service de Neurologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, F-34295 France
| | - Philippe Marin
- Centre National de la Recherche Scientifique, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France, Institut National de la Santé et de la Recherche Médicale, U661, Montpellier, F-34094 France, Université Montpellier 1, Montpellier, F-34094 France, Université Montpellier 2, Montpellier, F-34094 France, and Service de Neurologie, Centre Hospitalier Universitaire de Montpellier, Montpellier, F-34295 France
| |
Collapse
|
18
|
Ramaroson MF, Ruby J, Goshe MB, Liu HC. Changes in the Gallus gallus Proteome Induced by Marek’s Disease Virus. J Proteome Res 2008; 7:4346-58. [DOI: 10.1021/pr800268h] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Mialy F. Ramaroson
- Department of Molecular and Structural Biochemistry, and Department of Animal Science, North Carolina State University, Raleigh, North Carolina 27695
| | - James Ruby
- Department of Molecular and Structural Biochemistry, and Department of Animal Science, North Carolina State University, Raleigh, North Carolina 27695
| | - Michael B. Goshe
- Department of Molecular and Structural Biochemistry, and Department of Animal Science, North Carolina State University, Raleigh, North Carolina 27695
| | - Hsiao-Ching Liu
- Department of Molecular and Structural Biochemistry, and Department of Animal Science, North Carolina State University, Raleigh, North Carolina 27695
| |
Collapse
|
19
|
Petyuk VA, Qian WJ, Hinault C, Gritsenko MA, Singhal M, Monroe ME, Camp DG, Kulkarni RN, Smith RD. Characterization of the mouse pancreatic islet proteome and comparative analysis with other mouse tissues. J Proteome Res 2008; 7:3114-26. [PMID: 18570455 DOI: 10.1021/pr800205b] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The pancreatic islets of Langerhans, and especially the insulin-producing beta cells, play a central role in the maintenance of glucose homeostasis. Alterations in the expression of multiple proteins in the islets that contribute to the maintenance of islet function are likely to underlie the pathogenesis of types 1 and 2 diabetes. To identify proteins that constitute the islet proteome, we provide the first comprehensive proteomic characterization of pancreatic islets for mouse, the most commonly used animal model in diabetes research. Using strong cation exchange fractionation coupled with reversed phase LC-MS/MS we report the confident identification of 17,350 different tryptic peptides covering 2612 proteins having at least two unique peptides per protein. The data set also identified approximately 60 post-translationally modified peptides including oxidative modifications and phosphorylation. While many of the identified phosphorylation sites corroborate those previously known, the oxidative modifications observed on cysteinyl residues reveal potentially novel information suggesting a role for oxidative stress in islet function. Comparative analysis with 15 available proteomic data sets from other mouse tissues and cells revealed a set of 133 proteins predominantly expressed in pancreatic islets. This unique set of proteins, in addition to those with known functions such as peptide hormones secreted from the islets, contains several proteins with as yet unknown functions. The mouse islet protein and peptide database accessible at (http://ncrr.pnl.gov), provides an important reference resource for the research community to facilitate research in the diabetes and metabolism fields.
Collapse
Affiliation(s)
- Vladislav A Petyuk
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Wang Y, Muneton S, Sjövall J, Jovanovic JN, Griffiths WJ. The effect of 24S-hydroxycholesterol on cholesterol homeostasis in neurons: quantitative changes to the cortical neuron proteome. J Proteome Res 2008; 7:1606-14. [PMID: 18303831 DOI: 10.1021/pr7006076] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In humans, the brain represents only about 2% of the body's mass but contains about one-quarter of the body's free cholesterol. Cholesterol is synthesized de novo in brain and removed by metabolism to oxysterols. 24S-Hydoxycholesterol represents the major metabolic product of cholesterol in brain, being formed via the cytochrome P450 (CYP) enzyme CYP46A1. CYP46A1 is expressed exclusively in brain, normally by neurons. In this study, we investigated the effect of 24S-hydroxycholesterol on the proteome of rat cortical neurons. With the use of two-dimensional liquid chromatography linked to nanoelectrospray tandem mass spectrometry, over 1040 proteins were identified including members of the cholesterol, isoprenoid and fatty acid synthesis pathways. With the use of stable isotope labeling technology, the protein expression patterns of enzymes in these pathways were investigated. 24S-Hydroxycholesterol was found to down-regulate the expression of members of the cholesterol/isoprenoid synthesis pathways including 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (EC 2.3.3.10), diphosphomevalonate decarboxylase (EC 4.1.1.33), isopentenyl-diphosphate delta isomerase (EC 5.3.3.2), farnesyl-diphosphate synthase (Geranyl trans transferase, EC 2.5.1.10), and dedicated sterol synthesis enzymes, farnesyl-diphosphate farnesyltransferase 1 (squalene synthase, EC 2.5.1.21) and methylsterol monooxygenase (EC 1.14.13.72). The expression of many enzymes in the cholesterol/isoprenoid and fatty acid synthesis pathways are regulated by the membrane-bound transcription factors named sterol regulatory element-binding proteins (SREBPs), which themselves are both transcriptionally and post-transcriptionally regulated. The current proteomic data indicates that 24S-hydroxycholesterol down-regulates cholesterol synthesis in neurons, possibly, in a post-transcriptional manner through SREBP-2. In contrast to cholesterol metabolism, enzymes responsible for the synthesis of fatty acids were not found to be down-regulated in neurons treated with 24S-hydroxycholesterol, while apolipoprotein E (apo E), a cholesterol trafficking protein, was found to be up-regulated. Taken together, this data leads to the hypothesis that, in times of cholesterol excess, 24S-hydroxycholesterols signals down-regulation of cholesterol synthesis enzymes through SREBP-2, but up-regulates apo E synthesis (through the liver X receptor) leading to cholesterol storage and restoration of cholesterol balance.
Collapse
Affiliation(s)
- Yuqin Wang
- Institute of Mass Spectrometry, School of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP, UK.
| | | | | | | | | |
Collapse
|
21
|
McBee JK, Yu LR, Kinoshita Y, Uo T, Beyer RP, Veenstra TD, Morrison RS. Proteomic analysis of protein expression changes in a model of gliomagenesis. Proteomics Clin Appl 2007; 1:1485-98. [PMID: 21136645 DOI: 10.1002/prca.200700292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Loss of p53 function is a common event in a variety of human cancers including tumors of glial origin. Using an in vitro mouse model of malignant astrocyte transformation, three cleavable isotope coded affinity tag (cICAT) experiments were performed comparing cultured wild-type astrocytes and two p53(-/-) astrocyte cultures before and after malignant transformation. We identified and quantitated an average of 1366 proteins per experiment and demonstrated that the protein quantitation ratios in each individual cICAT experiment correlated well to ratios determined in the other two studies. These data were further supported by microarray analysis which also correlated to changes in protein expression. The results showed significant changes in protein expression in association with malignant transformation. Proteins overexpressed in malignant astrocytes were typically involved in ribosome biogenesis/protein synthesis and DNA replication, while underexpressed proteins were generally associated with the regulation of cell cycle checkpoint control, tumor suppression, and apoptosis. Among the significantly up-regulated proteins and transcripts in malignant mouse astrocytes were members of the minichromosome maintenance (MCM) family. Western blot analysis verified increased expression of MCM proteins in malignant human astrocytoma cell lines, which had not previously been described. These results demonstrate the usefulness of the cICAT approach for comparing differences in protein expression profiles between normal and malignant cells.
Collapse
Affiliation(s)
- Joshua K McBee
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA; Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | | | | | | |
Collapse
|
22
|
Fournier ML, Gilmore JM, Martin-Brown SA, Washburn MP. Multidimensional Separations-Based Shotgun Proteomics. Chem Rev 2007; 107:3654-86. [PMID: 17649983 DOI: 10.1021/cr068279a] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
23
|
Chen M, Ying W, Song Y, Liu X, Yang B, Wu S, Jiang Y, Cai Y, He F, Qian X. Analysis of human liver proteome using replicate shotgun strategy. Proteomics 2007; 7:2479-88. [PMID: 17623305 DOI: 10.1002/pmic.200600338] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this study, a liquid-based shotgun strategy was used to comprehensively identify the expression of human liver proteome. Proteins were extracted from human liver tissue and digested in-solution. The tryptic digest mixture was desalted and separated by off-line strong cation exchange (SCX) chromatography with a 60-min elution. The MS/MS spectra were acquired in data-dependent mode after an RP chromatographic separation combined with linear IT MS analysis. To obtain the most comprehensive human liver proteome, each SCX fraction was run six times in RPLC MS/MS manner. Finally, more than 6,000,000 MS/MS spectra were collected. Using a relatively strict filter criteria, 24,311 proteins (48.42% of the predicted human proteome from human International Protein Index (IPI) protein database 3.07) corresponding to 13,150 nonredundant proteins were successfully identified, in which 7001 proteins (53.24%) were identified by two or more peptides, which could be considered as a high-confident dataset. Among the 6149 proteins (46.76%) identified by single peptide, 3812 proteins (61.99%) were detected more than twice in six repeated runs. Comparative analysis between different runs shows that the overlap of identified proteins between any two runs ranged from 25 to 44%. Of the nonredundant proteins identified, 8919 proteins (67.83%) were detected more than twice and 4231 proteins (32.17%) were detected only once in six RPLC MS/MS runs. The Gene Ontology annotation shows that the identified proteins come from various subcellular components. In addition, a large number of low abundant proteins were identified. The dynamic range of the approach reached at least nine orders of magnitude by estimating the concentration of proteins.
Collapse
Affiliation(s)
- Ming Chen
- Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, PR China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Kadiu I, Ricardo-Dukelow M, Ciborowski P, Gendelman HE. Cytoskeletal protein transformation in HIV-1-infected macrophage giant cells. THE JOURNAL OF IMMUNOLOGY 2007; 178:6404-15. [PMID: 17475870 DOI: 10.4049/jimmunol.178.10.6404] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mechanisms linking HIV-1 replication, macrophage biology, and multinucleated giant cell formation are incompletely understood. With the advent of functional proteomics, the characterization, regulation, and transformation of HIV-1-infected macrophage-secreted proteins can be ascertained. To these ends, we performed proteomic analyses of culture fluids derived from HIV-1 infected monocyte-derived macrophages. Robust reorganization, phosphorylation, and exosomal secretion of the cytoskeletal proteins profilin 1 and actin were observed in conjunction with productive viral replication and giant cell formation. Actin and profilin 1 recruitment to the macrophage plasma membrane paralleled virus-induced cytopathicity, podosome formation, and cellular fusion. Poly-l-proline, an inhibitor of profilin 1-mediated actin polymerization, inhibited cytoskeletal transformations and suppressed, in part, progeny virion production. These data support the idea that actin and profilin 1 rearrangement along with exosomal secretion affect viral replication and cytopathicity. Such events favor the virus over the host cell and provide insights into macrophage defense mechanisms used to contain viral growth and how they may be affected during progressive HIV-1 infection.
Collapse
Affiliation(s)
- Irena Kadiu
- Laboratory of Neuroregeneration, Department of Pharmacology and Experimental Neuroscience, Center for Neurovirology and Neurodegenerative Disorders, University of Nebraska Medical Center, Omaha 68198, USA
| | | | | | | |
Collapse
|
25
|
Yu LR, Chan KC, Tahara H, Lucas DA, Chatterjee K, Issaq HJ, Veenstra TD. Quantitative proteomic analysis of human breast epithelial cells with differential telomere length. Biochem Biophys Res Commun 2007; 356:942-7. [PMID: 17395154 PMCID: PMC2268026 DOI: 10.1016/j.bbrc.2007.03.069] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Accepted: 03/14/2007] [Indexed: 10/23/2022]
Abstract
Telomeres play important functional roles in cell proliferation, cell cycle regulation, and genetic stability, in which telomere length is critical. In this study, quantitative proteome comparisons for the human breast epithelial cells with short and long telomeres (184-hTERTL vs. 184-hTERTS and 90P-hTERTL vs. 90P-hTERTS), resulting from transfection of the human telomerase reverse transcriptase (hTERT) gene, were performed using cleavable isotope-coded affinity tags. More than 2000 proteins were quantified in each comparative experiment, with approximately 77% of the proteins identified in both analyses. In the cells with long telomeres, significant and consistent alterations were observed in metabolism (amino acid, nucleotide, and lipid metabolism), genetic information transmission (transcription and translation regulation, spliceosome and ribosome complexes), and cell signaling. Interestingly, the DNA excision repair pathway is enhanced, while integrin and its ligands are downregulated in the cells with long telomeres. These results may provide valuable information related to telomere functions.
Collapse
Affiliation(s)
- Li-Rong Yu
- Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
- Address correspondence to: Dr. Li-Rong Yu, SAIC-Frederick, Inc., NCI-Frederick, P.O. Box B, Bldg. 434, Rm. 5E, Frederick, Maryland 21702. Phone: 301-846-7607; Fax: 301-846-6037; e-mail:
| | - King C. Chan
- Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Hiroshima University, Hiroshima 734-8551, Japan
| | - David A. Lucas
- Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Koushik Chatterjee
- Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Haleem J. Issaq
- Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
| | - Timothy D. Veenstra
- Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
- Dr. Timothy D. Veenstra, SAIC-Frederick, Inc., NCI-Frederick, P.O. Box B, Bldg. 469, Rm. 160, Frederick, Maryland 21702. Phone: 301-846-7286; Fax: 301-846-6037; e-mail:
| |
Collapse
|
26
|
Xue X, Wu S, Wang Z, Zhu Y, He F. Protein probabilities in shotgun proteomics: Evaluating different estimation methods using a semi-random sampling model. Proteomics 2006; 6:6134-45. [PMID: 17133366 DOI: 10.1002/pmic.200600070] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The calculation of protein probabilities is one of the most intractable problems in large-scale proteomic research. Current available estimating methods, for example, ProteinProphet, PROT_PROBE, Poisson model and two-peptide hits, employ different models trying to resolve this problem. Until now, no efficient method is used for comparative evaluation of the above methods in large-scale datasets. In order to evaluate these various methods, we developed a semi-random sampling model to simulate large-scale proteomic data. In this model, the identified peptides were sampled from the designed proteins and their cross-correlation scores were simulated according to the results from reverse database searching. The simulated result of 18 control proteins was consistent with the experimental one, demonstrating the efficiency of our model. According to the simulated results of human liver sample, ProteinProphet returned slightly higher probabilities and lower specificity than real cases. PROT_PROBE was a more efficient method with higher specificity. Predicted results from a Poisson model roughly coincide with real datasets, and the method of two-peptide hits seems solid but imprecise. However, the probabilities of identified proteins are strongly correlated with several experimental factors including spectra number, database size and protein abundance distribution.
Collapse
Affiliation(s)
- Xiaofang Xue
- Beijing Institute of Radiation Medicine, Beijing, China
| | | | | | | | | |
Collapse
|
27
|
Hood BL, Conrads TP, Veenstra TD. Mass spectrometric analysis of formalin-fixed paraffin-embedded tissue: unlocking the proteome within. Proteomics 2006; 6:4106-14. [PMID: 16800036 DOI: 10.1002/pmic.200600016] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The predominance of tissues stored worldwide in hospitals and clinical laboratories exist in formalin-fixed paraffin-embedded (FFPE) blocks that are generated by simple and well-established protocols. Although generation of FFPE tissues has facilitated their characterization by such techniques as histopathology, they have proven refractory to biomarker discovery investigations using state-of-the-art MS-based proteomic methodologies. Very recently new methods have been developed that enable proteins extracted from FFPE tissues to be analyzed by MS. This review will highlight and discuss those efforts that have led to this exciting recent progress. Although these developments are quite new, the ability to conduct MS-based proteomic analyses of FFPE tissues opens heretofore intractable clinical samples for discovery-based biomarker research.
Collapse
Affiliation(s)
- Brian L Hood
- Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., National Cancer Institute, Frederick, MD 21702, USA
| | | | | |
Collapse
|
28
|
Hu J, Qian J, Borisov O, Pan S, Li Y, Liu T, Deng L, Wannemacher K, Kurnellas M, Patterson C, Elkabes S, Li H. Optimized proteomic analysis of a mouse model of cerebellar dysfunction using amine-specific isobaric tags. Proteomics 2006; 6:4321-34. [PMID: 16800037 PMCID: PMC2553677 DOI: 10.1002/pmic.200600026] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Recent proteomic applications have demonstrated their potential for revealing the molecular mechanisms underlying neurodegeneration. The present study quantifies cerebellar protein changes in mice that are deficient in plasma membrane calcium ATPase 2 (PMCA2), an essential neuronal pump that extrudes calcium from cells and is abundantly expressed in Purkinje neurons. PMCA2-null mice display motor dyscoordination and unsteady gait deficits observed in neurological diseases such as multiple sclerosis and ataxia. We optimized an amine-specific isobaric tags (iTRAQ)-based shotgun proteomics workflow for this study. This workflow took consideration of analytical variance as a function of ion signal intensity and employed biological repeats to aid noise reduction. Even with stringent protein identification criteria, we could reliably quantify nearly 1000 proteins, including many neuronal proteins that are important for synaptic function. We identified 21 proteins that were differentially expressed in PMCA2-null mice. These proteins are involved in calcium homeostasis, cell structure and chromosome organization. Our findings shed light on the molecular changes that underlie the neurological deficits observed in PMCA2-null mice. The optimized workflow presented here will be valuable for others who plan to implement the iTRAQ method.
Collapse
Affiliation(s)
- Jun Hu
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Jin Qian
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Oleg Borisov
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Sanqiang Pan
- Department of Anatomy, Medical School of Jinan University, Guangzhou, Guangdong, P. R. China
| | - Yan Li
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Tong Liu
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Longwen Deng
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Kenneth Wannemacher
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Michael Kurnellas
- Department of Neurology and Neuroscience, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
- Neurology Service, Veterans Affairs, East Orange, NJ, USA
| | - Christa Patterson
- Department of Neurology and Neuroscience, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
- Neurology Service, Veterans Affairs, East Orange, NJ, USA
| | - Stella Elkabes
- Department of Neurology and Neuroscience, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
- Neurology Service, Veterans Affairs, East Orange, NJ, USA
| | - Hong Li
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| |
Collapse
|
29
|
Guo Z, Dai B, Jiang T, Xu K, Xie Y, Kim O, Nesheiwat I, Kong X, Melamed J, Handratta VD, Njar VCO, Brodie AMH, Yu LR, Veenstra TD, Chen H, Qiu Y. Regulation of androgen receptor activity by tyrosine phosphorylation. Cancer Cell 2006; 10:309-19. [PMID: 17045208 DOI: 10.1016/j.ccr.2006.08.021] [Citation(s) in RCA: 287] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Revised: 06/20/2006] [Accepted: 08/28/2006] [Indexed: 12/31/2022]
Abstract
The androgen receptor (AR) is essential for the growth of prostate cancer cells. Here, we report that tyrosine phosphorylation of AR is induced by growth factors and elevated in hormone-refractory prostate tumors. Mutation of the major tyrosine phosphorylation site in AR significantly inhibits the growth of prostate cancer cells under androgen-depleted conditions. The Src tyrosine kinase appears to be responsible for phosphorylating AR, and there is a positive correlation of AR tyrosine phosphorylation with Src tyrosine kinase activity in human prostate tumors. Our data collectively suggest that growth factors and their downstream tyrosine kinases, which are elevated during hormone-ablation therapy, can induce tyrosine phosphorylation of AR and such modification may be important for prostate tumor growth under androgen-depleted conditions.
Collapse
Affiliation(s)
- Zhiyong Guo
- Department of Pharmacology and Experimental Therapeutics, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Abstract
The brain is unquestionably the most fascinating organ. Despite tremendous progress, current knowledge falls short of being able to explain its function. An emerging approach toward improved understanding of the molecular mechanisms underlying brain function is neuroproteomics. Today's neuroscientists have access to a battery of versatile technologies both in transcriptomics and proteomics. The challenge is to choose the right strategy in order to generate new hypotheses on how the brain works. The goal of this review is therefore two-fold: first we recall the bewildering cellular, molecular, and functional complexity in the brain, as this knowledge is fundamental to any study design. In fact, an impressive complexity on the molecular level has recently re-emerged as a central theme in large-scale analyses. Then we review transcriptomics and proteomics technologies, as both are complementary. Finally, we comment on the most widely used proteomics techniques and their respective strengths and drawbacks. We conclude that for the time being, neuroproteomics should focus on its strengths, namely the identification of posttranslational modifications and protein-protein interactions, as well as the characterization of highly purified subproteomes. For global expression profiling, emphasis should be put on further development to significantly increase coverage.
Collapse
Affiliation(s)
- Michael Becker
- Abteilung Tierphysiologie, Fachbereich Biologie, Technische Universität Kaiserslautern, Germany
| | | | | |
Collapse
|
31
|
Park YM, Kim JY, Kwon KH, Lee SK, Kim YH, Kim SY, Park GW, Lee JH, Lee B, Yoo JS. Profiling human brain proteome by multi-dimensional separations coupled with MS. Proteomics 2006; 6:4978-86. [PMID: 16927429 DOI: 10.1002/pmic.200600098] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In our initial attempt to analyze the human brain proteome, we applied multi-dimensional protein separation and identification techniques using a combination of sample fractionation, 1-D SDS-PAGE, and MS analysis. The complexity of human brain proteome requires multiple fractionation strategies to extend the range and total number of proteins identified. According to the method of Klose (Methods Mol. Biol. 1999, 112, 67), proteins of the temporal lobe of human brain were fractionated into (i) cytoplasmic and nucleoplasmic, (ii) membrane and other structural, and (iii) DNA-binding proteins. Each fraction was then separated by SDS-PAGE, and the resulting gel line was cut into approximately 50 bands. After trypsin digestion, the resulting peptides from each band were analyzed by RP-LC/ESI-MS/MS using an LTQ spectrometer. The SEQUEST search program, which searched against the IPI database, was used for peptide sequence identification, and peptide sequences were validated by reversed sequence database search and filtered by the Protein Hit Score. Ultimately, 1533 proteins could be detected from the human brain. We classified the identified proteins according to their distribution on cellular components. Among these proteins, 24% were membrane proteins. Our results show that the multiple separation strategy is effective for high-throughput characterization of proteins from complex proteomic mixtures.
Collapse
Affiliation(s)
- Young Mok Park
- Proteomics Team, Korea Basic Science Institute, Daejeon, Republic of Korea
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Chertova E, Chertov O, Coren LV, Roser JD, Trubey CM, Bess JW, Sowder RC, Barsov E, Hood BL, Fisher RJ, Nagashima K, Conrads TP, Veenstra TD, Lifson JD, Ott DE. Proteomic and biochemical analysis of purified human immunodeficiency virus type 1 produced from infected monocyte-derived macrophages. J Virol 2006; 80:9039-52. [PMID: 16940516 PMCID: PMC1563931 DOI: 10.1128/jvi.01013-06] [Citation(s) in RCA: 354] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Accepted: 06/24/2006] [Indexed: 01/05/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infects CD4(+) T lymphocytes and monocytes/macrophages, incorporating host proteins in the process of assembly and budding. Analysis of the host cell proteins incorporated into virions can provide insights into viral biology. We characterized proteins in highly purified HIV-1 virions produced from human monocyte-derived macrophages (MDM), within which virus buds predominantly into intracytoplasmic vesicles, in contrast to the plasmalemmal budding of HIV-1 typically seen with infected T cells. Liquid chromatography-linked tandem mass spectrometry of highly purified virions identified many cellular proteins, including 33 previously described proteins in HIV-1 preparations from other cell types. Proteins involved in many different cellular structures and functions were present, including those from the cytoskeleton, adhesion, signaling, intracellular trafficking, chaperone, metabolic, ubiquitin/proteasomal, and immune response systems. We also identified annexins, annexin-binding proteins, Rab proteins, and other proteins involved in membrane organization, vesicular trafficking, and late endosomal function, as well as apolipoprotein E, which participates in cholesterol transport, immunoregulation, and modulation of cell growth and differentiation. Several tetraspanins, markers of the late endosomal compartment, were also identified. MDM-derived HIV contained 26 of 37 proteins previously found in exosomes, consistent with the idea that HIV uses the late endosome/multivesicular body pathway during virion budding from macrophages.
Collapse
Affiliation(s)
- Elena Chertova
- AIDS Vaccine Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Schindler J, Jung S, Niedner-Schatteburg G, Friauf E, Nothwang HG. Enrichment of integral membrane proteins from small amounts of brain tissue. J Neural Transm (Vienna) 2006; 113:995-1013. [PMID: 16835696 DOI: 10.1007/s00702-006-0508-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [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
Subcellular fractionation represents an essential technique for functional proteome analysis. Recently, we provided a subcellular fractionation protocol for minute amounts of tissue that yielded a nuclear fraction, a membrane and organelle fraction, and a cytosolic fraction. In the current study, we attempted to improve the protocol for the isolation of integral membrane proteins, as these are particularly important for brain function. In the membrane and organelle fraction, we increased the yield of membranes and organelles by about 50% by introducing a single re-extraction step. We then tested two protocols towards their capacity to enrich membrane proteins present in the membrane and organelle fraction. One protocol is based on sequential solubilization using subsequent increases of chaotropic conditions such as urea, thereby partitioning hydrophobic proteins from hydrophilic ones. The alternative protocol applies high-salt and high-pH washes to remove non-membrane proteins. The enrichment of membrane proteins by these procedures, as compared to the original membrane and organelle fraction, was evaluated by 16-BAC-SDS-PAGE followed by mass spectrometry of randomly selected spots. In the original membrane and organelle fraction, 7 of 50 (14%) identified proteins represented integral membrane proteins, and 15 (30%) were peripheral membrane proteins. In the urea-soluble fraction, 4 of 33 (12%) identified proteins represented integral membrane proteins, and 10 (30%) were peripheral membrane proteins. In the high-salt/high-pH resistant sediment, 12 of 45 (27%) identified proteins were integral membrane proteins and 13 (29%) represented peripheral membrane proteins. During the analysis, several proteins involved in neuroexocytosis were detected, including syntaxin, NSF, and Rab3-interaction protein 2. Taken together, differential centrifugation in combination with high-salt and high-pH washes resulted in the highest enrichment of integral membrane proteins and, therefore, represents an adequate technique for region-specific profiling of membrane proteins in the brain.
Collapse
Affiliation(s)
- J Schindler
- Abteilung Tierphysiologie, Fachbereich Biologie, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | | | | | | | | |
Collapse
|
34
|
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.
Collapse
Affiliation(s)
- F Tribl
- The National Parkinson Foundation (NPF) Research Laboratories, Miami, FL, USA.
| | | | | | | | | | | |
Collapse
|
35
|
Lukas TJ, Luo WW, Mao H, Cole N, Siddique T. Informatics-assisted Protein Profiling in a Transgenic Mouse Model of Amyotrophic Lateral Sclerosis. Mol Cell Proteomics 2006; 5:1233-44. [PMID: 16571896 DOI: 10.1074/mcp.m500431-mcp200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
One of the causes of amyotrophic lateral sclerosis (ALS) is due to mutations in Cu,Zn-superoxide dismutase (SOD1). The mutant protein exhibits a toxic gain of function that adversely affects the function of neurons in the spinal cord, brain stem, and motor cortex. A proteomic analysis of protein expression in a widely used mouse model of ALS was undertaken to identify differences in protein expression in the spinal cords of mice expressing a mutant protein with the G93A mutation found in human ALS. Protein profiling was done on soluble and particulate fractions of spinal cord extracts using high throughput two-dimensional liquid chromatography coupled to tandem mass spectrometry. An integrated proteomics-informatics platform was used to identify relevant differences in protein expression based upon the abundance of peptides identified by database searching of mass spectrometry data. Changes in the expression of proteins associated with mitochondria were particularly prevalent in spinal cord proteins from both mutant G93A-SOD1 and wild-type SOD1 transgenic mice. G93A-SOD1 mouse spinal cord also exhibited differences in proteins associated with metabolism, protein kinase regulation, antioxidant activity, and lysosomes. Using gene ontology analysis, we found an overlap of changes in mRNA expression in presymptomatic mice (from microarray analysis) in three different gene categories. These included selected protein kinase signaling systems, ATP-driven ion transport, and neurotransmission. Therefore, alterations in selected cellular processes are detectable before symptomatic onset in ALS mouse models. However, in late stage disease, mRNA expression analysis did not reveal significant changes in mitochondrial gene expression but did reveal concordant changes in lipid metabolism, lysosomes, and the regulation of neurotransmission. Thus, concordance of proteomic and mRNA expression data within multiple categories validates the use of gene ontology analysis to compare different types of "omic" data.
Collapse
Affiliation(s)
- Thomas J Lukas
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA.
| | | | | | | | | |
Collapse
|
36
|
Mor F, Cohen IR. How special is a pathogenic CNS autoantigen? Immunization to many CNS self-antigens does not induce autoimmune disease. J Neuroimmunol 2006; 174:3-11. [PMID: 16427143 DOI: 10.1016/j.jneuroim.2005.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Accepted: 12/05/2005] [Indexed: 01/01/2023]
Abstract
Recent work has shown neuro-protective effects of immunization with self-CNS antigens in animal models of Alzheimer's disease, prion diseases and CNS trauma. The major concern with such an approach is the inadvertent induction of autoimmune disease. The present work was initiated to study the incidence of autoimmune disease associated with the induction of T cell autoimmunity to a panel of 70 peptides derived from CNS proteins. Using a MHC class II motif developed in our laboratory to identify candidate peptides, we selected 70 peptides from 40 different CNS proteins. The proteins were selected randomly and represented various biological functions (surface receptors, structural proteins, synaptic proteins, neurodegeneration related proteins). Each peptide was emulsified in CFA and injected to autoimmune-prone Lewis rats. Immunogenicity was verified by peptide-specific LN cell proliferation. In addition, T cell lines were generated for many peptides and tested by adoptive transfer. Except for the previously reported pathogenicity of beta-synuclein, none of the 68 peptides from 39 proteins was found to induce CNS disease in recipient rats. These findings underscore the efficiency of immunological regulation in preventing CNS autoimmune disease, and confirm the uniqueness of the well-known pathogenic CNS auto-antigens.
Collapse
Affiliation(s)
- Felix Mor
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 76100, Israel.
| | | |
Collapse
|
37
|
Decker EL, Frank W, Sarnighausen E, Reski R. Moss systems biology en route: phytohormones in Physcomitrella development. PLANT BIOLOGY (STUTTGART, GERMANY) 2006; 8:397-405. [PMID: 16807833 DOI: 10.1055/s-2006-923952] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The moss Physcomitrella patens has become a powerful model system in modern plant biology. Highly standardized cell culture techniques, as well as the necessary tools for computational biology, functional genomics and proteomics have been established. Large EST collections are available and the complete moss genome will be released soon. A simple body plan and the small number of different cell types in Physcomitrella facilitate the study of developmental processes. In the filamentous juvenile moss tissue, developmental decisions rely on the differentiation of single cells. Developmental steps are controlled by distinct phytohormones and integration of environmental signals. Especially the phytohormones auxin, cytokinin, and abscisic acid have distinct effects on early moss development. In this article, we review current knowledge about phytohormone influences on early moss development in an attempt to fully unravel the complex regulatory signal transduction networks underlying the developmental decisions of single plant cells in a holistic systems biology approach.
Collapse
Affiliation(s)
- E L Decker
- Faculty of Biology, Plant Biotechnology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | | | | | | |
Collapse
|
38
|
Wang H, Qian WJ, Chin MH, Petyuk VA, Barry RC, Liu T, Gritsenko MA, Mottaz HM, Moore RJ, Camp Ii DG, Khan AH, Smith DJ, Smith RD. Characterization of the mouse brain proteome using global proteomic analysis complemented with cysteinyl-peptide enrichment. J Proteome Res 2006; 5:361-9. [PMID: 16457602 PMCID: PMC1850945 DOI: 10.1021/pr0503681] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a global proteomic approach for analyzing brain tissue and for the first time a comprehensive characterization of the whole mouse brain proteome. Preparation of the whole brain sample incorporated a highly efficient cysteinyl-peptide enrichment (CPE) technique to complement a global enzymatic digestion method. Both the global and the cysteinyl-enriched peptide samples were analyzed by SCX fractionation coupled with reversed phase LC-MS/MS analysis. A total of 48,328 different peptides were confidently identified (>98% confidence level), covering 7792 nonredundant proteins ( approximately 34% of the predicted mouse proteome). A total of 1564 and 1859 proteins were identified exclusively from the cysteinyl-peptide and the global peptide samples, respectively, corresponding to 25% and 31% improvements in proteome coverage compared to analysis of only the global peptide or cysteinyl-peptide samples. The identified proteins provide a broad representation of the mouse proteome with little bias evident due to protein pI, molecular weight, and/or cellular localization. Approximately 26% of the identified proteins with gene ontology (GO) annotations were membrane proteins, with 1447 proteins predicted to have transmembrane domains, and many of the membrane proteins were found to be involved in transport and cell signaling. The MS/MS spectrum count information for the identified proteins was used to provide a measure of relative protein abundances. The mouse brain peptide/protein database generated from this study represents the most comprehensive proteome coverage for the mammalian brain to date, and the basis for future quantitative brain proteomic studies using mouse models. The proteomic approach presented here may have broad applications for rapid proteomic analyses of various mouse models of human brain diseases.
Collapse
Affiliation(s)
- Haixing Wang
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Schindler J, Lewandrowski U, Sickmann A, Friauf E, Nothwang HG. Proteomic Analysis of Brain Plasma Membranes Isolated by Affinity Two-phase Partitioning. Mol Cell Proteomics 2006; 5:390-400. [PMID: 16249173 DOI: 10.1074/mcp.t500017-mcp200] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A comprehensive analysis of plasma membrane proteins is essential to in-depth understanding of brain development, function, and diseases. Proteomics offers the potential to perform such a comprehensive analysis, yet it requires efficient protocols for the purification of the plasma membrane compartment. Here, we present a novel and efficient protocol for the separation and enrichment of brain plasma membrane proteins. It lasts only 4 h and is easy to perform. It highly enriches plasma membrane proteins and can be applied to small amounts of brain tissue, such as the cerebellum of a single rat, which was used in the present study. The protocol is based on affinity partitioning of microsomes in an aqueous two-phase system. Marker enzyme assays demonstrated a more than 12-fold enrichment of plasma membranes and a strong reduction of other compartments, such as mitochondria and the endoplasmic reticulum. 506 different proteins were identified when the enriched proteins underwent LC-MS/MS analysis subsequent to protein separation by SDS-PAGE. Using gene ontology, 146 proteins were assigned to a subcellular compartment. Ninety-three of those (64%) were membrane proteins, and 49 (34%) were plasma membrane proteins. A combined literature and database search for all 506 identified proteins revealed subcellular information on 472 proteins, of which 197 (42%) were plasma membrane proteins. These comprised numerous transporters, channels, and neurotransmitter receptors, e.g. the inward rectifying potassium channel Kir7.1 and the cerebellum-specific gamma-aminobutyric acid receptor GABRA6. Surface proteins involved in cell-cell contact and disease-related proteins were also identified. Six of the 146 assigned proteins were derived from mitochondrial membranes and 5 from membranes of the endoplasmic reticulum. Taken together, our protocol represents a simple, rapid, and reproducible tool for the proteomic characterization of brain plasma membranes. Because it conserves membrane structure and protein interactions, it is also suitable to enrich multimeric protein complexes from the plasma membrane for subsequent analysis.
Collapse
Affiliation(s)
- Jens Schindler
- Animal Physiology Group, Department of Biology, University of Kaiserslautern, 67653 Kaiserslautern, Germany
| | | | | | | | | |
Collapse
|
40
|
Wilkins MR. How Proteomics Can Assist in the Detection and Avoidance of Adverse Drug Reactions. Transfus Med Hemother 2006. [DOI: 10.1159/000090205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
41
|
Tang HY, Ali-Khan N, Echan LA, Levenkova N, Rux JJ, Speicher DW. A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes. Proteomics 2005; 5:3329-42. [PMID: 16052622 DOI: 10.1002/pmic.200401275] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A novel strategy, termed protein array pixelation, is described for comprehensive profiling of human plasma and serum proteomes. This strategy consists of three sequential high-resolution protein prefractionation methods (major protein depletion, solution isoelectrofocusing, and 1-DE) followed by nanocapillary RP tryptic peptide separation prior to MS/MS analysis. The analysis generates a 2-D protein array where each pixel in the array contains a group of proteins with known pI and molecular weight range. Analysis of the HUPO samples using this strategy resulted in 575 and 2890 protein identifications from plasma and serum, respectively, based on HUPO-approved criteria for high-confidence protein assignments. Most importantly, a substantial number of low-abundance proteins (low ng/mL - pg/mL range) were identified. Although larger volumes were used in initial prefractionation steps, the protein identifications were derived from fractions equivalent to approximately 0.6 microL (45 microg) of plasma and 2.4 microL (204 microg) of serum. The time required for analyzing the entire protein array for each sample is comparable to some published shotgun analyses of plasma and serum proteomes. Therefore, protein array pixelation is a highly sensitive method capable of detecting proteins differing in abundance by up to nine orders of magnitude. With further refinement, this method has the potential for even higher capacity and higher throughput.
Collapse
|
42
|
Willis D, Li KW, Zheng JQ, Chang JH, Smit AB, Smit A, Kelly T, Merianda TT, Sylvester J, van Minnen J, Twiss JL. Differential transport and local translation of cytoskeletal, injury-response, and neurodegeneration protein mRNAs in axons. J Neurosci 2005; 25:778-91. [PMID: 15673657 PMCID: PMC6725618 DOI: 10.1523/jneurosci.4235-04.2005] [Citation(s) in RCA: 326] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Recent studies have begun to focus on the signals that regulate axonal protein synthesis and the functional significance of localized protein synthesis. However, identification of proteins that are synthesized in mammalian axons has been mainly based on predictions. Here, we used axons purified from cultures of injury-conditioned adult dorsal root ganglion (DRG) neurons and proteomics methodology to identify axonally synthesized proteins. Reverse transcription (RT)-PCR from axonal preparations was used to confirm that the mRNA for each identified protein extended into the DRG axons. Proteins and the encoding mRNAs for the cytoskeletal proteins beta-actin, peripherin, vimentin, gamma-tropomyosin 3, and cofilin 1 were present in the axonal preparations. In addition to the cytoskeletal elements, several heat shock proteins (HSP27, HSP60, HSP70, grp75, alphaB crystallin), resident endoplasmic reticulum (ER) proteins (calreticulin, grp78/BiP, ERp29), proteins associated with neurodegenerative diseases (ubiquitin C-terminal hydrolase L1, rat ortholog of human DJ-1/Park7, gamma-synuclein, superoxide dismutase 1), anti-oxidant proteins (peroxiredoxins 1 and 6), and metabolic proteins (e.g., phosphoglycerate kinase 1 (PGK 1), alpha enolase, aldolase C/Zebrin II) were included among the axonally synthesized proteins. Detection of the mRNAs encoding each of the axonally synthesized proteins identified by mass spectrometry in the axonal compartment indicates that the DRG axons have the potential to synthesize a complex population of proteins. Local treatment of the DRG axons with NGF or BDNF increased levels of cytoskeletal mRNAs into the axonal compartment by twofold to fivefold but had no effect on levels of the other axonal mRNAs studied. Neurotrophins selectively increased transport of beta-actin, peripherin, and vimentin mRNAs from the cell body into the axons rather than changing transcription or mRNA survival in the axonal compartment.
Collapse
Affiliation(s)
- Dianna Willis
- Nemours Biomedical Research, Alfred I. DuPont Hospital for Children, Wilmington, Delaware 19803, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Lowenthal MS, Mehta AI, Frogale K, Bandle RW, Araujo RP, Hood BL, Veenstra TD, Conrads TP, Goldsmith P, Fishman D, Petricoin EF, Liotta LA. Analysis of albumin-associated peptides and proteins from ovarian cancer patients. Clin Chem 2005; 51:1933-45. [PMID: 16099937 DOI: 10.1373/clinchem.2005.052944] [Citation(s) in RCA: 162] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Albumin binds low-molecular-weight molecules, including proteins and peptides, which then acquire its longer half-life, thereby protecting the bound species from kidney clearance. We developed an experimental method to isolate albumin in its native state and to then identify [mass spectrometry (MS) sequencing] the corresponding bound low-molecular-weight molecules. We used this method to analyze pooled sera from a human disease study set (high-risk persons without cancer, n = 40; stage I ovarian cancer, n = 30; stage III ovarian cancer, n = 40) to demonstrate the feasibility of this approach as a discovery method. METHODS Albumin was isolated by solid-phase affinity capture under native binding and washing conditions. Captured albumin-associated proteins and peptides were separated by gel electrophoresis and subjected to iterative MS sequencing by microcapillary reversed-phase tandem MS. Selected albumin-bound protein fragments were confirmed in human sera by Western blotting and immunocompetition. RESULTS In total, 1208 individual protein sequences were predicted from all 3 pools. The predicted sequences were largely fragments derived from proteins with diverse biological functions. More than one third of these fragments were identified by multiple peptide sequences, and more than one half of the identified species were in vivo cleavage products of parent proteins. An estimated 700 serum peptides or proteins were predicted that had not been reported in previous serum databases. Several proteolytic fragments of larger molecules that may be cancer-related were confirmed immunologically in blood by Western blotting and peptide immunocompetition. BRCA2, a 390-kDa low-abundance nuclear protein linked to cancer susceptibility, was represented in sera as a series of specific fragments bound to albumin. CONCLUSION Carrier-protein harvesting provides a rich source of candidate peptides and proteins with potential diverse tissue and cellular origins that may reflect important disease-related information.
Collapse
Affiliation(s)
- Mark S Lowenthal
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Hood BL, Darfler MM, Guiel TG, Furusato B, Lucas DA, Ringeisen BR, Sesterhenn IA, Conrads TP, Veenstra TD, Krizman DB. Proteomic analysis of formalin-fixed prostate cancer tissue. Mol Cell Proteomics 2005; 4:1741-53. [PMID: 16091476 DOI: 10.1074/mcp.m500102-mcp200] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue would enable retrospective biomarker investigations of this vast archive of pathologically characterized clinical samples that exist worldwide. These FFPE tissues are, however, refractory to proteomic investigations utilizing many state of the art methodologies largely due to the high level of covalently cross-linked proteins arising from formalin fixation. A novel tissue microdissection technique has been developed and combined with a method to extract soluble peptides directly from FFPE tissue for mass spectral analysis of prostate cancer (PCa) and benign prostate hyperplasia (BPH). Hundreds of proteins from PCa and BPH tissue were identified, including several known PCa markers such as prostate-specific antigen, prostatic acid phosphatase, and macrophage inhibitory cytokine-1. Quantitative proteomic profiling utilizing stable isotope labeling confirmed similar expression levels of prostate-specific antigen and prostatic acid phosphatase in BPH and PCa cells, whereas the expression of macrophage inhibitory cytokine-1 was found to be greater in PCa as compared with BPH cells.
Collapse
Affiliation(s)
- Brian L Hood
- Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., National Cancer Institute, Frederick, MD 21702, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Beer I, Barnea E, Admon A. Centralized data analysis of a large interlaboratory proteomics project: A feasibility study. Proteomics 2005; 5:3491-6. [PMID: 16052626 DOI: 10.1002/pmic.200401336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The human Plasma Proteome Project (PPP) is a large-scale collaboration between many laboratories. One of the most demanding tasks in the PPP involved the analysis of very large amounts of raw MS/MS data produced by the participants. The main approach for managing this task was letting the participants analyze their own data and submit the results to the central PPP repository as lists of identified proteins and peptides. To complement this distributed approach, we also performed centralized analysis of the raw MS/MS data provided by the participants. Due to the data redundancy inherent in such a project, centralized analysis has the potential to reduce the computational effort by reducing redundancy before the analysis. Centralized analysis can also unify the process and take advantage of data sharing among laboratories to improve protein identification and validation. The process we employed included removing low-quality spectra, clustering spectra by mutual similarity, and applying uniform peptide and protein identification procedures. To demonstrate the process, we analyzed 5.28 million MS/MS spectra derived by eight laboratories from tryptic peptides of serum and plasma proteins.
Collapse
Affiliation(s)
- Ilan Beer
- IBM Research Laboratory, Haifa, Israel.
| | | | | |
Collapse
|
46
|
Hood BL, Lucas DA, Kim G, Chan KC, Blonder J, Issaq HJ, Veenstra TD, Conrads TP, Pollet I, Karsan A. Quantitative analysis of the low molecular weight serum proteome using 18O stable isotope labeling in a lung tumor xenograft mouse model. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1221-30. [PMID: 15979327 DOI: 10.1016/j.jasms.2005.02.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2004] [Revised: 02/02/2005] [Accepted: 02/02/2005] [Indexed: 05/03/2023]
Abstract
With advancements in the analytical technologies and methodologies in proteomics, there is great interest in biomarker discovery in biofluids such as serum and plasma. Current hypotheses suggest that the low molecular weight (LMW) serum proteome possesses an archive of clipped and cleaved protein fragments that may provide insight into disease development. Though these biofluids represent attractive samples from which new and more accurate disease biomarkers may be found, the intrinsic person-to-person variability in these samples complicates their discovery. Mice are one of the most extensively used animal models for studying human disease because they represent a highly controllable experimental model system. In this study, the LMW serum proteome was compared between xenografted tumor-bearing mice and control mice by differential labeling utilizing trypsin-mediated incorporation of the stable isotope of oxygen, 18O. The digestates were combined, fractionated by strong cation exchange chromatography, and analyzed by nanoflow reversed-phase liquid chromatography coupled online with tandem mass spectrometry, resulting in the identification of 6003 proteins identified by at least a single, fully tryptic peptide. Almost 1650 proteins were identified and quantitated by two or more fully tryptic peptides. The methodology adopted in this work provides the means for future quantitative measurements in comparative animal models of disease and in human disease cohorts.
Collapse
Affiliation(s)
- Brian L Hood
- Laboratory of Proteomics and Analytical Technologies, National Cancer Institute at Frederick, SAIC-Frederick, Inc., Frederick, Maryland 21702, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Abstract
Shotgun proteomics has emerged as a powerful approach for the analysis of complex protein mixtures, including biofluids, tissues, cells, organelles or protein complexes. Having evolved from the integration of chromatography and mass spectrometry, innovations in sample preparation, multidimensional chromatography, mass spectrometry and proteomic informatics continually facilitate, enable and challenge shotgun proteomics. As a result, shotgun proteomics continues to evolve and enable new areas of biological research, and is beginning to impact human disease diagnosis and therapeutic intervention.
Collapse
Affiliation(s)
- Selene K Swanson
- Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA
| | | |
Collapse
|
48
|
Nielsen PA, Olsen JV, Podtelejnikov AV, Andersen JR, Mann M, Wisniewski JR. Proteomic mapping of brain plasma membrane proteins. Mol Cell Proteomics 2005; 4:402-8. [PMID: 15684408 DOI: 10.1074/mcp.t500002-mcp200] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteomics is potentially a powerful technology for elucidating brain function and neurodegenerative diseases. So far, the brain proteome has generally been analyzed by two-dimensional gel electrophoresis, which usually leads to the complete absence of membrane proteins. We describe a proteomic approach for profiling of plasma membrane proteins from mouse brain. The procedure consists of a novel method for extraction and fractionation of membranes, on-membrane digestion, diagonal separation of peptides, and high-sensitivity analysis by advanced MS. Breaking with the classical plasma membrane fractionation approach, membranes are isolated without cell compartment isolation, by stepwise depletion of nonmembrane molecules from entire tissue homogenate by high-salt, carbonate, and urea washes followed by treatment of the membranes with sublytic concentrations of digitonin. Plasma membrane is further enriched by of density gradient fractionation and protein digested on-membrane by endoproteinase Lys-C. Released peptides are separated, fractions digested by trypsin, and analyzed by LC-MS/MS. In single experiments, the developed technology enabled identification of 862 proteins from 150 mg of mouse brain cortex. Further development and miniaturization allowed analysis of 15 mg of hippocampus, revealing 1,685 proteins. More that 60% of the identified proteins are membrane proteins, including several classes of ion channels and neurotransmitter receptors. Our work now allows in-depth study of brain membrane proteomes, such as of mouse models of neurological disease.
Collapse
|
49
|
Yang B, Ying W, Gong Y, Zhang Y, Cai Y, Dong H, Qian X. Using cross-correlation normalized for peptide length to optimize peptide identification in shotgun proteomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2005; 19:2983-5. [PMID: 16178048 DOI: 10.1002/rcm.2137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
|
50
|
Johnson MD, Yu LR, Conrads TP, Kinoshita Y, Uo T, McBee JK, Veenstra TD, Morrison RS. The Proteomics of Neurodegeneration. ACTA ACUST UNITED AC 2005; 5:259-70. [PMID: 16078862 DOI: 10.2165/00129785-200505040-00006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The continuing improvement and refinement of proteomic and bioinformatic tools has made it possible to obtain increasing amounts of structural and functional information about proteins on a global scale. The emerging field of neuroproteomics promises to provide powerful strategies for further characterizing neuronal dysfunction and cell loss associated with neurodegenerative diseases. Neuroproteomic studies have thus far revealed relatively comprehensive quantitative changes and post-translational modifications (mostly oxidative damage) of high abundance proteins, confirming deficits in energy production, protein degradation, antioxidant protein function, and cytoskeletal regulation associated with neurodegenerative diseases such as Alzheimer and Parkinson disease. The identification of changes in low-abundance proteins and characterization of their functions based on protein-protein interactions still await further development of proteomic methodologies and more dedicated application of these technologies by neuroscientists. Once accomplished, however, the resulting information will certainly provide a truly comprehensive view of neurodegeneration-associated changes in protein expression, facilitating the identification of novel biomarkers for the early detection of neurodegenerative diseases and new targets for therapeutic intervention.
Collapse
Affiliation(s)
- Mark D Johnson
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington 98195-6470, USA
| | | | | | | | | | | | | | | |
Collapse
|