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Eddhif B, Lange J, Guignard N, Batonneau Y, Clarhaut J, Papot S, Geffroy-Rodier C, Poinot P. Study of a novel agent for TCA precipitated proteins washing - comprehensive insights into the role of ethanol/HCl on molten globule state by multi-spectroscopic analyses. J Proteomics 2018; 173:77-88. [DOI: 10.1016/j.jprot.2017.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/10/2017] [Accepted: 11/21/2017] [Indexed: 12/14/2022]
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2
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Kato Y, Jimbo M, Sakakibara Y, Onizuka R, Takahashi T, Matsuhashi S, Mita H, Amada K, Imahara Y, Tanabe K, Toda A, Kamiya H. Characterization of a novel allergenic protein from the octocoral Scleronephthya gracillima (Kuekenthal) that corresponds to a new GFP-like family named Akane. LUMINESCENCE 2017; 32:1009-1016. [PMID: 28378893 DOI: 10.1002/bio.3284] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/15/2016] [Accepted: 12/28/2016] [Indexed: 11/08/2022]
Abstract
Certain marine organisms have been known to cause allergic reactions among occupational fishermen. We have previously reported that bronchial asthma among the workers engaged in spiny lobster fishing in Japan was caused by octocorals such as Dendronephthya sp. and Scleronephthya gracillima (previously named Alcyonium gracillimum). Now we have found another octocoral, Scleronephthya gracillima (Kuekenthal), which causes the allergic disease in fishermen. The octocoral was characterized as a new green fluorescent protein (GFP)-like family. The new allergen has a molecular mass of 27 kDa in 1D and 2D SDS-PAGE under reduced conditions. The 27 kDa component was determined to be an allergen by western blotting, ECL immune staining method and absorption of patient sera with the antigen. Furthermore, the combination of analysis with LC-ESI-MS/MS and MASCOT search in the NCBInr database concluded the 27 kDa component had the sequence YPADI/LPDYFK, and that the 22 kDa component had the sequence QSFPEGFSWER, which both matched a GFP-like protein in Acropora aculeus and in Montastraea annularis. Further analysis by MALDI-TOF/MS/MS and MASCOT search in the NCBInr database of all 27 kDa eight spot components from 2D SDS-PAGE indicated that the sequence QSFPEGFSWER also matched as GFP-like protein in Lobophyllia hemprichii and Scleractinia sp. To our knowledge, this is the first report of the new allergenic protein that corresponds to a new GFP-like protein named Akane, and which has fluorescent emissions in the red and green part of the spectra at 628 nm and 508 nm, respectively.
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Affiliation(s)
- Yuko Kato
- Electronics Research Laboratory, Comprehensive Research Organization, Fukuoka Institute of Technology, Fukuoka, Japan
| | - Mitsuru Jimbo
- Department of Marine Biosciences, Schools of Marine Biosciences, Kitasato University, Japan
| | - Youichi Sakakibara
- Department of Biochemistry and Applied Biosciences, University of Miyazaki, Japan
| | - Reiko Onizuka
- National Hospital Organization, Miyazaki-Higashi Hospital, Japan
| | - Tatsuya Takahashi
- Department of Internal Medicine, Faculty of Medicine, Saga University, Japan
| | - Sachiko Matsuhashi
- Department of Internal Medicine, Faculty of Medicine, Saga University, Japan
| | - Hajime Mita
- Department of Life, Environment and Materials Science, Faculty of Engineering, Fukuoka Institute of Technology, Japan
| | - Kei Amada
- Department of Life, Environment and Materials Science, Faculty of Engineering, Fukuoka Institute of Technology, Japan
| | | | - Kimiko Tanabe
- Cooperative Research Center, University of Miyazaki, Japan
| | - Akihisa Toda
- Daiichi University of Pharmacy, Department of Health Science and Hygiene, Japan
| | - Hisao Kamiya
- Department of Marine Biosciences, Schools of Marine Biosciences, Kitasato University, Japan
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Fang F, Zhao Q, Li X, Liang Z, Zhang L, Zhang Y. Dissolving capability difference based sequential extraction: A versatile tool for in-depth membrane proteome analysis. Anal Chim Acta 2016; 945:39-46. [DOI: 10.1016/j.aca.2016.09.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/21/2016] [Accepted: 09/24/2016] [Indexed: 01/05/2023]
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Sjöström M, Ossola R, Breslin T, Rinner O, Malmström L, Schmidt A, Aebersold R, Malmström J, Niméus E. A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. J Proteome Res 2015; 14:2807-18. [DOI: 10.1021/acs.jproteome.5b00315] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | | | - Ruedi Aebersold
- Department
of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule, 8092 Zurich, Switzerland
| | | | - Emma Niméus
- Division
of Surgery, Skåne University Hospital, 221 85 Lund, Sweden
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Olsson N, Carlsson P, James P, Hansson K, Waldemarson S, Malmström P, Fernö M, Ryden L, Wingren C, Borrebaeck CAK. Grading breast cancer tissues using molecular portraits. Mol Cell Proteomics 2013; 12:3612-23. [PMID: 23982162 PMCID: PMC3861711 DOI: 10.1074/mcp.m113.030379] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Tumor progression and prognosis in breast cancer patients are difficult to assess using current clinical and laboratory parameters, where a pathological grading is indicative of tumor aggressiveness. This grading is based on assessments of nuclear grade, tubule formation, and mitotic rate. We report here the first protein signatures associated with histological grades of breast cancer, determined using a novel affinity proteomics approach. We profiled 52 breast cancer tissue samples by combining nine antibodies and label-free LC-MS/MS, which generated detailed quantified proteomic maps representing 1,388 proteins. The results showed that we could define in-depth molecular portraits of histologically graded breast cancer tumors. Consequently, a 49-plex candidate tissue protein signature was defined that discriminated between histological grades 1, 2, and 3 of breast cancer tumors with high accuracy. Highly biologically relevant proteins were identified, and the differentially expressed proteins indicated further support for the current hypothesis regarding remodeling of the tumor microenvironment during tumor progression. The protein signature was corroborated using meta-analysis of transcriptional profiling data from an independent patient cohort. In addition, the potential for using the markers to estimate the likelihood of long-term metastasis-free survival was also indicated. Taken together, these molecular portraits could pave the way for improved classification and prognostication of breast cancer.
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Affiliation(s)
- Niclas Olsson
- Department of Immunotechnology and CREATE HEALTH, Lund University, Medicon Village, SE-223 81 Lund, Sweden
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Ye X, Li L. Microwave-Assisted Protein Solubilization for Mass Spectrometry-Based Shotgun Proteome Analysis. Anal Chem 2012; 84:6181-91. [DOI: 10.1021/ac301169q] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Xiaoxia Ye
- Department of Chemistry, University of Alberta, Edmonton,
Alberta T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton,
Alberta T6G 2G2, Canada
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Wu F, Sun D, Wang N, Gong Y, Li L. Comparison of surfactant-assisted shotgun methods using acid-labile surfactants and sodium dodecyl sulfate for membrane proteome analysis. Anal Chim Acta 2011; 698:36-43. [DOI: 10.1016/j.aca.2011.04.039] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 04/13/2011] [Accepted: 04/18/2011] [Indexed: 01/11/2023]
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Sutton CW, Rustogi N, Gurkan C, Scally A, Loizidou MA, Hadjisavvas A, Kyriacou K. Quantitative proteomic profiling of matched normal and tumor breast tissues. J Proteome Res 2010; 9:3891-902. [PMID: 20560667 DOI: 10.1021/pr100113a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Proteomic analysis of breast cancer tissue has proven difficult due to its inherent histological complexity. This pilot study presents preliminary evidence for the ability to differentiate adenoma and invasive carcinoma by measuring changes in proteomic profile of matched normal and disease tissues. A dual lysis buffer method was used to maximize protein extraction from each biopsy, proteins digested with trypsin, and the resulting peptides iTRAQ labeled. After combining, the peptide mixtures they were separated using preparative IEF followed by RP nanoHPLC. Following MALDI MS/MS and database searching, identified proteins were combined into a nonredundant list of 481 proteins with associated normal/tumor iTRAQ ratios for each patient. Proteins were categorized by location as blood, extracellular, and cellular, and the iTRAQ ratios were normalized to enable comparison between patients. Of those proteins significantly changed (upper or lower quartile) between matched normal and disease tissues, those from two invasive carcinoma patients had >50% in common with each other but <22% in common with an adenoma patient. In invasive carcinoma patients, several cellular and extracellular proteins that were significantly increased (Periostin, Small breast epithelial mucin) or decreased (Kinectin) have previously been associated with breast cancer, thereby supporting this approach for a larger disease-stage characterization effort.
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Affiliation(s)
- Chris W Sutton
- Institute of Cancer Therapeutics, University of Bradford, West Yorkshire, United Kingdom.
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De Souza AG, MacCormack TJ, Wang N, Li L, Goss GG. Large-Scale Proteome Profile of the Zebrafish (Danio rerio) Gill for Physiological and Biomarker Discovery Studies. Zebrafish 2009; 6:229-38. [DOI: 10.1089/zeb.2009.0591] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Andrea G. De Souza
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Tyson J. MacCormack
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Nan Wang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Greg G. Goss
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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Wu F, Wang P, Young LC, Lai R, Li L. Proteome-wide identification of novel binding partners to the oncogenic fusion gene protein, NPM-ALK, using tandem affinity purification and mass spectrometry. THE AMERICAN JOURNAL OF PATHOLOGY 2009; 174:361-70. [PMID: 19131589 DOI: 10.2353/ajpath.2009.080521] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nucleophosmin-anaplastic lymphoma kinase (NPM-ALK), an oncogenic fusion gene protein that is characteristically found in a subset of anaplastic large cell lymphomas, promotes tumorigenesis through its functional and physical interactions with various biologically important proteins. The identification of these interacting proteins has proven to be useful to further our understanding of NPM-ALK-mediated tumorigenesis. For the first time, we performed a proteome-wide identification of NPM-ALK-binding proteins using tandem affinity purification and a highly sensitive mass spectrometric technique. Tandem affinity purification is a recently developed method that carries a lower background and higher sensitivity compared with the conventional immunoprecipitation-based protein purification protocols. The NPM-ALK gene was cloned into an HB-tagged vector and expressed in GP293 cells. Three independent experiments were performed and the reproducibility of the data was 68%. The vast majority of the previously reported NPM-ALK-binding proteins were detected. We also identified proteins that are involved in various cellular processes that were not previously described in association with NPM-ALK, such as MCM6 and MSH2 (DNA repair), Nup98 and importin 8 (subcellular protein transport), Stim1 (calcium signaling), 82Fip (RNA regulation), and BAG2 (proteosome degradation). We believe that these data highlight the functional diversity of NPM-ALK and provide new research directions for the study of the biology of this oncoprotein.
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Affiliation(s)
- Fang Wu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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