51
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Yamauchi KA, Herr AE. Subcellular western blotting of single cells. MICROSYSTEMS & NANOENGINEERING 2017; 3:16079. [PMID: 29333327 PMCID: PMC5764185 DOI: 10.1038/micronano.2016.79] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/28/2016] [Accepted: 10/10/2016] [Indexed: 05/04/2023]
Abstract
Although immunoassays are the de facto standard for determining subcellular protein localization in individual cells, antibody probe cross-reactivity and fixation artifacts remain confounding factors. To enhance selectivity while providing single-cell resolution, we introduce a subcellular western blotting technique capable of separately assaying proteins in the 14 pL cytoplasm and 2 pL nucleus of individual cells. To confer precision fluidic control, we describe a passive multilayer microdevice that leverages the rapid transport times afforded by miniaturization. After isolating single cells in microwells, we apply single-cell differential detergent fractionation to lyse and western blot the cytoplasmic lysate, whereas the nucleus remains intact in the microwell. Subsequently, we lyse the intact nucleus and western blot the nuclear lysate. To index each protein analysis to the originating subcellular compartment, we utilize bi-directional electrophoresis, a multidimensional separation that assays the lysate from each compartment in a distinct region of the separation axis. Single-cell bi-directional electrophoresis eliminates the need for semi-subjective image segmentation algorithms required in immunocytochemistry. The subcellular, single-cell western blot is demonstrated for six targets per cell, and successfully localizes spliceosome-associated proteins solubilized from large protein and RNA complexes, even for closely sized proteins (a 7 kDa difference). Measurement of NF-κB translocation dynamics in unfixed cells at 15-min intervals demonstrates reduced technical variance compared with immunofluorescence. This chemical cytometry assay directly measures the nucleocytoplasmic protein distribution in individual unfixed cells, thus providing insight into protein signaling in heterogeneous cell populations.
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Affiliation(s)
- Kevin A. Yamauchi
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
- The UC Berkeley—UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Amy E. Herr
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
- The UC Berkeley—UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA 94720, USA
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52
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Profiling Cell Lines Nuclear Sub-proteome. Methods Mol Biol 2017. [PMID: 28188521 DOI: 10.1007/978-1-4939-6747-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Proteins are very dynamic within the cell and their localization and trafficking between subcellular compartments are critical for their correct function. Indeed, the abnormal localization of a protein might lead to the pathogenesis of several diseases. The association of cell fractionation methods and mass spectrometry based proteomic methods allow both the localization and quantification of proteins in different sub-compartments. Here we present a detailed protocol for enrichment, identification, and quantitation of the nuclear proteome in cell lines combining nuclear subproteome enrichment by differential centrifugation and high-throughput proteomics.
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53
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Mathieu AA, Ohl-Séguy E, Dubois ML, Jean D, Jones C, Boudreau F, Boisvert FM. Subcellular proteomics analysis of different stages of colorectal cancer cell lines. Proteomics 2016; 16:3009-3018. [DOI: 10.1002/pmic.201600314] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/20/2016] [Accepted: 09/29/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Alex-Ane Mathieu
- Department of Anatomy and Cell Biology; Université de Sherbrooke; Sherbrooke Canada
| | - Emma Ohl-Séguy
- Department of Anatomy and Cell Biology; Université de Sherbrooke; Sherbrooke Canada
| | - Marie-Line Dubois
- Department of Anatomy and Cell Biology; Université de Sherbrooke; Sherbrooke Canada
| | - Dominique Jean
- Department of Anatomy and Cell Biology; Université de Sherbrooke; Sherbrooke Canada
| | - Christine Jones
- Department of Anatomy and Cell Biology; Université de Sherbrooke; Sherbrooke Canada
| | - François Boudreau
- Department of Anatomy and Cell Biology; Université de Sherbrooke; Sherbrooke Canada
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54
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Häupl B, Ihling CH, Sinz A. Protein Interaction Network of Human Protein Kinase D2 Revealed by Chemical Cross-Linking/Mass Spectrometry. J Proteome Res 2016; 15:3686-3699. [PMID: 27559607 DOI: 10.1021/acs.jproteome.6b00513] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated the interaction network of human PKD2 in the cytosol and in Golgi-enriched subcellular protein fractions by an affinity enrichment strategy combined with chemical cross-linking/mass spectrometry (MS). Analysis of the subproteomes revealed the presence of distinct proteins in the cytosolic and Golgi fractions. The covalent fixation of transient or weak interactors by chemical cross-linking allowed capturing interaction partners that might otherwise disappear during conventional pull-down experiments. In total, 31 interaction partners were identified for PKD2, including glycogen synthase kinase-3 beta (GSK3B), 14-3-3 protein gamma (YWHAG), and the alpha isoform of 55 kDa regulatory subunit B of protein phosphatase 2A (PPP2R2A). Remarkably, the entire seven-subunit Arp2/3 complex (ARPC1B, ARPC2, ARPC3, ARPC4, ARPC5, ACTR3, ACTR2) as well as ARPC1A and ARPC5L, which are putative substitutes of ARPC1B and ARPC5, were identified. We provide evidence of a direct protein-protein interaction between PKD2 and Arp2/3. Our findings will pave the way for further structural and functional studies of PKD2 complexes, especially the PKD2/Arp2/3 interaction, to elucidate the role of PKD2 for transport processes at the trans-Golgi network. Data are available via ProteomeXchange with identifiers PXD003909 (enrichment from cytosolic fractions), PXD003913 (enrichment from Golgi fractions), and PXD003917 (subcellular fractionation).
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Affiliation(s)
- Björn Häupl
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg , Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg , Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg , Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
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55
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MetaMass, a tool for meta-analysis of subcellular proteomics data. Nat Methods 2016; 13:837-40. [PMID: 27571551 DOI: 10.1038/nmeth.3967] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 07/21/2016] [Indexed: 11/08/2022]
Abstract
We report a tool for the analysis of subcellular proteomics data, called MetaMass, based on the use of standardized lists of subcellular markers. We analyzed data from 11 studies using MetaMass, mapping the subcellular location of 5,970 proteins. Our analysis revealed large variations in the performance of subcellular fractionation protocols as well as systematic biases in protein annotation databases. The Excel and R versions of MetaMass should enhance transparency and reproducibility in subcellular proteomics.
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56
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Yasueda Y, Tamura T, Fujisawa A, Kuwata K, Tsukiji S, Kiyonaka S, Hamachi I. A Set of Organelle-Localizable Reactive Molecules for Mitochondrial Chemical Proteomics in Living Cells and Brain Tissues. J Am Chem Soc 2016; 138:7592-602. [PMID: 27228550 DOI: 10.1021/jacs.6b02254] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein functions are tightly regulated by their subcellular localization in live cells, and quantitative evaluation of dynamically altered proteomes in each organelle should provide valuable information. Here, we describe a novel method for organelle-focused chemical proteomics using spatially limited reactions. In this work, mitochondria-localizable reactive molecules (MRMs) were designed that penetrate biomembranes and spontaneously concentrate in mitochondria, where protein labeling is facilitated by the condensation effect. The combination of this selective labeling and liquid chromatography-mass spectrometry (LC-MS) based proteomics technology facilitated identification of mitochondrial proteomes and the profile of the intrinsic reactivity of amino acids tethered to proteins expressed in live cultured cells, primary neurons and brain slices. Furthermore, quantitative profiling of mitochondrial proteins whose expression levels change significantly during an oxidant-induced apoptotic process was performed by combination of this MRMs-based method with a standard quantitative MS technique (SILAC: stable isotope labeling by amino acids in cell culture). The use of a set of MRMs represents a powerful tool for chemical proteomics to elucidate mitochondria-associated biological events and diseases.
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Affiliation(s)
- Yuki Yasueda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University , Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University , Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Alma Fujisawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University , Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University , Chikusa, Nagoya, 464-8602, Japan
| | - Shinya Tsukiji
- Frontier Research Institute for Materials Science (FRIMS), Nagoya Institute of Technology , Gokiso-cho, Showa-ku, Nagoya, 466-8555, Japan.,Department of Life Science and Applied Chemistry, Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology , Gokiso-cho, Showa-ku, Nagoya, 466-8555, Japan
| | - Shigeki Kiyonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University , Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University , Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan.,CREST (Core Research for Evolutional Science and Technology, JST) , Sanbancho, Chiyodaku, Tokyo, 102-0075, Japan
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57
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Vorapreeda T, Thammarongtham C, Laoteng K. Integrative computational approach for genome-based study of microbial lipid-degrading enzymes. World J Microbiol Biotechnol 2016; 32:122. [DOI: 10.1007/s11274-016-2067-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/05/2016] [Indexed: 01/19/2023]
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58
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Carraretto L, Teardo E, Checchetto V, Finazzi G, Uozumi N, Szabo I. Ion Channels in Plant Bioenergetic Organelles, Chloroplasts and Mitochondria: From Molecular Identification to Function. MOLECULAR PLANT 2016; 9:371-395. [PMID: 26751960 DOI: 10.1016/j.molp.2015.12.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/22/2015] [Accepted: 12/01/2015] [Indexed: 06/05/2023]
Abstract
Recent technical advances in electrophysiological measurements, organelle-targeted fluorescence imaging, and organelle proteomics have pushed the research of ion transport a step forward in the case of the plant bioenergetic organelles, chloroplasts and mitochondria, leading to the molecular identification and functional characterization of several ion transport systems in recent years. Here we focus on channels that mediate relatively high-rate ion and water flux and summarize the current knowledge in this field, focusing on targeting mechanisms, proteomics, electrophysiology, and physiological function. In addition, since chloroplasts evolved from a cyanobacterial ancestor, we give an overview of the information available about cyanobacterial ion channels and discuss the evolutionary origin of chloroplast channels. The recent molecular identification of some of these ion channels allowed their physiological functions to be studied using genetically modified Arabidopsis plants and cyanobacteria. The view is emerging that alteration of chloroplast and mitochondrial ion homeostasis leads to organelle dysfunction, which in turn significantly affects the energy metabolism of the whole organism. Clear-cut identification of genes encoding for channels in these organelles, however, remains a major challenge in this rapidly developing field. Multiple strategies including bioinformatics, cell biology, electrophysiology, use of organelle-targeted ion-sensitive probes, genetics, and identification of signals eliciting specific ion fluxes across organelle membranes should provide a better understanding of the physiological role of organellar channels and their contribution to signaling pathways in plants in the future.
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Affiliation(s)
- Luca Carraretto
- Department of Biology, University of Padova, Padova 35121, Italy
| | - Enrico Teardo
- Department of Biology, University of Padova, Padova 35121, Italy; CNR Institute of Neuroscience, University of Padova, Padova 35121, Italy
| | | | - Giovanni Finazzi
- UMR 5168 Laboratoire de Physiologie Cellulaire Végétale (LPCV) CNRS/ UJF / INRA / CEA, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), CEA Grenoble, 38054 Grenoble, France.
| | - Nobuyuki Uozumi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan.
| | - Ildiko Szabo
- Department of Biology, University of Padova, Padova 35121, Italy; CNR Institute of Neuroscience, University of Padova, Padova 35121, Italy.
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59
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Shang W, Lu H, Wan W, Fukuda T, Shen Y. Vision-based Nano Robotic System for High-throughput Non-embedded Cell Cutting. Sci Rep 2016; 6:22534. [PMID: 26941071 PMCID: PMC4778025 DOI: 10.1038/srep22534] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/17/2016] [Indexed: 12/25/2022] Open
Abstract
Cell cutting is a significant task in biology study, but the highly productive non-embedded cell cutting is still a big challenge for current techniques. This paper proposes a vision-based nano robotic system and then realizes automatic non-embedded cell cutting with this system. First, the nano robotic system is developed and integrated with a nanoknife inside an environmental scanning electron microscopy (ESEM). Then, the positions of the nanoknife and the single cell are recognized, and the distance between them is calculated dynamically based on image processing. To guarantee the positioning accuracy and the working efficiency, we propose a distance-regulated speed adapting strategy, in which the moving speed is adjusted intelligently based on the distance between the nanoknife and the target cell. The results indicate that the automatic non-embedded cutting is able to be achieved within 1–2 mins with low invasion benefiting from the high precise nanorobot system and the sharp edge of nanoknife. This research paves a way for the high-throughput cell cutting at cell’s natural condition, which is expected to make significant impact on the biology studies, especially for the in-situ analysis at cellular and subcellular scale, such as cell interaction investigation, neural signal transduction and low invasive cell surgery.
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Affiliation(s)
- Wanfeng Shang
- Mechanical Engineering Department, Xi'an University of Science and Technology, Xi'an 710054, China
| | - Haojian Lu
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong, China
| | - Wenfeng Wan
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong, China
| | - Toshio Fukuda
- School of Mechatronic Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Yajing Shen
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong, China.,City University of Hong Kong Shenzhen Research Institute, Shen Zhen 518057, China
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60
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Kustatscher G, Grabowski P, Rappsilber J. Multiclassifier combinatorial proteomics of organelle shadows at the example of mitochondria in chromatin data. Proteomics 2016; 16:393-401. [PMID: 26510496 PMCID: PMC4862026 DOI: 10.1002/pmic.201500267] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/03/2015] [Accepted: 10/15/2015] [Indexed: 12/31/2022]
Abstract
Subcellular localization is an important aspect of protein function, but the protein composition of many intracellular compartments is poorly characterized. For example, many nuclear bodies are challenging to isolate biochemically and thus remain inaccessible to proteomics. Here, we explore covariation in proteomics data as an alternative route to subcellular proteomes. Rather than targeting a structure of interest biochemically, we target it by machine learning. This becomes possible by taking data obtained for one organelle and searching it for traces of another organelle. As an extreme example and proof‐of‐concept we predict mitochondrial proteins based on their covariation in published interphase chromatin data. We detect about ⅓ of the known mitochondrial proteins in our chromatin data, presumably most as contaminants. However, these proteins are not present at random. We show covariation of mitochondrial proteins in chromatin proteomics data. We then exploit this covariation by multiclassifier combinatorial proteomics to define a list of mitochondrial proteins. This list agrees well with different databases on mitochondrial composition. This benchmark test raises the possibility that, in principle, covariation proteomics may also be applicable to structures for which no biochemical isolation procedures are available.
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Affiliation(s)
| | - Piotr Grabowski
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, UK.,Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, UK.,Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
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61
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Kwasnik A, Tonry C, Ardle AM, Butt AQ, Inzitari R, Pennington SR. Proteomes, Their Compositions and Their Sources. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:3-21. [DOI: 10.1007/978-3-319-41448-5_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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62
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Murphy S, Ohlendieck K. The biochemical and mass spectrometric profiling of the dystrophin complexome from skeletal muscle. Comput Struct Biotechnol J 2015; 14:20-7. [PMID: 26793286 PMCID: PMC4688399 DOI: 10.1016/j.csbj.2015.11.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/05/2015] [Accepted: 11/10/2015] [Indexed: 12/12/2022] Open
Abstract
The development of advanced mass spectrometric methodology has decisively enhanced the analytical capabilities for studies into the composition and dynamics of multi-subunit protein complexes and their associated components. Large-scale complexome profiling is an approach that combines the systematic isolation and enrichment of protein assemblies with sophisticated mass spectrometry-based identification methods. In skeletal muscles, the membrane cytoskeletal protein dystrophin of 427 kDa forms tight interactions with a variety of sarcolemmal, cytosolic and extracellular proteins, which in turn associate with key components of the extracellular matrix and the intracellular cytoskeleton. A major function of this enormous assembly of proteins, including dystroglycans, sarcoglycans, syntrophins, dystrobrevins, sarcospan, laminin and cortical actin, is postulated to stabilize muscle fibres during the physical tensions of continuous excitation-contraction-relaxation cycles. This article reviews the evidence from recent proteomic studies that have focused on the characterization of the dystrophin-glycoprotein complex and its central role in the establishment of the cytoskeleton-sarcolemma-matrisome axis. Proteomic findings suggest a close linkage of the core dystrophin complex with a variety of protein species, including tubulin, vimentin, desmin, annexin, proteoglycans and collagens. Since the almost complete absence of dystrophin is the underlying cause for X-linked muscular dystrophy, a more detailed understanding of the composition, structure and plasticity of the dystrophin complexome may have considerable biomedical implications.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
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63
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Paraizo Leite RE, Tenenholz Grinberg L. Closing the gap between brain banks and proteomics to advance the study of neurodegenerative diseases. Proteomics Clin Appl 2015; 9:832-7. [PMID: 26059592 DOI: 10.1002/prca.201400192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 05/01/2015] [Accepted: 05/27/2015] [Indexed: 11/05/2022]
Abstract
Neurodegenerative diseases (NDs), such as Alzheimer's disease and Parkinson's disease, are among the most debilitating neurological disorders, and as life expectancy rises quickly around the world, the scientific and clinical challenges of dealing with them will also increase dramatically, putting increased pressure on the biomedical community to come up with innovative solutions for the understanding, diagnosis, and treatment of these conditions. Despite several decades of intensive research, there is still little that can be done to prevent, cure, or even slow down the progression of NDs in most patients. There is an urgent need to develop new lines of basic and applied research that can be quickly translated into clinical application. One way to do this is to apply the tools of proteomics to well-characterized samples of human brain tissue, but a closer partnership must still be forged between proteomic scientists, brain banks, and clinicians to explore the maximum potential of this approach. Here, we analyze the challenges and potential benefits of using human brain tissue for proteomics research toward NDs.
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Affiliation(s)
- Renata Elaine Paraizo Leite
- Physiopathology in Aging Lab/Brazilian Aging Brain Study Group-LIM22, University of Sao Paulo Medical School, Sao Paulo, Brazil.,Discipline of Geriatrics, University of Sao Paulo Medical School, Sao Paulo, Brazil
| | - Lea Tenenholz Grinberg
- Physiopathology in Aging Lab/Brazilian Aging Brain Study Group-LIM22, University of Sao Paulo Medical School, Sao Paulo, Brazil.,Department of Neurology, Memory and Aging Center, University of California, San Francisco, CA, USA
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64
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Gonneaud A, Turgeon N, Boisvert FM, Boudreau F, Asselin C. Loss of histone deacetylase Hdac1 disrupts metabolic processes in intestinal epithelial cells. FEBS Lett 2015; 589:2776-83. [PMID: 26297832 DOI: 10.1016/j.febslet.2015.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 08/07/2015] [Indexed: 12/21/2022]
Abstract
By using acetyl-CoA as a substrate, acetyltransferases and histone deacetylases regulate protein acetylation by adding or removing an acetyl group on lysines. Nuclear-located Hdac1 is a regulator of intestinal homeostasis. We have previously shown that Hdac1 define specific intestinal epithelial cell basal and inflammatory-dependent gene expression patterns and control cell proliferation. We show here that Hdac1 depletion in cellulo leads to increased histone acetylation after metabolic stresses, and to metabolic disturbances resulting in impaired responses to oxidative stresses, AMPK kinase activation and mitochondrial biogenesis. Thus, nuclear Hdac1 may control intestinal epithelial cell metabolism by regulating the supply of acetyl groups.
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Affiliation(s)
- Alexis Gonneaud
- Département d'anatomie et biologie cellulaire, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Naomie Turgeon
- Département d'anatomie et biologie cellulaire, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - François-Michel Boisvert
- Département d'anatomie et biologie cellulaire, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - François Boudreau
- Département d'anatomie et biologie cellulaire, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Claude Asselin
- Département d'anatomie et biologie cellulaire, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada.
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65
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Horvatovich P, Végvári Á, Saul J, Park JG, Qiu J, Syring M, Pirrotte P, Petritis K, Tegeler TJ, Aziz M, Fuentes M, Diez P, Gonzalez-Gonzalez M, Ibarrola N, Droste C, De Las Rivas J, Gil C, Clemente F, Hernaez ML, Corrales FJ, Nilsson CL, Berven FS, Bischoff R, Fehniger TE, LaBaer J, Marko-Varga G. In Vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins. J Proteome Res 2015; 14:3441-51. [PMID: 26155874 DOI: 10.1021/acs.jproteome.5b00486] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Approximately 18% of all human genes purported to encode proteins have not been directly evidenced at the protein level, according to the validation criteria established by neXtProt, and are considered to be "missing" proteins. One of the goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to identify as many of these missing proteins as possible in human samples using mass spectrometry-based methods. To further this goal, a consortium of C-HPP teams (chromosomes 5, 10, 16, and 19) has joined forces to devise new strategies to identify missing proteins by use of a cell-free in vitro transcription/translation system (IVTT). The proposed strategy employs LC-MS/MS data-dependent acquisition (DDA) and targeted selective reaction monitoring (SRM) methods to scrutinize low-complexity samples derived from IVTT. The optimized assays are then applied to identify missing proteins in human cells and tissues. We describe the approach and show proof-of-concept results for development of LC-SRM assays for identification of 18 missing proteins. We believe that the IVTT system, when coupled with downstream mass spectrometric identification, can be applied to identify proteins that have eluded more traditional methods of detection.
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Affiliation(s)
- Péter Horvatovich
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ákos Végvári
- Department of Pharmacology & Toxicology, The University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555-1074, United States
| | - Justin Saul
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Jin G Park
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Ji Qiu
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Michael Syring
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | - Patrick Pirrotte
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | - Konstantinos Petritis
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States.,Pathology Research, Phoenix Children's Hospital , 1919 East Thomas Road, Phoenix, Arizona 85016, United States
| | - Tony J Tegeler
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | - Meraj Aziz
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | | | | | | | | | | | | | - Concha Gil
- Department of Microbiology & Proteomics Unit, University Complutense , 28040 Madrid, Spain
| | - Felipe Clemente
- Department of Microbiology & Proteomics Unit, University Complutense , 28040 Madrid, Spain
| | - Maria Luisa Hernaez
- Department of Microbiology & Proteomics Unit, University Complutense , 28040 Madrid, Spain
| | - Fernando J Corrales
- Center for Applied Medical Research (CIMA), University of Navarra, PRB2-ProteoRed-ISCIII, IDISNA, Ciberhed , 31008 Pamplona, Spain
| | - Carol L Nilsson
- Department of Pharmacology & Toxicology, The University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555-1074, United States
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen , Postbox 7804, N-5009 Bergen, Norway.,The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Postbox 1400, 5021 Bergen, Norway
| | - Rainer Bischoff
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | - Joshua LaBaer
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - György Marko-Varga
- First Department of Surgery, Tokyo Medical University , 6-7-1 Nishishinjuku Shinjuku-ku, 160-0023 Tokyo, Japan
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Murphy S, Henry M, Meleady P, Zweyer M, Mundegar RR, Swandulla D, Ohlendieck K. Simultaneous Pathoproteomic Evaluation of the Dystrophin-Glycoprotein Complex and Secondary Changes in the mdx-4cv Mouse Model of Duchenne Muscular Dystrophy. BIOLOGY 2015; 4:397-423. [PMID: 26067837 PMCID: PMC4498307 DOI: 10.3390/biology4020397] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/28/2015] [Indexed: 12/14/2022]
Abstract
In skeletal muscle, the dystrophin-glycoprotein complex forms a membrane-associated assembly of relatively low abundance, making its detailed proteomic characterization in normal versus dystrophic tissues technically challenging. To overcome this analytical problem, we have enriched the muscle membrane fraction by a minimal differential centrifugation step followed by the comprehensive label-free mass spectrometric analysis of microsomal membrane preparations. This organelle proteomic approach successfully identified dystrophin and its binding partners in normal versus dystrophic hind limb muscles. The introduction of a simple pre-fractionation step enabled the simultaneous proteomic comparison of the reduction in the dystrophin-glycoprotein complex and secondary changes in the mdx-4cv mouse model of dystrophinopathy in a single analytical run. The proteomic screening of the microsomal fraction from dystrophic hind limb muscle identified the full-length dystrophin isoform Dp427 as the most drastically reduced protein in dystrophinopathy, demonstrating the remarkable analytical power of comparative muscle proteomics. Secondary pathoproteomic expression patterns were established for 281 proteins, including dystrophin-associated proteins and components involved in metabolism, signalling, contraction, ion-regulation, protein folding, the extracellular matrix and the cytoskeleton. Key findings were verified by immunoblotting. Increased levels of the sarcolemmal Na+/K+-ATPase in dystrophic leg muscles were also confirmed by immunofluorescence microscopy. Thus, the reduction of sample complexity in organelle-focused proteomics can be advantageous for the profiling of supramolecular protein complexes in highly intricate systems, such as skeletal muscle tissue.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland.
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland.
| | - Margit Zweyer
- Department of Physiology II, University of Bonn, Bonn D-53115, Germany.
| | - Rustam R Mundegar
- Department of Physiology II, University of Bonn, Bonn D-53115, Germany.
| | - Dieter Swandulla
- Department of Physiology II, University of Bonn, Bonn D-53115, Germany.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
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67
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Gao W, Xu J, Wang F, Zhang L, Peng R, Shu Y, Wu J, Tang Q, Zhu Y. Plasma membrane proteomic analysis of human Gastric Cancer tissues: revealing flotillin 1 as a marker for Gastric Cancer. BMC Cancer 2015; 15:367. [PMID: 25948494 PMCID: PMC4525731 DOI: 10.1186/s12885-015-1343-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 04/22/2015] [Indexed: 02/07/2023] Open
Abstract
Background Gastric cancer remains the second leading cause of cancer-related deaths in the world. Successful early gastric cancer detection is hampered by lack of highly sensitive and specific biomarkers. Plasma membrane proteins participate and/or have a central role in the metastatic process of cancer cells and are potentially useful for cancer therapy due to easy accessibility of the targets. Methods In the present research, TMT method followed by mass spectrometry analysis was used to compare the relative expression levels of plasma membrane proteins between noncancer and gastric cancer tissues. Results Of a total data set that included 501 identified proteins, about 35% of the identified proteins were found to be plasma membrane and associated proteins. Among them, 82 proteins were at least 1.5-fold up- or down-regulated in gastric cancer compared with the adherent normal tissues. Conclusions A number of markers (e.g. annexin A6, caveolin 1, epidermal growth factor receptor, integrin beta 4) were previously reported as biomarkers of GC. Additionally, several potential biomarkers participated in endocytosis pathway and integrin signaling pathways were firstly identified as differentially expressed proteins in GC samples. Our findings also supported the notion that flotillin 1 is a potential biomarker that could be exploited for molecular imaging-based detection of gastric cancer. Together, the results show that subcellular proteomics of tumor tissue is a feasible and promising avenue for exploring oncogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1343-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wen Gao
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Road, Nanjing, 210029, China. .,Department of Oncology, The first affiliated hospital of Nanjing medical university, 300 GuangZhou Road, Nanjing, 210029, China.
| | - Jing Xu
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Road, Nanjing, 210029, China. .,Department of Oncology, The first affiliated hospital of Nanjing medical university, 300 GuangZhou Road, Nanjing, 210029, China.
| | - Fuqiang Wang
- Analysis Center of Nanjing Medical University, 104 Hanzhong Road, 210009, Nanjing, China.
| | - Long Zhang
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Road, Nanjing, 210029, China.
| | - Rui Peng
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Road, Nanjing, 210029, China.
| | - Yongqian Shu
- Department of Oncology, The first affiliated hospital of Nanjing medical university, 300 GuangZhou Road, Nanjing, 210029, China.
| | - Jindao Wu
- Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Department of Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, 300 GuangZhou Road, Nanjing, 210029, China.
| | - Qiyun Tang
- Department of Gastroenterology, The first affiliated hospital of Nanjing medical university, 300 GuangZhou Road, Nanjing, 210029, China.
| | - Yunxia Zhu
- Analysis Center of Nanjing Medical University, 104 Hanzhong Road, 210009, Nanjing, China.
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Moorman NJ, Murphy EA. Roseomics: a blank slate. Curr Opin Virol 2014; 9:188-93. [PMID: 25437230 PMCID: PMC4268339 DOI: 10.1016/j.coviro.2014.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/23/2014] [Accepted: 09/26/2014] [Indexed: 11/24/2022]
Abstract
Recent technological advances have led to an explosion in the system-wide profiling of biological processes in the study of herpesvirus biology, herein referred to as '-omics'. In many cases these approaches have revealed novel virus-induced changes to host cell biology that can be targeted with new antiviral therapeutics. Despite these successes, -omics approaches are not widely applied in the study of roseoloviruses. Here we describe examples of how -omics studies have shaped our understanding of herpesvirus biology, and discuss how these approaches might be used to identify host and viral factors that mediate roseolovirus pathogenesis.
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Affiliation(s)
- Nathaniel J Moorman
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eain A Murphy
- Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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69
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Wu W, Fu Y, Therkildsen M, Li XM, Dai RT. Molecular Understanding of Meat Quality Through Application of Proteomics. FOOD REVIEWS INTERNATIONAL 2014. [DOI: 10.1080/87559129.2014.961073] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Truman AW, Kristjansdottir K, Wolfgeher D, Ricco N, Mayampurath A, Volchenboum SL, Clotet J, Kron SJ. Quantitative proteomics of the yeast Hsp70/Hsp90 interactomes during DNA damage reveal chaperone-dependent regulation of ribonucleotide reductase. J Proteomics 2014; 112:285-300. [PMID: 25452130 DOI: 10.1016/j.jprot.2014.09.028] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 09/05/2014] [Accepted: 09/27/2014] [Indexed: 12/11/2022]
Abstract
UNLABELLED The highly conserved molecular chaperones Hsp90 and Hsp70 are indispensible for folding and maturation of a significant fraction of the proteome, including many proteins involved in signal transduction and stress response. To examine the dynamics of chaperone-client interactions after DNA damage, we applied quantitative affinity-purification mass spectrometry (AP-MS) proteomics to characterize interactomes of the yeast Hsp70 isoform Ssa1 and Hsp90 isoform Hsp82 before and after exposure to methyl methanesulfonate. Of 256 proteins identified and quantified via (16)O(/18)O labeling and LC-MS/MS, 142 are novel Hsp70/90 interactors. Nearly all interactions remained unchanged or decreased after DNA damage, but 5 proteins increased interactions with Ssa1 and/or Hsp82, including the ribonucleotide reductase (RNR) subunit Rnr4. Inhibiting Hsp70 or 90 chaperone activity destabilized Rnr4 in yeast and its vertebrate homolog hRMM2 in breast cancer cells. In turn, pre-treatment of cancer cells with chaperone inhibitors sensitized cells to the RNR inhibitor gemcitabine, suggesting a novel chemotherapy strategy. All MS data have been deposited in the ProteomeXchange with identifier PXD001284. BIOLOGICAL SIGNIFICANCE This study provides the dynamic interactome of the yeast Hsp70 and Hsp90 under DNA damage which suggest key roles for the chaperones in a variety of signaling cascades. Importantly, the cancer drug target ribonucleotide reductase was shown to be a client of Hsp70 and Hsp90 in both yeast and breast cancer cells. As such, this study highlights the potential of a novel cancer therapeutic strategy that exploits the synergy of chaperone and ribonucleotide reductase inhibitors.
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Affiliation(s)
- Andrew W Truman
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | | | - Donald Wolfgeher
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Natalia Ricco
- Departament de Ciències Bàsiques, Universitat Internacional de Catalunya, Barcelona, Catalunya, Spain
| | - Anoop Mayampurath
- Computation Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Samuel L Volchenboum
- Computation Institute, The University of Chicago, Chicago, IL 60637, USA; Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA
| | - Josep Clotet
- Departament de Ciències Bàsiques, Universitat Internacional de Catalunya, Barcelona, Catalunya, Spain
| | - Stephen J Kron
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA.
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71
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Recent advances in stable isotope labeling based techniques for proteome relative quantification. J Chromatogr A 2014; 1365:1-11. [PMID: 25246102 DOI: 10.1016/j.chroma.2014.08.098] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 08/24/2014] [Accepted: 08/27/2014] [Indexed: 12/27/2022]
Abstract
The large scale relative quantification of all proteins expressed in biological samples under different states is of great importance for discovering proteins with important biological functions, as well as screening disease related biomarkers and drug targets. Therefore, the accurate quantification of proteins at proteome level has become one of the key issues in protein science. Herein, the recent advances in stable isotope labeling based techniques for proteome relative quantification were reviewed, from the aspects of metabolic labeling, chemical labeling and enzyme-catalyzed labeling. Furthermore, the future research direction in this field was prospected.
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72
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Igarashi M. Proteomic identification of the molecular basis of mammalian CNS growth cones. Neurosci Res 2014; 88:1-15. [PMID: 25066522 DOI: 10.1016/j.neures.2014.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 06/13/2014] [Accepted: 07/02/2014] [Indexed: 11/28/2022]
Abstract
The growth cone, which is a unique structure with high motility that forms at the tips of extending axons and dendrites, is crucial to neuronal network formation. Axonal growth of the mammalian CNS is most likely achieved by the complicated coordination of cytoskeletal rearrangement and vesicular trafficking via many proteins. Before recent advances, no methods to identify numerous proteins existed; however, proteomics revolutionarily resolved such problems. In this review, I summarize the profiles of the mammalian growth cone proteins revealed by proteomics as the molecular basis of the growth cone functions, with molecular mapping. These results should be used as a basis for understanding the mechanisms of the complex mammalian CNS developmental process.
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Affiliation(s)
- Michihiro Igarashi
- Department of Neurochemistry and Molecular Cell Biology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan; Trans-disciplinary Program, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan.
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Gatto L, Breckels LM, Burger T, Nightingale DJH, Groen AJ, Campbell C, Nikolovski N, Mulvey CM, Christoforou A, Ferro M, Lilley KS. A foundation for reliable spatial proteomics data analysis. Mol Cell Proteomics 2014; 13:1937-52. [PMID: 24846987 DOI: 10.1074/mcp.m113.036350] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Quantitative mass-spectrometry-based spatial proteomics involves elaborate, expensive, and time-consuming experimental procedures, and considerable effort is invested in the generation of such data. Multiple research groups have described a variety of approaches for establishing high-quality proteome-wide datasets. However, data analysis is as critical as data production for reliable and insightful biological interpretation, and no consistent and robust solutions have been offered to the community so far. Here, we introduce the requirements for rigorous spatial proteomics data analysis, as well as the statistical machine learning methodologies needed to address them, including supervised and semi-supervised machine learning, clustering, and novelty detection. We present freely available software solutions that implement innovative state-of-the-art analysis pipelines and illustrate the use of these tools through several case studies involving multiple organisms, experimental designs, mass spectrometry platforms, and quantitation techniques. We also propose sound analysis strategies for identifying dynamic changes in subcellular localization by comparing and contrasting data describing different biological conditions. We conclude by discussing future needs and developments in spatial proteomics data analysis.
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Affiliation(s)
- Laurent Gatto
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom; §Computational Proteomics Unit, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Lisa M Breckels
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom; §Computational Proteomics Unit, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Thomas Burger
- ¶Université Grenoble-Alpes, CEA (iRSTV/BGE), INSERM (U1038), CNRS (FR3425), F-38054 Grenoble, France
| | - Daniel J H Nightingale
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Arnoud J Groen
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Callum Campbell
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Nino Nikolovski
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Claire M Mulvey
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Andy Christoforou
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom
| | - Myriam Ferro
- ¶Université Grenoble-Alpes, CEA (iRSTV/BGE), INSERM (U1038), CNRS (FR3425), F-38054 Grenoble, France
| | - Kathryn S Lilley
- From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom;
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