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Yang P, Bi Q, Li Y, Liao J, Ding Y, Huang D, Luo X, Huang Y, Yao C, Zhang J, Wei W, Li Z, Meng J, Guo D. Identification of Five Gelatins Based on Marker Peptides from Type I Collagen by Mass Spectrum in Multiple Reaction Monitoring Mode. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5851-5860. [PMID: 37010496 DOI: 10.1021/acs.jafc.3c00151] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
In this study, a novel pseudo-targeted peptidomics strategy, integrating the transition list generated by an in-house software (Pep-MRMer) and the retention time transfer by high-abundance ion-based retention time calibration (HAI-RT-cal), was developed to screen marker peptides of gelatins from five closely related animal species, including porcine, bovine, horse, mule, and donkey. Five marker peptides were screened from the molecular phenotypic differences of type I collagen. Furthermore, a simple and robust 10 min multiple reaction monitoring (MRM) method was established and performed well in distinguishing different gelatins, particularly in discerning horse-hide gelatin (HHG) and mule-hide gelatin (MHG) from donkey-hide gelatin (DHG). The market investigation revealed the serious adulteration of DHG. Meantime, the pseudo-targeted peptidomics could be used to screen marker peptides of other gelatin foods.
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Affiliation(s)
- Peilei Yang
- Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, People's Republic of China
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Qirui Bi
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Yun Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Jingmei Liao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Yelin Ding
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Dongdong Huang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, People's Republic of China
| | - Xiaoxiao Luo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Yong Huang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Changliang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Jianqing Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Wenlong Wei
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Zhenwei Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Jiang Meng
- Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, People's Republic of China
| | - Dean Guo
- Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, People's Republic of China
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, People's Republic of China
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Comparative Secretomics Analysis Reveals the Major Components of Penicillium oxalicum 16 and Trichoderma reesei RUT-C30. Microorganisms 2021; 9:microorganisms9102042. [PMID: 34683363 PMCID: PMC8538001 DOI: 10.3390/microorganisms9102042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/16/2021] [Accepted: 09/24/2021] [Indexed: 11/23/2022] Open
Abstract
In this study, the major secretome components of Penicillium oxalicum 16 and Trichoderma reesei RUT-C30 under wheat bran (WB) and rice straw (RS) solid-state fermentation were systematically analyzed. The activities of the major components, e.g., cellulase, hemicellulase, and amylase, were consistent with their abundance in the secretomes. P. oxalicum 16 secreted more abundant glycoside hydrolases than T. reesei RUT-C30. The main up-regulated proteins from the induction of WB, compared with that from RS, were amylase, pectinase, and protease, whereas the main down-regulated enzymes were cellulase, hemicellulase, swollenin, and lytic polysaccharide monooxygenase (LPMO). Specifically, WB induced more β-1,4-glucosidases, namely, S8B0F3 (UniProt ID), and A0A024RWA5 than RS, but RS induced more β-1,4-exoglucanases and β-1,4-endoglucanases, namely, A0A024RXP8, A024SH76, S7B6D6, S7ZP52, A024SH20, A024S2H5, S8BGM3, S7ZX22, and S8AIJ2. The P. oxalicum 16 xylanases S8AH74 and S7ZA57 were the major components responsible for degrading soluble xylan, and S8BDN2 probably acted on solid-state hemicellulose instead of soluble xylan. The main hemicellulase component of T. reesei RUT-C30 in RS was the xyloglucanase A0A024S9Z6 with an abundance of 16%, but T. reesei RUT-C30 lacked the hemicellulase mannanase and had a small amount of the hemicellulase xylanase. P. oxalicum 16 produced more amylase than T. reesei RUT-C30, and the results suggest amylase S7Z6T2 may degrade soluble starch. The percentage of the glucoamylase S8B6D7 did not significantly change, and reached an average abundance of 5.5%. The major auxiliary degradation enzymes of P. oxalicum 16 were LPMOs S7Z716 and S7ZPW1, whereas those of T. reesei RUT-C30 were swollenin and LPMOs A0A024SM10, A0A024SFJ2, and A0A024RZP7.
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Yang Y, Zhang Y, Yang C, Fang F, Wang Y, Chang H, Chen Z, Chen P. Differential mitochondrial proteomic analysis of A549 cells infected with avian influenza virus subtypes H5 and H9. Virol J 2021; 18:39. [PMID: 33602268 PMCID: PMC7891018 DOI: 10.1186/s12985-021-01512-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/08/2021] [Indexed: 01/14/2023] Open
Abstract
Background Both the highly pathogenic avian influenza (HPAI) H5N1 and low pathogenic avian influenza (LPAI) H9N2 viruses have been reported to cross species barriers to infect humans. H5N1 viruses can cause severe damage and are associated with a high mortality rate, but H9N2 viruses do not cause such outcomes. Our purpose was to use proteomics technology to study the differential expression of mitochondrial-related proteins related to H5N1 and H9N2 virus infections.
Methods According to the determined viral infection titer, A549 cells were infected with 1 multiplicity of infection virus, and the mitochondria were extracted after 24 h of incubation. The protein from lysed mitochondria was analyzed by the BCA method to determine the protein concentration, as well as SDS-PAGE (preliminary analysis), two-dimensional gel electrophoresis, and mass spectrometry. Differential protein spots were selected, and Western blotting was performed to verify the proteomics results. The identified proteins were subjected to GO analysis for subcellular localization, KEGG analysis for functional classification and signaling pathways assessment, and STRING analysis for functional protein association network construction. Results In the 2-D gel electrophoresis analysis, 227 protein spots were detected in the H5N1-infected group, and 169 protein spots were detected in the H9N2-infected group. Protein spots were further subjected to mass spectrometry identification and removal of redundancy, and 32 differentially expressed proteins were identified. Compared with the H9N2 group, the H5N1-infected group had 16 upregulated mitochondrial proteins and 16 downregulated proteins. The differential expression of 70-kDa heat shock protein analogs, short-chain enoyl-CoA hydratase, malate dehydrogenase, and ATP synthase was verified by Western blot, and the results were consistent with the proteomics findings. Functional analysis indicated that these differentially expressed proteins were primarily involved in apoptosis and metabolism. Conclusions Compared with their expression in the H9N2 group, the differential expression of eight mitochondrial proteins in the H5N1 group led to host T cell activation, antigen presentation, stress response, ATP synthesis and cell apoptosis reduction, leading to higher pathogenicity of H5N1 than H9N2. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01512-4.
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Affiliation(s)
- Yuting Yang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Yun Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Changcheng Yang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Fang Fang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Ying Wang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Haiyan Chang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China.
| | - Ze Chen
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China. .,Shanghai Institute of Biological Products, Shanghai, 200052, China.
| | - Ping Chen
- College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China.
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Li Y, Qin H, Ye M. An overview on enrichment methods for cell surface proteome profiling. J Sep Sci 2019; 43:292-312. [PMID: 31521063 DOI: 10.1002/jssc.201900700] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/17/2022]
Abstract
Cell surface proteins are essential for many important biological processes, including cell-cell interactions, signal transduction, and molecular transportation. With the characteristics of low abundance, high hydrophobicity, and high heterogeneity, it is difficult to get a comprehensive view of cell surface proteome by direct analysis. Thus, it is important to selectively enrich the cell surface proteins before liquid chromatography with mass spectrometry analysis. In recent years, a variety of enrichment methods have been developed. Based on the separation mechanism, these methods could be mainly classified into three types. The first type is based on their difference in the physicochemical property, such as size, density, charge, and hydrophobicity. The second one is based on the bimolecular affinity interaction with lectin or antibody. And the third type is based on the chemical covalent coupling to free side groups of surface-exposed proteins or carbohydrate chains, such as primary amines, carboxyl groups, glycan side chains. In addition, metabolic labeling and enzymatic reaction-based methods have also been employed to selectively isolate cell surface proteins. In this review, we will provide a comprehensive overview of the enrichment methods for cell surface proteome profiling.
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Affiliation(s)
- Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China
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5
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Tube-Gel: A Fast and Effective Sample Preparation Method for High-Throughput Quantitative Proteomics. Methods Mol Biol 2019. [PMID: 30852819 DOI: 10.1007/978-1-4939-9164-8_8] [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
Sample preparation is a key step in proteomics workflows. Tube-gel (TG) is a fast and repeatable sample preparation method that consists in the instantaneous trapping of the sample in a polyacrylamide gel matrix. It takes advantage of in-gel sample preparations by allowing the use of high concentrations of sodium-dodecyl sulfate but avoids the time-consuming step of electrophoresis. Therefore, TG limits the sample handling and is thus particularly suitable for high-throughput quantitative proteomics when large sample numbers have to be processed, as it is often the case in biomarker research and clinical proteomics projects.
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6
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Wang X, Liang S. Gel Absorption-Based Sample Preparation Method for Shotgun Analysis of Membrane Proteome. Methods Mol Biol 2019; 1855:483-490. [PMID: 30426442 DOI: 10.1007/978-1-4939-8793-1_41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Membrane proteins solubilized in a starting buffer containing high concentration of SDS are directly entrapped and immobilized into gel matrix when the membrane protein solution is absorbed by the vacuum-dried polyacrylamide gel. After the detergent and other salts are removed by washing, the proteins are subjected to in-gel digestion, and the tryptic peptides are extracted and analyzed by CapLC-MS/MS. The newly developed method not only avoids protein loss and the adverse protein modifications during gel-embedment but also improves the subsequent in-gel digestion and the recovery of tryptic peptides, particularly hydrophobic peptides. Thus, this method facilitates the identification of membrane proteins, especially integral membrane proteins.
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Affiliation(s)
- Xianchun Wang
- College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, China.
| | - Songping Liang
- College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, China
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7
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Muller L, Fornecker L, Chion M, Van Dorsselaer A, Cianférani S, Rabilloud T, Carapito C. Extended investigation of tube-gel sample preparation: a versatile and simple choice for high throughput quantitative proteomics. Sci Rep 2018; 8:8260. [PMID: 29844437 PMCID: PMC5974325 DOI: 10.1038/s41598-018-26600-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/10/2018] [Indexed: 11/09/2022] Open
Abstract
Sample preparation for quantitative proteomics is a crucial step to ensure the repeatability and the accuracy of the results. However, there is no universal method compatible with the wide variety of protein extraction buffers currently used. We have recently demonstrated the compatibility of tube-gel with SDS-based buffers and its efficiency for label-free quantitative proteomics by comparing it to stacking gel and liquid digestion. Here, we investigated the compatibility of tube-gel with alternatives to SDS-based buffers allowing notably the extraction of proteins in various pH conditions. We also explored the use of photopolymerization to extend the number of possibilities, as it is compatible with a wide range of pH and is non-oxidative. To achieve this goal, we compared six extraction buffers in combination with two polymerization conditions to further optimize the tube-gel protocol and evaluate its versatility. Identification and quantitative results demonstrated the compatibility of tube-gel with all tested conditions by overall raising quite comparable results. In conclusion, tube-gel is a versatile and simple sample preparation method for large-scale quantitative proteomics applications. Complete datasets are available via ProteomeXchange with identifier PXD008656.
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Affiliation(s)
- Leslie Muller
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 25 rue Becquerel, 67087, Strasbourg, France
| | - Luc Fornecker
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 25 rue Becquerel, 67087, Strasbourg, France
| | - Marie Chion
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 25 rue Becquerel, 67087, Strasbourg, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 25 rue Becquerel, 67087, Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 25 rue Becquerel, 67087, Strasbourg, France
| | - Thierry Rabilloud
- Laboratoire de Chimie et Biologie des Métaux, UMR CNRS-CEA-UGA 5249, iRTSV/LCBM, CEA Grenoble, Grenoble, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 25 rue Becquerel, 67087, Strasbourg, France.
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8
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Muller L, Fornecker L, Van Dorsselaer A, Cianférani S, Carapito C. Benchmarking sample preparation/digestion protocols reveals tube-gel being a fast and repeatable method for quantitative proteomics. Proteomics 2016; 16:2953-2961. [DOI: 10.1002/pmic.201600288] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/23/2016] [Accepted: 10/12/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Leslie Muller
- Laboratoire de Spectrométrie de Masse BioOrganique; Université de Strasbourg; CNRS, IPHC UMR 7178 Strasbourg France
| | - Luc Fornecker
- Laboratoire de Spectrométrie de Masse BioOrganique; Université de Strasbourg; CNRS, IPHC UMR 7178 Strasbourg France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique; Université de Strasbourg; CNRS, IPHC UMR 7178 Strasbourg France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique; Université de Strasbourg; CNRS, IPHC UMR 7178 Strasbourg France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique; Université de Strasbourg; CNRS, IPHC UMR 7178 Strasbourg France
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9
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Liu Y, Yan G, Gao M, Deng C, Zhang X. Membrane protein isolation and identification by covalent binding for proteome research. Proteomics 2015; 15:3892-900. [DOI: 10.1002/pmic.201400572] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 08/21/2015] [Accepted: 09/11/2015] [Indexed: 02/02/2023]
Affiliation(s)
- Yiying Liu
- Department of Chemistry, Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Guoquan Yan
- Department of Chemistry, Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Mingxia Gao
- Department of Chemistry, Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Chunhui Deng
- Department of Chemistry, Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
| | - Xiangmin Zhang
- Department of Chemistry, Institutes of Biomedical Sciences; Fudan University; Shanghai P. R. China
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10
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Alfonso-Garrido J, Garcia-Calvo E, Luque-Garcia JL. Sample preparation strategies for improving the identification of membrane proteins by mass spectrometry. Anal Bioanal Chem 2015; 407:4893-905. [PMID: 25967148 DOI: 10.1007/s00216-015-8732-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 04/15/2015] [Accepted: 04/22/2015] [Indexed: 12/31/2022]
Abstract
Despite enormous advances in the mass spectrometry and proteomics fields during the last two decades, the analysis of membrane proteins still remains a challenge for the proteomic community. Membrane proteins play a wide number of key roles in several cellular events, making them relevant target molecules to study in a significant variety of investigations (e.g., cellular signaling, immune surveillance, drug targets, vaccine candidates, etc.). Here, we critically review the several attempts that have been carried out on the different steps of the sample preparation procedure to improve and modify existing conventional proteomic strategies in order to make them suitable for the study of membrane proteins. We also revise novel techniques that have been designed to tackle the difficult but relevant task of identifying and characterizing membrane proteins.
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Affiliation(s)
- Javier Alfonso-Garrido
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, Av. Complutense s/n, 28004, Madrid, Spain
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11
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Lee YC, Gajdosik MS, Josic D, Clifton JG, Logothetis C, Yu-Lee LY, Gallick GE, Maity SN, Lin SH. Secretome analysis of an osteogenic prostate tumor identifies complex signaling networks mediating cross-talk of cancer and stromal cells within the tumor microenvironment. Mol Cell Proteomics 2014; 14:471-83. [PMID: 25527621 DOI: 10.1074/mcp.m114.039909] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A distinct feature of human prostate cancer (PCa) is the development of osteoblastic (bone-forming) bone metastases. Metastatic growth in the bone is supported by factors secreted by PCa cells that activate signaling networks in the tumor microenvironment that augment tumor growth. To better understand these signaling networks and identify potential targets for therapy of bone metastases, we characterized the secretome of a patient-derived xenograft, MDA-PCa-118b (PCa-118b), generated from osteoblastic bone lesion. PCa-118b induces osteoblastic tumors when implanted either in mouse femurs or subcutaneously. To study signaling molecules critical to these unique tumor/microenvironment-mediated events, we performed mass spectrometry on conditioned media of isolated PCa-118b tumor cells, and identified 26 secretory proteins, such as TGF-β2, GDF15, FGF3, FGF19, CXCL1, galectins, and β2-microglobulin, which represent both novel and previously published secreted proteins. RT-PCR using human versus mouse-specific primers showed that TGFβ2, GDF15, FGF3, FGF19, and CXCL1 were secreted from PCa-118b cells. TGFβ2, GDF15, FGF3, and FGF19 function as both autocrine and paracrine factors on tumor cells and stromal cells, that is, endothelial cells and osteoblasts. In contrast, CXCL1 functions as a paracrine factor through the CXCR2 receptor expressed on endothelial cells and osteoblasts. Thus, our study reveals a complex PCa bone metastasis secretome with paracrine and autocrine signaling functions that mediate cross-talk among multiple cell types within the tumor microenvironment.
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Affiliation(s)
- Yu-Chen Lee
- From the Departments of ‡Translational Molecular Pathology
| | | | - Djuro Josic
- ****Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - James G Clifton
- ‡‡Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02903
| | - Christopher Logothetis
- §Genitourinary Medical Oncology, University of Texas, M.D. Anderson Cancer Center, Houston, TX
| | - Li-Yuan Yu-Lee
- ¶Department of Medicine, Baylor College of Medicine, Houston, Texas 77030
| | - Gary E Gallick
- §Genitourinary Medical Oncology, University of Texas, M.D. Anderson Cancer Center, Houston, TX
| | - Sankar N Maity
- §Genitourinary Medical Oncology, University of Texas, M.D. Anderson Cancer Center, Houston, TX
| | - Sue-Hwa Lin
- From the Departments of ‡Translational Molecular Pathology,
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12
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McShane AJ, Bajrami B, Ramos AA, Diego-Limpin PA, Farrokhi V, Coutermarsh BA, Stanton BA, Jensen T, Riordan JR, Wetmore D, Joseloff E, Yao X. Targeted proteomic quantitation of the absolute expression and turnover of cystic fibrosis transmembrane conductance regulator in the apical plasma membrane. J Proteome Res 2014; 13:4676-85. [PMID: 25227318 PMCID: PMC4227562 DOI: 10.1021/pr5006795] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Deficient
chloride transport through cystic fibrosis (CF) transmembrane
conductance regulator (CFTR) causes lethal complications in CF patients.
CF is the most common autosomal recessive genetic disease, which is
caused by mutations in the CFTR gene; thus, CFTR mutants can serve
as primary targets for drugs to modulate and rescue the ion channel’s
function. The first step of drug modulation is to increase the expression
of CFTR in the apical plasma membrane (PM); thus, accurate measurement
of CFTR in the PM is desired. This work reports a tandem enrichment
strategy to prepare PM CFTR and uses a stable isotope labeled CFTR
sample as the quantitation reference to measure the absolute amount
of apical PM expression of CFTR in CFBE 41o- cells. It was found that
CFBE 41o- cells expressing wild-type CFTR (wtCFTR), when cultured
on plates, had 2.9 ng of the protein in the apical PM per million
cells; this represented 10% of the total CFTR found in the cells.
When these cells were polarized on filters, the apical PM expression
of CFTR increased to 14%. Turnover of CFTR in the apical PM of baby
hamster kidney cells overexpressing wtCFTR (BHK-wtCFTR) was also quantified
by targeted proteomics based on multiple reaction monitoring mass
spectrometry; wtCFTR had a half-life of 29.0 ± 2.5 h in the apical
PM. This represents the first direct measurement of CFTR turnover
using stable isotopes. The absolute quantitation and turnover measurements
of CFTR in the apical PM can significantly facilitate understanding
the disease mechanism of CF and thus the development of new disease-modifying
drugs. Absolute CFTR quantitation allows for direct result comparisons
among analyses, analysts, and laboratories and will greatly amplify
the overall outcome of CF research and therapy.
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Affiliation(s)
- Adam J McShane
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
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Hyperthermia-Conditioned OECs Serum-Free–Conditioned Medium Induce NSC Differentiation Into Neuron More Efficiently by the Upregulation of HIF-1 Alpha and Binding Activity. Transplantation 2014; 97:1225-32. [DOI: 10.1097/tp.0000000000000118] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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14
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Wang YJ, Han DY, Tabib T, Yates JR, Mu TW. Identification of GABA(C) receptor protein homeostasis network components from three tandem mass spectrometry proteomics approaches. J Proteome Res 2013; 12:5570-86. [PMID: 24079818 DOI: 10.1021/pr400535z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
γ-Amino butyric acid type C (GABA(C)) receptors inhibit neuronal firing primarily in retina. Maintenance of GABA(C) receptor protein homeostasis in cells is essential for its function. However, a systematic study of GABA(C) receptor protein homeostasis (proteostasis) network components is absent. Here coimmunoprecipitation of human GABA(C)-ρ1-receptor complexes was performed in HEK293 cells overexpressing ρ1 receptors. To enhance the coverage and reliability of identified proteins, immunoisolated ρ1-receptor complexes were subjected to three tandem mass spectrometry (MS)-based proteomic analyses, namely, gel-based tandem MS (GeLC-MS/MS), solution-based tandem MS (SoLC-MS/MS), and multidimensional protein identification technology (MudPIT). From the 107 identified proteins, we assembled GABA(C)-ρ1-receptor proteostasis network components, including proteins with protein folding, degradation, and trafficking functions. We studied representative individual ρ1-receptor-interacting proteins, including calnexin, a lectin chaperone that facilitates glycoprotein folding, and LMAN1, a glycoprotein trafficking receptor, and global effectors that regulate protein folding in cells based on bioinformatics analysis, including HSF1, a master regulator of the heat shock response, and XBP1, a key transcription factor of the unfolded protein response. Manipulating selected GABA(C) receptor proteostasis network components is a promising strategy to regulate GABA(C) receptor folding, trafficking, degradation and thus function to ameliorate related retinal diseases.
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Affiliation(s)
- Ya-Juan Wang
- Center for Proteomics and Bioinformatics and Department of Epidemiology and Biostatistics and ‡Department of Physiology and Biophysics, Case Western Reserve University School of Medicine , 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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15
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Cao L, Clifton JG, Reutter W, Josic D. Mass spectrometry-based analysis of rat liver and hepatocellular carcinoma Morris hepatoma 7777 plasma membrane proteome. Anal Chem 2013; 85:8112-20. [PMID: 23909495 PMCID: PMC3840720 DOI: 10.1021/ac400774g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gel-based proteomic analysis of plasma membranes from rat liver and chemically induced, malignant hepatocellular carcinoma Morris hepatoma 7777 was systematically optimized to yield the maximum number of proteins containing transmembrane domains (TMDs). Incorporation of plasma membrane proteins into a polyacrylamide "tube gel" followed by in-gel digestion of "tube gel" pieces significantly improved detection by electrospray ionization-liquid chromatography-tandem mass spectrometry. Removal of less hydrophobic proteins by washing isolated plasma membranes with 0.1 M sodium carbonate enables detection of a higher number of hydrophobic proteins containing TMDs in both tissues. Subsequent treatment of plasma membranes by a proteolytic enzyme (trypsin) causes the loss of some of the proteins that are detected after washing with sodium carbonate, but it enables the detection of other hydrophobic proteins containing TMDs. Introduction of mass spectrometers with higher sensitivity, higher mass resolution and mass accuracy, and a faster scan rate significantly improved detection of membrane proteins, but the improved sample preparation is still useful and enables detection of additional hydrophobic proteins. Proteolytic predigestion of plasma membranes enables detection of additional hydrophobic proteins and better sequence coverage of TMD-containing proteins in plasma membranes from both tissues.
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Affiliation(s)
- Lulu Cao
- Proteomics Core, COBRE Center for Cancer Research Development, Rhode Island Hospital, Providence, RI 02903 USA
| | - James G. Clifton
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02903, USA
| | - Werner Reutter
- Institut für Laboratoriumsmedizin und Klinische Chemie, Charité-Universitätsmedizin Campus Benjamin Franklin, D-14195 Berlin, Germany
| | - Djuro Josic
- Department of Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
- Department of Biotechnology, University of Rijeka, HR-51000 Rijeka, Croatia
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16
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Ong DST, Wang YJ, Tan YL, Yates JR, Mu TW, Kelly JW. FKBP10 depletion enhances glucocerebrosidase proteostasis in Gaucher disease fibroblasts. ACTA ACUST UNITED AC 2013; 20:403-15. [PMID: 23434032 DOI: 10.1016/j.chembiol.2012.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 11/14/2012] [Accepted: 11/21/2012] [Indexed: 12/20/2022]
Abstract
Lysosomal storage diseases (LSDs) are often caused by mutations compromising lysosomal enzyme folding in the endoplasmic reticulum (ER), leading to degradation and loss of function. Mass spectrometry analysis of Gaucher fibroblasts treated with mechanistically distinct molecules that increase LSD enzyme folding, trafficking, and function resulted in the identification of nine commonly downregulated and two jointly upregulated proteins, which we hypothesized would be critical proteostasis network components for ameliorating loss-of-function diseases. LIMP-2 and FK506 binding protein 10 (FKBP10) were validated as such herein. Increased FKBP10 levels accelerated mutant glucocerebrosidase degradation over folding and trafficking, whereas decreased ER FKBP10 concentration led to more LSD enzyme partitioning into the calnexin profolding pathway, enhancing folding and activity to levels thought to ameliorate LSDs. Thus, targeting FKBP10 appears to be a heretofore unrecognized therapeutic strategy to ameliorate LSDs.
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Affiliation(s)
- Derrick Sek Tong Ong
- Departments of Chemistry and Molecular and Experimental Medicine and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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17
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Lin Y, Liu H, Liu Z, Liu Y, He Q, Chen P, Wang X, Liang S. Development and evaluation of an entirely solution-based combinative sample preparation method for membrane proteomics. Anal Biochem 2013; 432:41-8. [DOI: 10.1016/j.ab.2012.09.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 08/31/2012] [Accepted: 09/17/2012] [Indexed: 10/27/2022]
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18
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Proteomic analysis of the cilia membrane of Paramecium tetraurelia. J Proteomics 2012; 78:113-22. [PMID: 23146917 DOI: 10.1016/j.jprot.2012.09.040] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 08/21/2012] [Accepted: 09/30/2012] [Indexed: 02/01/2023]
Abstract
Channels, pumps, receptors, cyclases and other membrane proteins modulate the motility and sensory function of cilia, but these proteins are generally under-represented in proteomic analyses of cilia. Studies of these ciliary membrane proteins would benefit from a protocol to greatly enrich for integral and lipidated membrane proteins. We used LC-MS/MS to compare the proteomes of unfractionated cilia (C), the ciliary membrane (CM) and the ciliary membrane in the detergent phase (DP) of Triton X-114 phase separation. 55% of the proteins in DP were membrane proteins (i.e. predicted transmembrane or membrane-associated through lipid modifications) and 31% were transmembrane. This is to be compared to 23% membrane proteins with 9% transmembrane in CM and 9% membrane proteins with 3% transmembrane in C. 78% of the transmembrane proteins in the DP were found uniquely in DP, and not in C or CM. There were ion channels, cyclases, plasma membrane pumps, Ca(2+) dependent protein kinases, and Rab GTPases involved in the signal transduction in DP that were not identified in the other C and CM preparations. Of 267 proteins unique to the DP, 147 were novel, i.e. not found in other proteomic and genomic studies of cilia.
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19
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Liver plasma membranes: an effective method to analyze membrane proteome. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 909:113-23. [PMID: 22903712 DOI: 10.1007/978-1-61779-959-4_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Plasma membrane proteins are critical for the maintenance of biological systems and represent important targets for the treatment of disease. The hydrophobicity and low abundance of plasma membrane proteins make them difficult to analyze. The protocols given here are the efficient isolation/digestion procedures for liver plasma membrane proteomic analysis. Both protocol for the isolation of plasma membranes and protocol for the in-gel digestion of gel-embedded plasma membrane proteins are presented. The later method allows the use of a high detergent concentration to achieve efficient solubilization of hydrophobic plasma membrane proteins while avoiding interference with the subsequent LC-MS/MS analysis.
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20
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Cao R, Chen K, Song Q, Zang Y, Li J, Wang X, Chen P, Liang S. Quantitative proteomic analysis of membrane proteins involved in astroglial differentiation of neural stem cells by SILAC labeling coupled with LC-MS/MS. J Proteome Res 2012; 11:829-38. [PMID: 22149100 DOI: 10.1021/pr200677z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane proteins play a critical role in the process of neural stem cell self-renewal and differentiation. Here, we apply the SILAC (stable isotope labeling by amino acids in cell culture) approach to quantitatively compare the membrane proteome of the self-renewing and the astroglial differentiating cells. High-resolution analysis on a linear ion trap-Orbitrap instrument (LTQ-Orbitrap) at sub-ppm mass accuracy resulted in confident identification and quantitation of more than 700 distinct membrane proteins during the astroglial differentiation. Of the 735 quantified proteins, seven cell surface proteins display significantly higher expression levels in the undifferentiated state membrane compared to astroglial differentiating membrane. One cell surface protein transferrin receptor protein 1 may serve as a new candidate for NSCs surface markers. Functional clustering of differentially expressed proteins by Ingenuity Pathway Analysis revealed that most of overexpressed membrane proteins in the astroglial differentiation neural stem cells are involved in cellular growth, nervous system development, and energy metabolic pathway. Taken together, this study increases our understanding of the underlying mechanisms that modulate complex biological processes of neural stem cell proliferation and differentiation.
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Affiliation(s)
- Rui Cao
- Key Laboratory of Protein Chemistry and Developmental Biology of Education Committee, College of Life Sciences, Hunan Normal University , Changsha 410081, PR China.
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21
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Liu Y, Lin Y, Yan Y, Li J, He Q, Chen P, Wang X, Liang S. Electrophoretically driven SDS removal and protein fractionation in the shotgun analysis of membrane proteomes. Electrophoresis 2012; 33:316-24. [PMID: 22222976 DOI: 10.1002/elps.201100364] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yi Liu
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
| | - Yong Lin
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha, P. R. China
| | - Yizhong Yan
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
| | - Jianjun Li
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
| | - Quanze He
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
| | - Ping Chen
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
| | - Xianchun Wang
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
| | - Songping Liang
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
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22
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Wang X, Liang S. Gel-absorption-based sample preparation method for shotgun analysis of membrane proteome. Methods Mol Biol 2012; 869:385-392. [PMID: 22585502 DOI: 10.1007/978-1-61779-821-4_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Membrane proteins solubilized in a starting buffer containing high concentration of sodium dodecyl sulfate (SDS) are directly entrapped and immobilized into gel matrix when the membrane protein solution is absorbed by the vacuum-dried polyacrylamide gel. After the detergent and other salts are removed by washing, the proteins are subjected to in-gel digestion and the tryptic peptides are extracted and analyzed by CapLC-MS/MS. The newly developed method not only avoids protein loss and the adverse protein modifications during gel-embedment but also improves the subsequent in-gel digestion and the recovery of tryptic peptides, particularly the hydrophobic peptides. Thus, this method facilitates the identification of membrane proteins especially the integral membrane proteins.
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Affiliation(s)
- Xianchun Wang
- Hunan Normal University, Changsha, Hunan, People's Republic of China.
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23
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Rucevic M, Hixson D, Josic D. Mammalian plasma membrane proteins as potential biomarkers and drug targets. Electrophoresis 2011; 32:1549-64. [PMID: 21706493 DOI: 10.1002/elps.201100212] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Defining the plasma membrane proteome is crucial to understand the role of plasma membrane in fundamental biological processes. Change in membrane proteins is one of the first events that take place under pathological conditions, making plasma membrane proteins a likely source of potential disease biomarkers with prognostic or diagnostic potential. Membrane proteins are also potential targets for monoclonal antibodies and other drugs that block receptors or inhibit enzymes essential to the disease progress. Despite several advanced methods recently developed for the analysis of hydrophobic proteins and proteins with posttranslational modifications, integral membrane proteins are still under-represented in plasma membrane proteome. Recent advances in proteomic investigation of plasma membrane proteins, defining their roles as diagnostic and prognostic disease biomarkers and as target molecules in disease treatment, are presented.
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Affiliation(s)
- Marijana Rucevic
- COBRE Center for Cancer Research Development, Rhode Island Hospital, Providence, RI, USA
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24
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Zhou H, Wang F, Wang Y, Ning Z, Hou W, Wright TG, Sundaram M, Zhong S, Yao Z, Figeys D. Improved recovery and identification of membrane proteins from rat hepatic cells using a centrifugal proteomic reactor. Mol Cell Proteomics 2011; 10:O111.008425. [PMID: 21749988 DOI: 10.1074/mcp.o111.008425] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Despite their importance in many biological processes, membrane proteins are underrepresented in proteomic analysis because of their poor solubility (hydrophobicity) and often low abundance. We describe a novel approach for the identification of plasma membrane proteins and intracellular microsomal proteins that combines membrane fractionation, a centrifugal proteomic reactor for streamlined protein extraction, protein digestion and fractionation by centrifugation, and high performance liquid chromatography-electrospray ionization-tandem MS. The performance of this approach was illustrated for the study of the proteome of ER and Golgi microsomal membranes in rat hepatic cells. The centrifugal proteomic reactor identified 945 plasma membrane proteins and 955 microsomal membrane proteins, of which 63 and 47% were predicted as bona fide membrane proteins, respectively. Among these proteins, >800 proteins were undetectable by the conventional in-gel digestion approach. The majority of the membrane proteins only identified by the centrifugal proteomic reactor were proteins with ≥ 2 transmembrane segments or proteins with high molecular mass (e.g. >150 kDa) and hydrophobicity. The improved proteomic reactor allowed the detection of a group of endocytic and/or signaling receptor proteins on the plasma membrane, as well as apolipoproteins and glycerolipid synthesis enzymes that play a role in the assembly and secretion of apolipoprotein B100-containing very low density lipoproteins. Thus, the centrifugal proteomic reactor offers a new analytical tool for structure and function studies of membrane proteins involved in lipid and lipoprotein metabolism.
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Affiliation(s)
- Hu Zhou
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Canada
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25
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Zhou J, Li J, Li J, Chen P, Wang X, Liang S. Dried polyacrylamide gel absorption: a method for efficient elimination of the interferences from SDS-solubilized protein samples in mass spectrometry-based proteome analysis. Electrophoresis 2011; 31:3816-22. [PMID: 21064138 DOI: 10.1002/elps.201000255] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Sample preparation holds an important place in MS-based proteome analysis. For effective proteolysis and MS analysis, it is essential to eliminate the interferences while extracting the analytes of interest from complex mixtures. To address this, herein we describe a new dried polyacrylamide gel absorption method. In this method, the protein sample prepared using high concentration of SDS was directly and completely absorbed by vacuum-dried polyacrylamide gel, and then the interfering substances including SDS and some other salts were efficiently removed by in-gel washing steps while retaining the denatured proteins in the gel, thus offering a clean environment amenable to downstream buffer exchange, proteolytic digestion and digest recovery, etc. In combination with in-gel digestion and LC-MS/MS, the newly developed method was applied to the proteome analyses of membrane-enriched fraction and whole tissue homogenate. It was demonstrated that the method is suitable for the analysis of a complex biological sample and can be widely used for sample cleanup in shotgun proteome analyses.
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Affiliation(s)
- Jian Zhou
- The Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, PR China
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26
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Gel absorption-based sample preparation for the analysis of membrane proteome by mass spectrometry. Anal Biochem 2010; 404:204-10. [DOI: 10.1016/j.ab.2010.05.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 05/14/2010] [Accepted: 05/18/2010] [Indexed: 11/17/2022]
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27
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Cao R, Liu Y, Chen P, Lv R, Song Q, Sheng T, He Q, Wang Y, Wang X, Liang S. Improvement of hydrophobic integral membrane protein identification by mild performic acid oxidation-assisted digestion. Anal Biochem 2010; 407:196-204. [PMID: 20732293 DOI: 10.1016/j.ab.2010.08.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 08/11/2010] [Accepted: 08/17/2010] [Indexed: 10/19/2022]
Abstract
Integral membrane proteins (IMPs) are critical for the maintenance of biological systems and represent important targets for the treatment of disease. The hydrophobicity and low abundance of IMPs make them difficult to analyze. In proteomic analyses, hydrophobic peptides including transmembrane domains are often underrepresented, and this reduces the sequence coverage and reliability of the identified IMPs. Here we report a new strategy, mild performic acid oxidation treatment (mPAOT), for improvement of IMP identification. In the mPAOT strategy, the hydrophobicity of IMPs is significantly decreased by oxidizing their methionine and cysteine residues with performic acid, thereby improving the solubility and enzymolysis of these proteins. The application of the mPAOT strategy to the analysis of IMPs from human nasopharyngeal carcinoma CNE1 cell line demonstrated that many IMPs, including those with high hydrophobicity, could be reliably identified.
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Affiliation(s)
- Rui Cao
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha 410081, People's Republic of China
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28
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Proteomics analysis of plasma membrane from liver sinusoidal endothelial cells after partial hepatectomy by an improved two-dimensional electrophoresis. Mol Cell Biochem 2010; 344:137-50. [PMID: 20607590 DOI: 10.1007/s11010-010-0537-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 06/24/2010] [Indexed: 01/17/2023]
Abstract
Liver regeneration is an angiogenesis-associated phenomenon. To identify key plasma membrane (PM) proteins of endothelial cells involved in the initiation of angiogenesis during liver regeneration, the PM of liver sinusoidal endothelial cells (LSEC) at 72 h after partial hepatectomy was enriched by an established in vivo membrane density perturbation method. The differentially expressed membrane proteins compared to those from sham operation were quantified using an improved two-dimensional 16-BAC/SDS-PAGE and identified by LC-MS/MS. Several proteins were further confirmed by cICAT labeling quantitative strategy. A total of 47 proteins were identified including known and novel proteins involved in angiogenesis or liver regeneration, such as inducible nitric oxide synthase, type IV collagen, and integrin beta3. Our results indicated that the combination of the membrane density perturbation strategy and the improved two-dimensional electrophoresis (2-DE) method are useful for investigating the endothelial dysfunctions in vivo.
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29
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Casado-Vela J, Muries B, Carvajal M, Iloro I, Elortza F, Martínez-Ballesta M. Analysis of Root Plasma Membrane Aquaporins from Brassica oleracea: Post-Translational Modifications, de novo Sequencing and Detection of Isoforms by High Resolution Mass Spectrometry. J Proteome Res 2010; 9:3479-94. [DOI: 10.1021/pr901150g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- J. Casado-Vela
- Plataforma de Proteómica, CIC bioGUNE, CIBERehd, ProteoRed, Parque Tecnológico de Bizkaia, Edifício 800, 48160, Bizkaia, Spain, and Departamento de Nutrición Vegetal, Centro de Edafología y Biología Aplicada del Segura - CSIC, Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
| | - B. Muries
- Plataforma de Proteómica, CIC bioGUNE, CIBERehd, ProteoRed, Parque Tecnológico de Bizkaia, Edifício 800, 48160, Bizkaia, Spain, and Departamento de Nutrición Vegetal, Centro de Edafología y Biología Aplicada del Segura - CSIC, Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
| | - M. Carvajal
- Plataforma de Proteómica, CIC bioGUNE, CIBERehd, ProteoRed, Parque Tecnológico de Bizkaia, Edifício 800, 48160, Bizkaia, Spain, and Departamento de Nutrición Vegetal, Centro de Edafología y Biología Aplicada del Segura - CSIC, Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
| | - I. Iloro
- Plataforma de Proteómica, CIC bioGUNE, CIBERehd, ProteoRed, Parque Tecnológico de Bizkaia, Edifício 800, 48160, Bizkaia, Spain, and Departamento de Nutrición Vegetal, Centro de Edafología y Biología Aplicada del Segura - CSIC, Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
| | - F. Elortza
- Plataforma de Proteómica, CIC bioGUNE, CIBERehd, ProteoRed, Parque Tecnológico de Bizkaia, Edifício 800, 48160, Bizkaia, Spain, and Departamento de Nutrición Vegetal, Centro de Edafología y Biología Aplicada del Segura - CSIC, Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
| | - M.C. Martínez-Ballesta
- Plataforma de Proteómica, CIC bioGUNE, CIBERehd, ProteoRed, Parque Tecnológico de Bizkaia, Edifício 800, 48160, Bizkaia, Spain, and Departamento de Nutrición Vegetal, Centro de Edafología y Biología Aplicada del Segura - CSIC, Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
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30
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Zhang Q, Schulenborg T, Tan T, Lang B, Friauf E, Fecher-Trost C. Proteome analysis of a plasma membrane-enriched fraction at the placental feto-maternal barrier. Proteomics Clin Appl 2010; 4:538-49. [DOI: 10.1002/prca.200900048] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 12/17/2009] [Accepted: 12/18/2009] [Indexed: 12/15/2022]
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31
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Falcón-Pérez JM, Lu SC, Mato JM. Sub-proteome approach to the knowledge of liver. Proteomics Clin Appl 2010; 4:407-15. [PMID: 21137060 DOI: 10.1002/prca.200900123] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 08/12/2009] [Indexed: 11/08/2022]
Abstract
In the recent years, global proteomics approaches have been widely used to characterize a number of tissue proteomes including plasma and liver; however, the elevated complexity of these samples in combination with the high abundance of some specific proteins make the study of the lowest abundant proteins difficult. This review is focused on different strategies that have been developed to extend the proteome focused on these two tissues, as, for example, the analysis of sub-cellular proteomes. In this regard, two special kind of extracellular vesicles--exosomes and membrane plasma shedding vesicles--are emerging as excellent biological source both to extend the liver and plasma proteomes and to be applied in the discovery of non-invasive liver-specific disease biomarkers.
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Affiliation(s)
- Juan M Falcón-Pérez
- Metabolomics Unit, CICbioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Bizkaia, Spain.
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32
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Codarin E, Renzone G, Poz A, Avellini C, Baccarani U, Lupo F, di Maso V, Crocè SL, Tiribelli C, Arena S, Quadrifoglio F, Scaloni A, Tell G. Differential Proteomic Analysis of Subfractioned Human Hepatocellular Carcinoma Tissues. J Proteome Res 2009; 8:2273-84. [DOI: 10.1021/pr8009275] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Erika Codarin
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Giovanni Renzone
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Alessandra Poz
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Claudio Avellini
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Umberto Baccarani
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Francesco Lupo
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Vittorio di Maso
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Saveria Lory Crocè
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Claudio Tiribelli
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Simona Arena
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Franco Quadrifoglio
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Andrea Scaloni
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Gianluca Tell
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
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Scaloni A, Codarin E, Di Maso V, Arena S, Renzone G, Tiribelli C, Quadrifoglio F, Tell G. Modern strategies to identify new molecular targets for the treatment of liver diseases: The promising role of Proteomics and Redox Proteomics investigations. Proteomics Clin Appl 2009; 3:242-62. [DOI: 10.1002/prca.200800169] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Indexed: 12/16/2022]
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Dowling P, Walsh N, Clynes M. Membrane and membrane-associated proteins involved in the aggressive phenotype displayed by highly invasive cancer cells. Proteomics 2009; 8:4054-65. [PMID: 18780347 DOI: 10.1002/pmic.200800098] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Invasion, the penetration of tumour cells into adjacent tissues, is a fundamental characteristic of malignant carcinomas and a first step in the metastatic process. The molecular mechanisms involved in tumour cell invasion are complex, but over the last couple of decades the knowledge base has grown quite considerably and many proteins with important roles in invasion have been identified and characterised. Benign tumours typically are encapsulated, which inhibits their ability to behave in a malignant manner, meaning these tumours do not grow in a location-limited less aggressive manner, do not invade surrounding tissues and do not metastasise. The ability of malignant tumours to invade and metastasise is the major cause of death for cancer patients. A greater insight into the molecular basis of cancer invasion and metastasis will lead to the development of novel therapies and specific panels of biomarkers for use in the treatment and diagnosis/monitoring in many types of metastatic cancer.
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Affiliation(s)
- Paul Dowling
- The National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland.
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Abstract
The Gene Ontology (GO) is widely recognized as the premier tool for the organization and functional annotation of molecular aspects of cellular systems. However, for many immunologists the use of GO is a very foreign concept. Indeed, as a controlled vocabulary, GO can almost be considered a new language, and it can be difficult to appreciate the use and value of this approach for understanding the immune system. This review reflects on the application of GO to the field of immunology and explains the process of GO annotation. Finally, this review hopes to inspire immunologists to invest time and energy in improving both the content of the GO and the quality of GO annotations associated with genes of immunological interest.
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Affiliation(s)
- Ruth C Lovering
- Department of Medicine, University College London, Rayne Institute, London, UK
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36
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Li X, Xie C, Cao J, He Q, Cao R, Lin Y, Jin Q, Chen P, Wang X, Liang S. An in Vivo Membrane Density Perturbation Strategy for Identification of Liver Sinusoidal Surface Proteome Accessible from the Vasculature. J Proteome Res 2008; 8:123-32. [DOI: 10.1021/pr8006683] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Xuanwen Li
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, 410081, P.R. China
| | - Chunliang Xie
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, 410081, P.R. China
| | - Jia Cao
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, 410081, P.R. China
| | - Quanyuan He
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, 410081, P.R. China
| | - Rui Cao
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, 410081, P.R. China
| | - Yong Lin
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, 410081, P.R. China
| | - Qihui Jin
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, 410081, P.R. China
| | - Ping Chen
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, 410081, P.R. China
| | - Xianchun Wang
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, 410081, P.R. China
| | - Songping Liang
- Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, 410081, P.R. China
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Abstract
Gene Ontology (GO) provides a controlled vocabulary to describe the attributes of genes and gene products in any organism. Although one might initially wonder what relevance a ‘controlled vocabulary’ might have for cardiovascular science, such a resource is proving highly useful for researchers investigating complex cardiovascular disease phenotypes as well as those interpreting results from high-throughput methodologies. GO enables the current functional knowledge of individual genes to be used to annotate genomic or proteomic datasets. In this way, the GO data provides a very effective way of linking biological knowledge with the analysis of the large datasets of post-genomics research. Consequently, users of high-throughput methodologies such as expression arrays or proteomics will be the main beneficiaries of such annotation sets. However, as GO annotations increase in quality and quantity, groups using small-scale approaches will gradually begin to benefit too. For example, genome wide association scans for coronary heart disease are identifying novel genes, with previously unknown connections to cardiovascular processes, and the comprehensive annotation of these novel genes might provide clues to their cardiovascular link. At least 4000 genes, to date, have been implicated in cardiovascular processes and an initiative is underway to focus on annotating these genes for the benefit of the cardiovascular community. In this article we review the current uses of Gene Ontology annotation to highlight why Gene Ontology should be of interest to all those involved in cardiovascular research.
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