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de Jong E, Kocer A. Current Methods for Identifying Plasma Membrane Proteins as Cancer Biomarkers. MEMBRANES 2023; 13:409. [PMID: 37103836 PMCID: PMC10142483 DOI: 10.3390/membranes13040409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 06/19/2023]
Abstract
Plasma membrane proteins are a special class of biomolecules present on the cellular membrane. They provide the transport of ions, small molecules, and water in response to internal and external signals, define a cell's immunological identity, and facilitate intra- and intercellular communication. Since they are vital to almost all cellular functions, their mutants, or aberrant expression is linked to many diseases, including cancer, where they are a part of cancer cell-specific molecular signatures and phenotypes. In addition, their surface-exposed domains make them exciting biomarkers for targeting by imaging agents and drugs. This review looks at the challenges in identifying cancer-related cell membrane proteins and the current methodologies that solve most of the challenges. We classified the methodologies as biased, i.e., search cells for the presence of already known membrane proteins. Second, we discuss the unbiased methods that can identify proteins without prior knowledge of what they are. Finally, we discuss the potential impact of membrane proteins on the early detection and treatment of cancer.
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2
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Zhang B, Guo M, Wang H, Wang Z, Zhang L, Zhang Y, Cao C, Xiao H. Metal Organic Framework Nanomaterial-Based Extraction and Proteome Analysis of Membrane and Membrane-Associated Proteins. Anal Chem 2021; 93:15922-15930. [PMID: 34817162 DOI: 10.1021/acs.analchem.1c03219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Membrane proteins (MPs) play a key role in various biological processes, while difficulties still exist in the extraction because of their inherent low abundance and poor solubility caused by high hydrophobicity. Metal organic framework (MOF) materials with good hydrophobic properties have the ability to absorb MPs, especially zeolitic imidazolate framework (ZIF) materials. Here, two MOF materials (ZIF-8 and ZIF-67) were compared for MP extraction, and our results revealed that higher yield was obtained with ZIF-67. After method development, the optimal enrichment effect was obtained when the mass ratio of proteins and ZIF-67 reached 1:20 with 100 mM NaCl in 20% ethanol at 4 °C and pH 9.0. When compared with a commercial kit, the extraction yield increased by 88.11% and the average number of identified MPs elevated by 29.17% with the developed ZIF method. Normal lung cell MRC5 was employed to verify the effectiveness of the ZIF method. Results showed 45.13% increase in yield and 22.88% increase in average number of identified MPs by the ZIF method. Our method was further applied to the enrichment of MPs for high-metastatic (95D) and low-metastatic (95C) human lung cancer cells. A total of 1732 (95D) and 1711 (95C) MPs were identified, among which 710 MPs were dysregulated significantly; 441 upregulated MPs in 95D cells were found to be closely related to the growth, proliferation, and migration of lung cancer cells. Our results collectively demonstrated that ZIF-67 was an ideal material for MP extraction, which might be helpful for analysis of cancer proteomics and discovery of cancer migration associated MPs.
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Affiliation(s)
- Baohui Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Miao Guo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zeyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lu Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chengxi Cao
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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3
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Zhong L, Zhu L, Cai ZW. Mass Spectrometry-based Proteomics and Glycoproteomics in COVID-19 Biomarkers Identification: A Mini-review. JOURNAL OF ANALYSIS AND TESTING 2021; 5:298-313. [PMID: 34513131 PMCID: PMC8423835 DOI: 10.1007/s41664-021-00197-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/27/2021] [Indexed: 12/11/2022]
Abstract
The first corona-pandemic, coronavirus disease 2019 (COVID-19) caused a huge health crisis and incalculable damage worldwide. Knowledge of how to cure the disease is urgently needed. Emerging immune escaping mutants of the virus suggested that it may be potentially persistent in human society as a regular health threat as the flu virus. Therefore, it is imperative to identify appropriate biomarkers to indicate pathological and physiological states, and more importantly, clinic outcomes. Proteins are the performers of life functions, and their abundance and modification status can directly reflect the immune status. Protein glycosylation serves a great impact in modulating protein function. The use of both unmodified and glycosylated proteins as biomarkers has also been proved feasible in the studies of SARS, Zika virus, influenza, etc. In recent years, mass spectrometry-based glycoproteomics, as well as proteomics approaches, advanced significantly due to the evolution of mass spectrometry. We focus on the current development of the mass spectrometry-based strategy for COVID-19 biomarkers' investigation. Potential application of glycoproteomics approaches and challenges in biomarkers identification are also discussed.
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Affiliation(s)
- Li Zhong
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, China
| | - Lin Zhu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, China
| | - Zong-Wei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, 224 Waterloo Road, Kowloon Tong, Hong Kong SAR, China
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4
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Laxmivandana R, Patole C, Sharma TR, Sharma KK, Naskar S. Differential proteins associated with plasma membrane in X- and/or Y-chromosome bearing spermatozoa in indicus cattle. Reprod Domest Anim 2021; 56:928-935. [PMID: 33829570 DOI: 10.1111/rda.13936] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/05/2021] [Indexed: 11/29/2022]
Abstract
The differential proteins associated with plasma membrane of spermatozoa are less known, identification of which shall help overcome limitations of currently used methods of sperm sexing, considered as a high priority for livestock sector of many countries. This study has reported plasma membrane proteomics of unsorted spermatozoa and differential expression of plasma membrane-associated proteins between X- and Y-chromosome bearing spermatozoa of indicus cattle (Bos indicus). Isolation of plasma membrane fraction using percoll gradient, relatively a rapid method, from bovine spermatozoa has been reported to enrich isolation of plasma membrane proteins. Significant enrichment for plasma membrane-associated proteins was observed in plasma membrane fraction (p < .05) as compared to the total cell lysate using LC-MS/MS. Furthermore, these experiments were conducted in flow cytometry sorted, sexed-semen samples. Thirteen proteins were identified as differentially abundant between X- and Y-sorted spermatozoa. Among these, two proteins were downregulated in Y-sorted spermatozoa compared to the X-sorted spermatozoa (p < .05), while four and seven proteins could be noted in X- and Y-sorted spermatozoa, respectively. Proteins that are presumed to support sperm capacitation and sperm migration velocity were found to be abundant in Y-sorted spermatozoa while those associated with structural molecule activity were identified as abundant in X-sorted spermatozoa in the present study. Our study provides better insight into the plasma membrane proteomics of spermatozoa of indicus cattle and furnishes data that might aid in design and development of alternate and open technology for sex-sorting of semen.
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Affiliation(s)
| | | | - Tilak Raj Sharma
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | | | - Soumen Naskar
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
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5
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A Protocol for the Plasma Membrane Proteome Analysis of Rice Leaves. Methods Mol Biol 2020. [PMID: 32462581 DOI: 10.1007/978-1-0716-0528-8_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
Subcellular proteome analysis is one of the most effective ways to reduce the complexity of total proteome. With the advancement in protein extraction methodologies, it is now possible to fractionate and isolate the proteins from subcellular compartments without significant contamination from the cytoplasm and other organelles. Of the different subcellular proteomes, plasma membrane remained largely uncharacterized because of the difficulties in isolation of contamination free plasma membrane proteins. Moreover, proteome analysis in the past two decades majorly relied on the two-dimensional gel electrophoresis which showed limited protein loading ability and poor separation of highly hydrophobic plasma membrane proteins. Development of shotgun proteomics methods has facilitated the identification and quantification of hydrophobic proteins isolated from plasma membrane or other cellular membranes. Here, we present a simplified procedure for the isolation of plasma membrane proteins by a two-phase partitioning method and their identification by shotgun proteomics approach using rice as a model plant.
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6
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Improved sensitivity in cell surface protein detection by combining chemical labeling with mechanical lysis in a colorectal cancer cell model. Biotechnol Lett 2020; 42:683-695. [DOI: 10.1007/s10529-020-02824-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/26/2020] [Indexed: 10/25/2022]
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7
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Li J, Han S, Li H, Udeshi ND, Svinkina T, Mani DR, Xu C, Guajardo R, Xie Q, Li T, Luginbuhl DJ, Wu B, McLaughlin CN, Xie A, Kaewsapsak P, Quake SR, Carr SA, Ting AY, Luo L. Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators. Cell 2020; 180:373-386.e15. [PMID: 31955847 DOI: 10.1016/j.cell.2019.12.029] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 01/12/2023]
Abstract
Molecular interactions at the cellular interface mediate organized assembly of single cells into tissues and, thus, govern the development and physiology of multicellular organisms. Here, we developed a cell-type-specific, spatiotemporally resolved approach to profile cell-surface proteomes in intact tissues. Quantitative profiling of cell-surface proteomes of Drosophila olfactory projection neurons (PNs) in pupae and adults revealed global downregulation of wiring molecules and upregulation of synaptic molecules in the transition from developing to mature PNs. A proteome-instructed in vivo screen identified 20 cell-surface molecules regulating neural circuit assembly, many of which belong to evolutionarily conserved protein families not previously linked to neural development. Genetic analysis further revealed that the lipoprotein receptor LRP1 cell-autonomously controls PN dendrite targeting, contributing to the formation of a precise olfactory map. These findings highlight the power of temporally resolved in situ cell-surface proteomic profiling in discovering regulators of brain wiring.
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Affiliation(s)
- Jiefu Li
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| | - Shuo Han
- Departments of Genetics, Biology, and Chemistry, Chan Zuckerberg Biohub, Stanford University, Stanford, CA 94305, USA
| | - Hongjie Li
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Namrata D Udeshi
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tanya Svinkina
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - D R Mani
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chuanyun Xu
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ricardo Guajardo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Qijing Xie
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Tongchao Li
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - David J Luginbuhl
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Bing Wu
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Colleen N McLaughlin
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Anthony Xie
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Pornchai Kaewsapsak
- Departments of Genetics, Biology, and Chemistry, Chan Zuckerberg Biohub, Stanford University, Stanford, CA 94305, USA
| | - Stephen R Quake
- Departments of Bioengineering and Applied Physics, Chan Zuckerberg Biohub, Stanford University, Stanford, CA 94305, USA
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alice Y Ting
- Departments of Genetics, Biology, and Chemistry, Chan Zuckerberg Biohub, Stanford University, Stanford, CA 94305, USA.
| | - Liqun Luo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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8
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Yoneten KK, Kasap M, Akpinar G, Kanli A, Karaoz E. Comparative Proteomics Analysis of Four Commonly Used Methods for Identification of Novel Plasma Membrane Proteins. J Membr Biol 2019; 252:587-608. [PMID: 31346646 DOI: 10.1007/s00232-019-00084-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/17/2019] [Indexed: 11/25/2022]
Abstract
Plasma membrane proteins perform a variety of important tasks in the cells. These tasks can be diverse as carrying nutrients across the plasma membrane, receiving chemical signals from outside the cell, translating them into intracellular action, and anchoring the cell in a particular location. When these crucial roles of plasma membrane proteins are considered, the need for their characterization becomes inevitable. Certain characteristics of plasma membrane proteins such as hydrophobicity, low solubility, and low abundance limit their detection by proteomic analyses. Here, we presented a comparative proteomics study in which the most commonly used plasma membrane protein enrichment methods were evaluated. The methods that were utilized include biotinylation, selective CyDye labeling, temperature-dependent phase partition, and density-gradient ultracentrifugation. Western blot analysis was performed to assess the level of plasma membrane protein enrichment using plasma membrane and cytoplasmic protein markers. Quantitative evaluation of the level of enrichment was performed by two-dimensional electrophoresis (2-DE) and benzyldimethyl-n-hexadecylammonium chloride/sodium dodecyl sulfate polyacrylamide gel electrophoresis (16-BAC/SDS-PAGE) from which the protein spots were cut and identified. Results from this study demonstrated that density-gradient ultracentrifugation method was superior when coupled with 16-BAC/SDS-PAGE. This work presents a valuable contribution and provides a future direction to the membrane sub-proteome research by evaluating commonly used methods for plasma membrane protein enrichment.
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Affiliation(s)
| | - Murat Kasap
- Department of Medical Biology, School of Medicine, Kocaeli University, 41380, Kocaeli, Turkey.
| | - Gurler Akpinar
- Department of Medical Biology, School of Medicine, Kocaeli University, 41380, Kocaeli, Turkey
| | - Aylin Kanli
- Department of Medical Biology, School of Medicine, Kocaeli University, 41380, Kocaeli, Turkey
| | - Erdal Karaoz
- Department of Histology and Embryology, School of Medicine, Istinye University, 34010, Istanbul, Turkey
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9
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Molecular phenotyping of the surfaceome of migratory chondroprogenitors and mesenchymal stem cells using biotinylation, glycocapture and quantitative LC-MS/MS proteomic analysis. Sci Rep 2019; 9:9018. [PMID: 31227739 PMCID: PMC6588563 DOI: 10.1038/s41598-019-44957-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 04/24/2019] [Indexed: 12/16/2022] Open
Abstract
The complement of cell surface proteins, collectively referred to as the surfaceome, is a useful indicator of normal differentiation processes, and the development of pathologies such as osteoarthritis (OA). We employed biochemical and proteomic tools to explore the surfaceome and to define biomarkers in chondrogenic progenitor cells (CPC) derived from human OA knee articular cartilage. These cells have great therapeutic potential, but their unexplored biology limits their clinical application. We performed biotinylation combined with glycocapture and high throughput shotgun proteomics to define the surface proteome of human bone marrow mesenchymal stem cells (MSCs) and human CPCs. We prepared cell surface protein-enriched fractions from MSCs and CPCs, and then a proteomic approach was used to compare and evaluate protein changes between undifferentiated MSCs and CPCs. 1256 proteins were identified in the study, of which 791 (63%) were plasma membrane, cell surface or extracellular matrix proteins. Proteins constituting the surfaceome were annotated and categorized. Our results provide, for the first time, a repository of quantitative proteomic data on the surfaceome of two closely related cell types relevant to cartilage biology and OA. These results may provide novel insights into the transformation of the surfaceome during chondrogenic differentiation and phenotypic changes during OA development.
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10
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Kwan TOC, Reis R, Siligardi G, Hussain R, Cheruvara H, Moraes I. Selection of Biophysical Methods for Characterisation of Membrane Proteins. Int J Mol Sci 2019; 20:E2605. [PMID: 31137900 PMCID: PMC6566885 DOI: 10.3390/ijms20102605] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 02/01/2023] Open
Abstract
Over the years, there have been many developments and advances in the field of integral membrane protein research. As important pharmaceutical targets, it is paramount to understand the mechanisms of action that govern their structure-function relationships. However, the study of integral membrane proteins is still incredibly challenging, mostly due to their low expression and instability once extracted from the native biological membrane. Nevertheless, milligrams of pure, stable, and functional protein are always required for biochemical and structural studies. Many modern biophysical tools are available today that provide critical information regarding to the characterisation and behaviour of integral membrane proteins in solution. These biophysical approaches play an important role in both basic research and in early-stage drug discovery processes. In this review, it is not our objective to present a comprehensive list of all existing biophysical methods, but a selection of the most useful and easily applied to basic integral membrane protein research.
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Affiliation(s)
- Tristan O C Kwan
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
| | - Rosana Reis
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Harish Cheruvara
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
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11
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Moritz CP, Tholance Y, Rosier C, Reynaud-Federspiel E, Svahn J, Camdessanché JP, Antoine JC. Completing the Immunological Fingerprint by Refractory Proteins: Autoantibody Screening via an Improved Immunoblotting Technique. Proteomics Clin Appl 2019; 13:e1800157. [PMID: 30768763 DOI: 10.1002/prca.201800157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/30/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE Identifying autoantigens of serological autoantibodies requires expensive methods, such as protein microarrays or IP+MS. Thus, sera are commonly pre-screened for interesting immunopatterns via immunocytochemistry/immunohistochemistry. However, distinguishing immunopatterns can be difficult and intracellular antigens are less accessible. Therefore, a simple and cheap immunoblot screening able to distinguish immunopatterns and to detect refractory proteins is presented. EXPERIMENTAL DESIGN Five steps of immunoblotting-based autoantigen screening are revised: (1) choice of protein source, (2) protein extraction, (3) protein separation, (4) protein transfer, (5) antigen detection. Thereafter, 52 patients' sera with chronic inflammatory demyelinating polyneuropathy (CIDP) and 45 controls were screened. RESULTS The protein source impacts the detected antigen set. Steps 2-4 can be adapted for refractory proteins. Furthermore, longitudinal cutting of protein lanes saves ≥75% of time and material and allows for exact comparison of band patterns. As the latter are individually specific and temporarily constant, we call them "immunological fingerprints". In a proof-of-principle, a 155 kDa immunoband was detected with two anti-neurofascin-155-positive CIDP sera and two further immunobands (120/220 kDa) specific to a subgroup of 3-6 of 52 CIDP patients. CONCLUSIONS AND CLINICAL RELEVANCE Adapted immunoblotting is a cheap and simple method for accurate serum screening including refractory and intracellular antigens.
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Affiliation(s)
- Christian P Moritz
- Synaptopathies and Autoantibodies, Faculty of Medicine Jacques Lisfranc, University Jean Monnet, University of Lyon, 42270, Saint-Priest en Jarez, France.,Institut NeuroMyoGene INSERM U1217/CNRS UMR 5310, University Jean Monnet, University of Lyon, 42270, Saint-Priest en Jarez, France
| | - Yannick Tholance
- Synaptopathies and Autoantibodies, Faculty of Medicine Jacques Lisfranc, University Jean Monnet, University of Lyon, 42270, Saint-Priest en Jarez, France.,Institut NeuroMyoGene INSERM U1217/CNRS UMR 5310, University Jean Monnet, University of Lyon, 42270, Saint-Priest en Jarez, France.,Biochemistry Laboratory, Centre Hospitalier Universitaire de Saint-Étienne, 42055, Saint-Étienne, France
| | - Carole Rosier
- Synaptopathies and Autoantibodies, Faculty of Medicine Jacques Lisfranc, University Jean Monnet, University of Lyon, 42270, Saint-Priest en Jarez, France.,Neurology Department, Centre Hospitalier Universitaire de Saint-Étienne, 42055, Saint-Étienne, France
| | - Evelyne Reynaud-Federspiel
- Synaptopathies and Autoantibodies, Faculty of Medicine Jacques Lisfranc, University Jean Monnet, University of Lyon, 42270, Saint-Priest en Jarez, France.,Institut NeuroMyoGene INSERM U1217/CNRS UMR 5310, University Jean Monnet, University of Lyon, 42270, Saint-Priest en Jarez, France
| | - Juliette Svahn
- Synaptopathies and Autoantibodies, Faculty of Medicine Jacques Lisfranc, University Jean Monnet, University of Lyon, 42270, Saint-Priest en Jarez, France
| | - Jean-Philippe Camdessanché
- Synaptopathies and Autoantibodies, Faculty of Medicine Jacques Lisfranc, University Jean Monnet, University of Lyon, 42270, Saint-Priest en Jarez, France.,Institut NeuroMyoGene INSERM U1217/CNRS UMR 5310, University Jean Monnet, University of Lyon, 42270, Saint-Priest en Jarez, France.,Neurology Department, Centre Hospitalier Universitaire de Saint-Étienne, 42055, Saint-Étienne, France
| | - Jean-Christophe Antoine
- Synaptopathies and Autoantibodies, Faculty of Medicine Jacques Lisfranc, University Jean Monnet, University of Lyon, 42270, Saint-Priest en Jarez, France.,Institut NeuroMyoGene INSERM U1217/CNRS UMR 5310, University Jean Monnet, University of Lyon, 42270, Saint-Priest en Jarez, France.,Neurology Department, Centre Hospitalier Universitaire de Saint-Étienne, 42055, Saint-Étienne, France
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12
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Jankovskaja S, Kamiie J, Rezeli M, Gustavsson L, Sugihara Y, Miliotis T, Ruzgas T, Marko-Varga G. Optimization of sample preparation for transporter protein quantification in tissues by LC-MS/MS. J Pharm Biomed Anal 2019; 164:9-15. [PMID: 30339949 DOI: 10.1016/j.jpba.2018.10.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 11/25/2022]
Abstract
BACKGROUND Reproducible quantification of drug transporter protein expression in tissues is important for predicting transporter mediated drug disposition. Many mass-spectrometry based transporter protein quantification methods result in high variability of the estimated transporter quantities. Therefore, we aimed to evaluate and optimize mass spectrometry-based quantification method for drug transporter proteins in tissues. MATERIALS AND METHODS Plasma membrane (PM) proteins from mouse tissues were isolated by applying three extraction protocols: commercial plasma membrane extraction kit, tissue homogenization by Potter-Elvehjem homogenizer in combination with sucrose-cushion ultracentrifugation, and PM enrichment with Tween 40. Moreover, five different protein digestion protocols were applied on the same PM fraction. PM isolation and digestion protocols were evaluated by measuring the amount of transporter proteins by liquid chromatography-tandem mass spectrometry in selected reaction monitoring mode. RESULTS Mouse liver homogenization by Potter-Elvehjem homogenizer in combination with sucrose-cushion ultracentrifugation and PM enrichment with Tween 40 resulted in two times higher transporter protein quantity (Breast cancer resistance protein (Bcrp) 18.0 fmol/μg protein) in comparison with the PM samples isolated by extraction kit (Bcrp 9.8 fmol/μg protein). The evaluation of protein digestion protocols revealed that the most optimal protocol for PM protein digestion is with Lys-C and trypsin, in combination with trypsin enhancer and heat denaturation. Overall, quantities of Bcrp and Na+/K + ATPase proteins evaluated in mouse liver and kidney cortex by using our optimized PM isolation method, as well as, established digestion protocol were two to three times higher than previously reported and coefficient of variation (CV) for technical replicates was below 10%. CONCLUSION We have established an improved transporter protein quantification methodology by optimizing PM isolation and protein digestion procedures. The optimized procedure resulted in a higher transporter protein yield and improved precision.
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Affiliation(s)
- Skaidre Jankovskaja
- Clinical Protein Science and Imaging, Department of Biomedical Engineering, Lund University, Lund, Sweden; Department of Biomedical Science, Faculty of Health and Society, Malmö University, Malmö, Sweden; Biofilms -Research Center for Biointerfaces, Malmö University, Malmö, Sweden
| | - Junichi Kamiie
- Clinical Protein Science and Imaging, Department of Biomedical Engineering, Lund University, Lund, Sweden; Laboratory of Veterinary Pathology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Melinda Rezeli
- Clinical Protein Science and Imaging, Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Lena Gustavsson
- Department of Drug Metabolism, H. Lundbeck A/S, Valby, Denmark
| | - Yutaka Sugihara
- Clinical Protein Science and Imaging, Department of Biomedical Engineering, Lund University, Lund, Sweden; Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Tasso Miliotis
- Clinical Protein Science and Imaging, Department of Biomedical Engineering, Lund University, Lund, Sweden; Translational Science, Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Tautgirdas Ruzgas
- Department of Biomedical Science, Faculty of Health and Society, Malmö University, Malmö, Sweden; Biofilms -Research Center for Biointerfaces, Malmö University, Malmö, Sweden
| | - György Marko-Varga
- Clinical Protein Science and Imaging, Department of Biomedical Engineering, Lund University, Lund, Sweden; Centre of Excellence in Biological and Medical Mass Spectrometry "CEBMMS", Biomedical Centre D13, Lund University, Lund, Sweden.
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13
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Buchegger B, Kreutzer J, Axmann M, Mayr S, Wollhofen R, Plochberger B, Jacak J, Klar TA. Proteins on Supported Lipid Bilayers Diffusing around Proteins Fixed on Acrylate Anchors. Anal Chem 2018; 90:12372-12376. [PMID: 30350628 PMCID: PMC6222595 DOI: 10.1021/acs.analchem.8b02588] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/16/2018] [Indexed: 01/04/2023]
Abstract
Mobility of proteins and lipids plays a major role in physiological processes. Platforms which were developed to study protein interaction between immobilized and mobile proteins suffer from shortcomings such as fluorescence quenching or complicated fabrication methods. Here we report a versatile platform comprising immobilized histidine-tagged proteins and biotinylated proteins in a mobile phase. Importantly, multiphoton photolithography was used for easy and fast fabrication of the platform and allows, in principle, extension of its application to three dimensions. The platform, which is made up of functionalized polymer structures embedded in a mobile lipid bilayer, shows low background fluorescence and allows for mobility of arbitrary proteins.
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Affiliation(s)
- Bianca Buchegger
- Institute
of Applied Physics, Johannes Kepler University
Linz, Altenberger Straße 69, 4040 Linz, Austria
| | - Johannes Kreutzer
- Institute
of Applied Physics, Johannes Kepler University
Linz, Altenberger Straße 69, 4040 Linz, Austria
| | - Markus Axmann
- Institute
of Medical Chemistry, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Währinger Straße 10, 1090 Vienna, Austria
| | - Sandra Mayr
- School
of Medical Engineering and Applied Social Sciences, University of Applied Sciences Upper Austria, Garnisonstraße 21, 4020 Linz, Austria
| | - Richard Wollhofen
- Institute
of Applied Physics, Johannes Kepler University
Linz, Altenberger Straße 69, 4040 Linz, Austria
| | - Birgit Plochberger
- School
of Medical Engineering and Applied Social Sciences, University of Applied Sciences Upper Austria, Garnisonstraße 21, 4020 Linz, Austria
| | - Jaroslaw Jacak
- Institute
of Applied Physics, Johannes Kepler University
Linz, Altenberger Straße 69, 4040 Linz, Austria
- School
of Medical Engineering and Applied Social Sciences, University of Applied Sciences Upper Austria, Garnisonstraße 21, 4020 Linz, Austria
| | - Thomas A. Klar
- Institute
of Applied Physics, Johannes Kepler University
Linz, Altenberger Straße 69, 4040 Linz, Austria
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14
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Fujinaka CM, Waas M, Gundry RL. Mass Spectrometry-Based Identification of Extracellular Domains of Cell Surface N-Glycoproteins: Defining the Accessible Surfaceome for Immunophenotyping Stem Cells and Their Derivatives. Methods Mol Biol 2018; 1722:57-78. [PMID: 29264798 DOI: 10.1007/978-1-4939-7553-2_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Human stem cells and their progeny are valuable for a variety of research applications and have the potential to revolutionize approaches to regenerative medicine. However, we currently have limited tools to permit live isolation of homogeneous populations of cells apt for mechanistic studies or cellular therapies. While these challenges can be overcome through the use of immunophenotyping based on accessible cell surface markers, the success of this process depends on the availability of reliable antibodies and well-characterized markers, which are lacking for most stem cell lineages. This chapter outlines an iterative process for the development of new cell surface marker barcodes for identifying and selecting stem cell derived progeny of specific cell types, subtypes, and maturation stages, where antibody-independent identification of cell surface proteins is achieved using a modern chemoproteomic approach to specifically identify N-glycoproteins localized to the cell surface. By taking advantage of a large repository of available cell surfaceome data, proteins that are unlikely to confer cell type specificity can be rapidly eliminated from consideration. Subsequently, targeted quantitation by mass spectrometry can be used to refine candidates of interest, and a bioinformatic visualization tool is key to mapping experimental data to candidate protein sequences for the purpose of epitope selection during the antibody development phase. Overall, the process of developing cell surface barcodes for immunophenotyping is iterative and can include multiple rounds of discovery, refinement, and validation depending on the phenotypic resolution required.
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Affiliation(s)
- Chelsea M Fujinaka
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.
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15
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Özkan Küçük NE, Şanal E, Tan E, Mitchison T, Özlü N. Labeling Carboxyl Groups of Surface-Exposed Proteins Provides an Orthogonal Approach for Cell Surface Isolation. J Proteome Res 2018; 17:1784-1793. [PMID: 29651847 DOI: 10.1021/acs.jproteome.7b00825] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Quantitative profiling of cell surface proteins is critically important for the understanding of cell-cell communication, signaling, tissue development, and homeostasis. Traditional proteomics methods are challenging for cell surface proteins due to their hydrophobic nature and low abundance, necessitating alternative methods to efficiently identify and quantify this protein group. Here we established carboxyl-reactive biotinylation for selective and efficient biotinylation and isolation of surface-exposed proteins of living cells. We assessed the efficiency of carboxyl-reactive biotinylation for plasma membrane proteins by comparing it with a well-established protocol, amine-reactive biotinylation, using SILAC (stable isotope labeling in cell culture). Our results show that carboxyl-reactive biotinylation of cell surface proteins is both more selective and more efficient than amine-reactive biotinylation. We conclude that it is a useful approach, which is partially orthogonal to amine-reactive biotinylation, allowing us to cast a wider net for a comprehensive profiling of cell surface proteins.
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Affiliation(s)
- Nazlı E Özkan Küçük
- Department of Molecular Biology and Genetics , Koç University , Istanbul 34450 , Turkey
| | - Erdem Şanal
- Department of Molecular Biology and Genetics , Koç University , Istanbul 34450 , Turkey
| | - Edwin Tan
- Department of Systems Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Timothy Mitchison
- Department of Systems Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Nurhan Özlü
- Department of Molecular Biology and Genetics , Koç University , Istanbul 34450 , Turkey
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16
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Thimiri Govinda Raj DB, Khan NA. Surface functionalization dependent subcellular localization of Superparamagnetic nanoparticle in plasma membrane and endosome. NANO CONVERGENCE 2018; 5:4. [PMID: 29492374 PMCID: PMC5813047 DOI: 10.1186/s40580-018-0136-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/31/2018] [Indexed: 05/22/2023]
Abstract
In this article, we elaborate the application of thermal decomposition based synthesis of Fe3O4 superparamagnetic nanoparticle (SPMNP) in subcellular fractionation context. Here, we performed surface functionalization of SPMNP with phospholipids and dimercaptosuccinic acid. Surprisingly, we observed surface functionalization dependent SPMNP localization in subcellular compartments such as plasma membrane, endosomes and lysosomes. By using SPMNP based subcellular localization with pulse-chase methodology, we could use SPMNP for high pure-high yield organelle (plasma membrane, endosomes and lysosome) fractionation. Further, SPMNP that are distinctly localized in subcellular compartments can be used as technology for subcellular fractionation that can complement existing tools for cell biology research. As a future perspective, isolated magnetic organelles can be extended to protein/protein complex purification for biochemical and structural biology studies.
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Affiliation(s)
- Deepak B. Thimiri Govinda Raj
- Envirotransgene® Bio-solutions Global Chennai, Tamil Nadu, India
- Biotechnology Centre for Oslo, Centre for Molecular Medicine Norway (NCMM), Blindern, P.O. Box 1137, 0318 Oslo, Norway
| | - Niamat Ali Khan
- Laboratory of Lipid Metabolism and Cancer, O&N I, Herestraat 49, Box 902, 3000 Louvain, Belgium
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17
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Mini-Scale Isolation and Preparation of Plasma Membrane Proteins from Potato Roots for LC/MS Analysis. Methods Mol Biol 2018; 1696:195-204. [PMID: 29086405 DOI: 10.1007/978-1-4939-7411-5_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Plasma membrane (PM) proteins are of special interest due to their function in exchanging material and information with the external environment as well as their role in cellular regulation. In quantitative proteomic studies PM proteins are underrepresented mostly because they constitute only small percent of all membrane proteins. Strong demand is placed on plasma membrane enrichment methods. For decades two-phase partitioning Dextran T500/PEG 3350 isolation protocols were applied for many different animal and plant species and also a variety of tissue types. The typical quantity of material used in the enrichment protocols is 10-30 g of fresh weight. The main difficulty of working with in vitro cultivated plants is the low amount of material, especially when roots are examined. In addition, roots are frequently characterized by low protein concentrations. Our protocol established for roots of in vitro cultivated potato plants is adjusted to amounts of fresh weight not exceeding 7.5 g and allows studying the plasma membrane proteome by LC-MS.
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18
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Nimthong-Roldán A, Sripa P, Wattanakanjana Y. Crystal structure of chlorido-[1-(4-nitro-phen-yl)thio-urea-κ S]bis-(tri-phenyl-phosphane-κ P)silver(I). Acta Crystallogr E Crystallogr Commun 2017; 73:829-831. [PMID: 28638637 PMCID: PMC5458302 DOI: 10.1107/s2056989017006405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/28/2017] [Indexed: 12/05/2022]
Abstract
In the title compound, [AgCl(C7H7N3O2S)(C18H15P)2], the AgI ion is in a distorted tetra-hedral coordination environment formed by P atoms from two tri-phenyl-phosphane ligands, one terminal S atom from the 1-(4-nitro-phen-yl)thio-urea ligand and a chloride ion. In the crystal, bifurcated (N-H)2⋯Cl hydrogen bonds [with graph-set motif R21(6)] connect complex mol-ecules, forming zigzag chains along [001]. These chains are linked via weak C-H⋯O hydrogen bonds, forming a two-dimensional network parallel to (100). An intra-molecular N-H⋯Cl hydrogen bond forming an S(6) ring is also observed.
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Affiliation(s)
| | - Paramee Sripa
- Department of Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112 , Thailand
| | - Yupa Wattanakanjana
- Department of Chemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112 , Thailand
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19
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Chandler KB, Costello CE. Glycomics and glycoproteomics of membrane proteins and cell-surface receptors: Present trends and future opportunities. Electrophoresis 2016; 37:1407-19. [PMID: 26872045 PMCID: PMC4889498 DOI: 10.1002/elps.201500552] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/02/2016] [Accepted: 02/02/2016] [Indexed: 12/16/2022]
Abstract
Membrane proteins mediate cell-cell interactions and adhesion, the transfer of ions and metabolites, and the transmission of signals from the extracellular environment to the cell interior. The extracellular domains of most cell membrane proteins are glycosylated, often at multiple sites. There is a growing awareness that glycosylation impacts the structure, interaction, and function of membrane proteins. The application of glycoproteomics and glycomics methods to membrane proteins has great potential. However, challenges also arise from the unique physical properties of membrane proteins. Successful analytical workflows must be developed and disseminated to advance functional glycoproteomics and glycomics studies of membrane proteins. This review explores the opportunities and challenges related to glycomic and glycoproteomic analysis of membrane proteins, including discussion of sample preparation, enrichment, and MS/MS analyses, with a focus on recent successful workflows for analysis of N- and O-linked glycosylation of mammalian membrane proteins.
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Affiliation(s)
- Kevin Brown Chandler
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
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20
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Richards MJ, Hsia CY, Singh RR, Haider H, Kumpf J, Kawate T, Daniel S. Membrane Protein Mobility and Orientation Preserved in Supported Bilayers Created Directly from Cell Plasma Membrane Blebs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:2963-74. [PMID: 26812542 DOI: 10.1021/acs.langmuir.5b03415] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Membrane protein interactions with lipids are crucial for their native biological behavior, yet traditional characterization methods are often carried out on purified protein in the absence of lipids. We present a simple method to transfer membrane proteins expressed in mammalian cells to an assay-friendly, cushioned, supported lipid bilayer platform using cell blebs as an intermediate. Cell blebs, expressing either GPI-linked yellow fluorescent proteins or neon-green fused transmembrane P2X2 receptors, were induced to rupture on glass surfaces using PEGylated lipid vesicles, which resulted in planar supported membranes with over 50% mobility for multipass transmembrane proteins and over 90% for GPI-linked proteins. Fluorescent proteins were tracked, and their diffusion in supported bilayers characterized, using single molecule tracking and moment scaling spectrum (MSS) analysis. Diffusion was characterized for individual proteins as either free or confined, revealing details of the local lipid membrane heterogeneity surrounding the protein. A particularly useful result of our bilayer formation process is the protein orientation in the supported planar bilayer. For both the GPI-linked and transmembrane proteins used here, an enzymatic assay revealed that protein orientation in the planar bilayer results in the extracellular domains facing toward the bulk, and that the dominant mode of bleb rupture is via the "parachute" mechanism. Mobility, orientation, and preservation of the native lipid environment of the proteins using cell blebs offers advantages over proteoliposome reconstitution or disrupted cell membrane preparations, which necessarily result in significant scrambling of protein orientation and typically immobilized membrane proteins in SLBs. The bleb-based bilayer platform presented here is an important step toward integrating membrane proteomic studies on chip, especially for future studies aimed at understanding fundamental effects of lipid interactions on protein activity and the roles of membrane proteins in disease pathways.
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Affiliation(s)
- Mark J Richards
- School of Chemical and Biomolecular Engineering, and ‡Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
| | - Chih-Yun Hsia
- School of Chemical and Biomolecular Engineering, and ‡Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
| | - Rohit R Singh
- School of Chemical and Biomolecular Engineering, and ‡Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
| | - Huma Haider
- School of Chemical and Biomolecular Engineering, and ‡Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
| | - Julia Kumpf
- School of Chemical and Biomolecular Engineering, and ‡Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
| | - Toshimitsu Kawate
- School of Chemical and Biomolecular Engineering, and ‡Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
| | - Susan Daniel
- School of Chemical and Biomolecular Engineering, and ‡Department of Molecular Medicine, Cornell University , Ithaca, New York 14853, United States
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21
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Kuo CP, Chang KS, Hsu JL, Tsai IF, Lin AB, Wei TY, Wu CL, Lu YT. Analysis of the immune response of human dendritic cells to Mycobacterium tuberculosis by quantitative proteomics. Proteome Sci 2016; 14:5. [PMID: 26957948 PMCID: PMC4782377 DOI: 10.1186/s12953-016-0095-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 03/01/2016] [Indexed: 12/27/2022] Open
Abstract
Background The cellular immune response for Mycobacterium tuberculosis (M. tuberculosis) infection remained incompletely understood. To uncover membrane proteins involved in this infection mechanism, an integrated approach consisting of an organic solvent-assisted membrane protein digestion, stable-isotope dimethyl labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis was used to comparatively profile the membrane protein expression of human dendritic cells upon heat-killed M. tuberculosis (HKTB) treatment. Results Organic solvent-assisted trypsin digestion coupled with stable-isotope labeling and LC-MS/MS analysis was applied to quantitatively analyze the membrane protein expression of THP-1 derived dendritic cells. We evaluated proteins that were upregulated in response to HKTB treatment, and applied STRING website database to analyze the correlations between these proteins. Of the investigated proteins, aminopeptidase N (CD13) was found to be largely expressed after HKTB treatment. By using confocal microscopy and flow cytometry, we found that membranous CD13 expression was upregulated and was capable of binding to live mycobacteria. Treatment dendritic cell with anti-CD13 antibody during M. tuberculosis infection enhanced the ability of T cell activation. Conclusions Via proteomics data and STRING analysis, we demonstrated that the highly-expressed CD13 is also associated with proteins involved in the antigen presenting process, especially with CD1 proteins. Increasing expression of CD13 on dendritic cells while M. tuberculosis infection and enhancement of T cell activation after CD13 treated with anti-CD13 antibody indicates CD13 positively involved in the pathogenesis of M. tuberculosis. Electronic supplementary material The online version of this article (doi:10.1186/s12953-016-0095-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chiu-Ping Kuo
- Division of Chest Medicine, Department of Internal Medicine, Mackay Memorial Hospital, 92, Sec 2, Chungshan North Road, Taipei, Taiwan
| | - Kuo-Song Chang
- Department of Emergency Medicine, Mackay Memorial Hospital, Taipei, Taiwan.,Mackay Junior College of Medicine, Nursing, and Management, Taipei, Taiwan
| | - Jue-Liang Hsu
- Graduate Institute of Biotechnology, National Pingtung University of Science and Technology, Pingtung, 91201 Taiwan
| | - I-Fang Tsai
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Andrew Boyd Lin
- Biology Department, Case Western Reserve University, Cleveland, OH USA
| | - Tsai-Yin Wei
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Chien-Liang Wu
- Division of Chest Medicine, Department of Internal Medicine, Mackay Memorial Hospital, 92, Sec 2, Chungshan North Road, Taipei, Taiwan.,Mackay Junior College of Medicine, Nursing, and Management, Taipei, Taiwan
| | - Yen-Ta Lu
- Division of Chest Medicine, Department of Internal Medicine, Mackay Memorial Hospital, 92, Sec 2, Chungshan North Road, Taipei, Taiwan.,Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
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22
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Matta C, Zhang X, Liddell S, Smith JR, Mobasheri A. Label-free proteomic analysis of the hydrophobic membrane protein complement in articular chondrocytes: a technique for identification of membrane biomarkers. Biomarkers 2016; 20:572-89. [PMID: 26864288 PMCID: PMC4819840 DOI: 10.3109/1354750x.2015.1130191] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CONTEXT There is insufficient knowledge about the chondrocyte membranome and its molecular composition. OBJECTIVE To develop a Triton X-114 based separation technique using nanoLC-MS/MS combined with shotgun proteomics to identify chondrocyte membrane proteins. MATERIALS AND METHODS Articular chondrocytes from equine metacarpophalangeal joints were separated into hydrophobic and hydrophilic fractions; trypsin-digested proteins were analysed by nanoLC-MS/MS. RESULTS A total of 315 proteins were identified. The phase extraction method yielded a high proportion of membrane proteins (56%) including CD276, S100-A6 and three VDAC isoforms. DISCUSSION Defining the chondrocyte membranome is likely to reveal new biomarker targets for conventional and biological drug discovery.
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Affiliation(s)
- Csaba Matta
- a Department of Veterinary Preclinical Sciences , School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey , Guildford , Surrey , UK .,b Department of Anatomy , Histology and Embryology, Faculty of Medicine, University of Debrecen , Debrecen , Hungary
| | - Xiaofei Zhang
- c Proteomics Laboratory, School of Biosciences, University of Nottingham , Sutton Bonington , UK
| | - Susan Liddell
- c Proteomics Laboratory, School of Biosciences, University of Nottingham , Sutton Bonington , UK
| | | | - Ali Mobasheri
- a Department of Veterinary Preclinical Sciences , School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey , Guildford , Surrey , UK .,e Arthritis Research UK Centre for Sport, Exercise and Osteoarthritis, Arthritis Research UK Pain Centre, Medical Research Council and Arthritis Research UK Centre for Musculoskeletal Ageing Research, University of Nottingham, Queen's Medical Centre , Nottingham , UK , and.,f Center of Excellence in Genomic Medicine Research (CEGMR), King Fahd Medical Research Centre (KFMRC), Faculty of Applied Medical Sciences, King AbdulAziz University , Jeddah , Kingdom of Saudi Arabia
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23
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Zheng L, Abhyankar W, Ouwerling N, Dekker HL, van Veen H, van der Wel NN, Roseboom W, de Koning LJ, Brul S, de Koster CG. Bacillus subtilis Spore Inner Membrane Proteome. J Proteome Res 2016; 15:585-94. [PMID: 26731423 DOI: 10.1021/acs.jproteome.5b00976] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The endospore is the dormant form of Bacillus subtilis and many other Firmicutes. By sporulation, these spore formers can survive very harsh physical and chemical conditions. Yet, they need to go through germination to return to their growing form. The spore inner membrane (IM) has been shown to play an essential role in triggering the initiation of germination. In this study, we isolated the IM of bacterial spores, in parallel with the isolation of the membrane of vegetative cells. With the use of GeLC-MS/MS, over 900 proteins were identified from the B. subtilis spore IM preparations. By bioinformatics-based membrane protein predictions, ca. one-third could be predicted to be membrane-localized. A large number of unique proteins as well as proteins common to the two membrane proteomes were identified. In addition to previously known IM proteins, a number of IM proteins were newly identified, at least some of which are likely to provide new insights into IM physiology, unveiling proteins putatively involved in spore germination machinery and hence putative germination inhibition targets.
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Affiliation(s)
| | | | | | | | - Henk van Veen
- Electron Microscopy Centre Amsterdam, Department of Cell Biology and Histology, Academic Medical Center , 1105 AZ Amsterdam, The Netherlands
| | - Nicole N van der Wel
- Electron Microscopy Centre Amsterdam, Department of Cell Biology and Histology, Academic Medical Center , 1105 AZ Amsterdam, The Netherlands
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24
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Hörmann K, Stukalov A, Müller AC, Heinz LX, Superti-Furga G, Colinge J, Bennett KL. A Surface Biotinylation Strategy for Reproducible Plasma Membrane Protein Purification and Tracking of Genetic and Drug-Induced Alterations. J Proteome Res 2016; 15:647-58. [PMID: 26699813 DOI: 10.1021/acs.jproteome.5b01066] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plasma membrane (PM) proteins contribute to the identity of a cell, mediate contact and communication, and account for more than two-thirds of known drug targets.1-8 In the past years, several protocols for the proteomic profiling of PM proteins have been described. Nevertheless, comparative analyses have mainly focused on different variations of one approach.9-11 We compared sulfo-NHS-SS-biotinylation, aminooxy-biotinylation, and surface coating with silica beads to isolate PM proteins for subsequent analysis by one-dimensional gel-free liquid chromatography mass spectrometry. Absolute and relative numbers of PM proteins and reproducibility parameters on a qualitative and quantitative level were assessed. Sulfo-NHS-SS-biotinylation outperformed aminooxy-biotinylation and surface coating using silica beads for most of the monitored criteria. We further simplified this procedure by a competitive biotin elution strategy achieving an average PM annotated protein fraction of 54% (347 proteins). Computational analysis using additional databases and prediction tools revealed that in total over 90% of the purified proteins were associated with the PM, mostly as interactors. The modified sulfo-NHS-SS-biotinylation protocol was validated by tracking changes in the plasma membrane proteome composition induced by genetic alteration and drug treatment. Glycosylphosphatidylinositol (GPI)-anchored proteins were depleted in PM purifications from cells deficient in the GPI transamidase component PIGS, and treatment of cells with tunicamycin significantly reduced the abundance of N-glycoproteins in surface purifications.
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Affiliation(s)
- Katrin Hörmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , 1090 Vienna, Austria
| | - Alexey Stukalov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , 1090 Vienna, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , 1090 Vienna, Austria
| | - Leonhard X Heinz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , 1090 Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , 1090 Vienna, Austria.,Center for Physiology and Pharmacology, Medical University of Vienna , 1090 Vienna, Austria
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , 1090 Vienna, Austria
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , 1090 Vienna, Austria
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25
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Chen S, Luo Y, Ding G, Xu F. Comparative analysis of Brassica napus plasma membrane proteins under phosphorus deficiency using label-free and MaxQuant-based proteomics approaches. J Proteomics 2015; 133:144-152. [PMID: 26746009 DOI: 10.1016/j.jprot.2015.12.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/14/2015] [Accepted: 12/18/2015] [Indexed: 12/27/2022]
Abstract
UNLABELLED Phosphorus (P) deficiency is a primary constraint for plant growth in terrestrial ecosystems. To better understand the genotypic differences in the adaptation mechanism of Brassica napus to P deficiency, we purified the plasma membrane (PM) from the roots of two genotypes: P-efficient "Eyou Changjia" and P-inefficient "B104-2". Combining label-free quantitative proteomics with the MaxQuant approach, a total of 71 proteins that significantly changed in abundances were identified in the two genotypes in response to P-free starvation, including 31 in "Eyou Changjia" and 40 in "B104-2". Based on comparative genomics study, 28 proteins were mapped to the confidence intervals of quantitative trait loci (QTLs) for P efficiency related traits. Seven decreased proteins with transporter activity were found to be located in the PM by subcellular localization analyses. These proteins involved in intracellular protein transport and ATP hydrolysis coupled proton transport were mapped to the QTL for P content and dry weight. Compared with "B104-2", more decreased proteins referring to transporter activity were found in "Eyou Changjia", showing that substance exchange was decreased in response to short-term P-free starvation. Together with the finding, more decreased proteins functioning in signal transduction and protein synthesis/degradation suggested that "Eyou Changjia" could slow the progression of growth and save more P in response to short-term P-free starvation. BIOLOGICAL SIGNIFICANCE P deficiency seriously limits the production and quality of B. napus. Roots absorb water and nutrients and anchor the plant in the soil. Therefore, to study root PM proteome under P stress would be helpful to understand the adaptation mechanism for P deficiency. However, PM proteome analysis in B. napus has been seldom reported due to the high hydrophobicity and low abundance of PM. Thus, we herein investigated the PM proteome alteration of roots in two B. napus genotypes, with different P deficient tolerances, in response to P-free starvation. The present study offers new insights and novel information for better understanding the adaptative response to P deficiency in B. napus.
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Affiliation(s)
- Shuisen Chen
- National Key Laboratory of Crop Genetic Improvement, and Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biological Science and Technology, Shenyang Agricultural University, Shenyang 110866, China
| | - Ying Luo
- National Key Laboratory of Crop Genetic Improvement, and Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, and Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, and Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China.
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Stöckmann H, Marin VL, Nimmer P, Balut CM, Davidson DJ, Richardson PL, Vasudevan A. Glycan-Mediated, Ligand-Controlled Click Chemistry for Drug-Target Identification. Chembiochem 2015; 17:150-4. [DOI: 10.1002/cbic.201500590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Henning Stöckmann
- Discovery Chemistry and Technology; Oncology Discovery; Integrated Sciences and Technology; AbbVie Inc.; 1 North Waukegan Road North Chicago IL 60064 USA
| | - Violeta L. Marin
- Discovery Chemistry and Technology; Oncology Discovery; Integrated Sciences and Technology; AbbVie Inc.; 1 North Waukegan Road North Chicago IL 60064 USA
| | - Paul Nimmer
- Discovery Chemistry and Technology; Oncology Discovery; Integrated Sciences and Technology; AbbVie Inc.; 1 North Waukegan Road North Chicago IL 60064 USA
| | - Corina M. Balut
- Discovery Chemistry and Technology; Oncology Discovery; Integrated Sciences and Technology; AbbVie Inc.; 1 North Waukegan Road North Chicago IL 60064 USA
| | - Donald J. Davidson
- Discovery Chemistry and Technology; Oncology Discovery; Integrated Sciences and Technology; AbbVie Inc.; 1 North Waukegan Road North Chicago IL 60064 USA
| | - Paul L. Richardson
- Discovery Chemistry and Technology; Oncology Discovery; Integrated Sciences and Technology; AbbVie Inc.; 1 North Waukegan Road North Chicago IL 60064 USA
| | - Anil Vasudevan
- Discovery Chemistry and Technology; Oncology Discovery; Integrated Sciences and Technology; AbbVie Inc.; 1 North Waukegan Road North Chicago IL 60064 USA
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27
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Abstract
The local structure and composition of the outer membrane of an animal cell are important factors in the control of many membrane processes and mechanisms. These include signaling, sorting, and exo- and endocytic processes that are occurring all the time in a living cell. Paradoxically, not only are the local structure and composition of the membrane matters of much debate and discussion, the mechanisms that govern its genesis remain highly controversial. Here, we discuss a swathe of new technological advances that may be applied to understand the local structure and composition of the membrane of a living cell from the molecular scale to the scale of the whole membrane.
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Affiliation(s)
- Thomas S van Zanten
- National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore, 560065, India
| | - Satyajit Mayor
- National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore, 560065, India
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28
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Takakura D, Tada M, Kawasaki N. Membrane glycoproteomics of fetal lung fibroblasts using LC/MS. Proteomics 2015; 16:47-59. [PMID: 26439794 DOI: 10.1002/pmic.201500003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 07/29/2015] [Accepted: 09/28/2015] [Indexed: 11/05/2022]
Abstract
Some aberrant N-glycosylations are being used as tumor markers, and glycoproteomics is expected to provide novel diagnosis markers and targets of drug developments. However, one has trouble in mass spectrometric glycoproteomics of membrane fraction because of lower intensity of glycopeptides in the existence of surfactants. Previously, we developed a glycopeptide enrichment method by acetone precipitation, and it was successfully applied to human serum glycoproteomics. In this study, we confirmed that this method is useful to remove the surfactants and applicable to membrane glycoproteomics. The glycoproteomic approach to the human fetal lung fibroblasts membrane fraction resulted in the identification of over 272 glycoforms on 63 sites of the 44 glycoproteins. According to the existing databases, the structural features on 41 sites are previously unreported. The most frequently occurring forms at N-glycosylation site were high-mannose type containing nine mannose residues (M9) and monosialo-fucosylated biantennary oligosaccharides. Several unexpected N-glycans, such as fucosylated complex-type and fucosylated high-mannose and/or fucosylated pauci-mannose types were found in ER and lysosome proteins. Our method provides new insights into transport, biosynthesis, and degradation of glycoproteins.
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Affiliation(s)
- Daisuke Takakura
- Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
| | - Minoru Tada
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, Setagaya-ku, Tokyo, Japan
| | - Nana Kawasaki
- Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
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29
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Tian Y, Koganti T, Yao Z, Cannon P, Shah P, Pietrovito L, Modesti A, Aiyetan P, DeLeon-Pennell K, Ma Y, Halade GV, Hicks C, Zhang H, Lindsey ML. Cardiac extracellular proteome profiling and membrane topology analysis using glycoproteomics. Proteomics Clin Appl 2015; 8:595-602. [PMID: 24920555 DOI: 10.1002/prca.201400009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 05/23/2014] [Accepted: 06/06/2014] [Indexed: 01/23/2023]
Abstract
PURPOSE Extracellular proteins are easily accessible, which presents a subproteome of molecular targets that have high diagnostic and therapeutic potential. Efforts have been made to catalog the cardiac extracellular matridome and analyze the topology of identified proteins for the design of therapeutic targets. Although many bioinformatics tools have been developed to predict protein topology, topology has been experimentally validated for only a very small portion of membrane proteins. The aim of this study was to use a glycoproteomics and MS approach to identify glycoproteins in the extracellular matridome of the infarcted left ventricle (LV) and provide experimental evidence for topological determination. EXPERIMENTAL DESIGN Glycoproteomics analysis was performed on eight biological replicates of LV samples from wild-type mice at 7 days following myocardial infarction using SPE of glycopeptides, followed by mass spectrometric identification of N-linked glycosylation sites for topology assessment. RESULTS We identified hundreds of glycoproteins, and the identified N-glycosylation sites provide novel information on the correct topology for membrane proteins present in the infarct setting. CONCLUSIONS AND CLINICAL RELEVANCE Our data provide the foundation for future studies of the LV infarct extracellular matridome, which may facilitate the discovery of drug targets and biomarkers.
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Affiliation(s)
- Yuan Tian
- San Antonio Cardiovascular Proteomics Center, San Antonio, TX, USA; Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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30
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Kasvandik S, Sillaste G, Velthut-Meikas A, Mikelsaar AV, Hallap T, Padrik P, Tenson T, Jaakma Ü, Kõks S, Salumets A. Bovine sperm plasma membrane proteomics through biotinylation and subcellular enrichment. Proteomics 2015; 15:1906-20. [PMID: 25603787 DOI: 10.1002/pmic.201400297] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/01/2014] [Accepted: 01/15/2015] [Indexed: 12/27/2022]
Abstract
A significant proportion of mammalian fertilization is mediated through the proteomic composition of the sperm surface. These protein constituents can present as biomarkers to control and regulate breeding of agricultural animals. Previous studies have addressed the bovine sperm cell apical plasma membrane (PM) proteome with nitrogen cavitation enrichment. Alternative workflows would enable to expand the compositional data more globally around the entire sperm's surface. We used a cell surface biotin-labeling in combination with differential centrifugation to enrich sperm surface proteins. Using nano-LC MS/MS, 338 proteins were confidently identified in the PM-enriched proteome. Functional categories of sperm-egg interaction, protein turnover, metabolism as well as molecular transport, spermatogenesis, and signal transduction were represented by proteins with high quantitative signal in our study. A highly significant degree of enrichment was found for transmembrane and PM-targeted proteins. Among them, we also report proteins previously not described on bovine sperm (CPQ, CD58, CKLF, CPVL, GLB1L3, and LPCAT2B) of which CPQ and CPVL cell surface localization was further validated. A descriptive overview of the bovine sperm PM integral and peripheral proteins is provided to complement future studies on animal reproduction and its relation to sperm cell surface. All MS data have been deposited in the ProteomeXchange with identifier PXD001096 (http://proteomecentral.proteomexchange.org/dataset/PXD001096).
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Affiliation(s)
- Sergo Kasvandik
- Proteomics Core Facility, Institute of Technology, University of Tartu, Tartu, Estonia.,Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia.,Department of Obstetrics and Gynaecology, University of Tartu, Tartu, Estonia
| | - Gerly Sillaste
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
| | - Agne Velthut-Meikas
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia.,Department of Obstetrics and Gynaecology, University of Tartu, Tartu, Estonia.,Center for Biology of Integrated Systems, Tallinn University of Technology, Tallinn, Estonia
| | - Aavo-Valdur Mikelsaar
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Triin Hallap
- Department of Reproductive Biology, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Peeter Padrik
- Animal Breeders Association of Estonia, Keava, Kehtna vald, Raplamaa, Estonia
| | - Tanel Tenson
- Proteomics Core Facility, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Ülle Jaakma
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia.,Department of Reproductive Biology, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Sulev Kõks
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia.,Department of Obstetrics and Gynaecology, University of Tartu, Tartu, Estonia.,Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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31
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Musunuri S, Kultima K, Richard BC, Ingelsson M, Lannfelt L, Bergquist J, Shevchenko G. Micellar extraction possesses a new advantage for the analysis of Alzheimer's disease brain proteome. Anal Bioanal Chem 2014; 407:1041-57. [PMID: 25416231 DOI: 10.1007/s00216-014-8320-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/30/2014] [Accepted: 11/03/2014] [Indexed: 12/11/2022]
Abstract
Integral membrane proteins (MPs), such as transporters, receptors, and ion channels, are of great interest because of their participation in various vital cellular functions including cell-cell interactions, ion transport, and signal transduction. However, studies of MPs are complicated because of their hydrophobic nature, heterogeneity, and low abundance. Cloud-point extraction (CPE) with the non-ionic surfactant Triton X-114 was performed to simultaneously extract and phase separate hydrophobic and hydrophilic proteins from Alzheimer's disease (AD) and unaffected control brain tissue. Quantitative proteomics analysis of temporal neocortex samples of AD patients and controls was performed using a shotgun approach based on stable isotope dimethyl labeling (DML) quantification technique followed by nanoLC-MS/MS analysis. A total of 1096 unique proteins were identified and quantified, with 40.3 % (211/524) predicted as integral MPs with at least one transmembrane domain (TMD) found in the detergent phase, and 10 % (80/798) in the detergent-depleted phase. Among these, 62 proteins were shown to be significantly altered (p-value <0.05), in AD versus control samples. In the detergent fraction, we found 10 hydrophobic transmembrane proteins containing up to 14 putative TMDs that were significantly up- or down-regulated in AD compared with control brains. Changes in four of these proteins, alpha-enolase (ENOA), lysosome-associated membrane glycoprotein 1 (LAMP1), 14-3-3 protein gamma (1433G), and sarcoplasmic/endoplasmic reticulum calcium ATPase2 (AT2A2) were validated by immunoblotting. Our results emphasize that separating hydrophobic MPs in CPE contributes to an increased understanding of the underlying molecular mechanisms in AD. Such knowledge can become useful for the development of novel disease biomarkers.
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Affiliation(s)
- Sravani Musunuri
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
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32
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Mermelekas G, Zoidakis J. Mass spectrometry-based membrane proteomics in cancer biomarker discovery. Expert Rev Mol Diagn 2014; 14:549-63. [DOI: 10.1586/14737159.2014.917965] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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33
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Sun B, Hood L. Protein-centric N-glycoproteomics analysis of membrane and plasma membrane proteins. J Proteome Res 2014; 13:2705-14. [PMID: 24754784 PMCID: PMC4053080 DOI: 10.1021/pr500187g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The advent of proteomics technology
has transformed our understanding
of biological membranes. The challenges for studying membrane proteins
have inspired the development of many analytical and bioanalytical
tools, and the techniques of glycoproteomics have emerged as an effective
means to enrich and characterize membrane and plasma-membrane proteomes.
This Review summarizes the development of various glycoproteomics
techniques to overcome the hurdles formed by the unique structures
and behaviors of membrane proteins with a focus on N-glycoproteomics.
Example contributions of N-glycoproteomics to the understanding of
membrane biology are provided, and the areas that require future technical
breakthroughs are discussed.
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Affiliation(s)
- Bingyun Sun
- Department of Chemistry, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia V5A1S6, Canada
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34
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Battle KN, Uba FI, Soper SA. Microfluidics for the analysis of membrane proteins: How do we get there? Electrophoresis 2014; 35:2253-66. [DOI: 10.1002/elps.201300625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/16/2014] [Accepted: 02/17/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Katrina N. Battle
- Department of Chemistry; Louisiana State University; Baton Rouge LA USA
| | - Franklin I. Uba
- Department of Chemistry; University of North Carolina; Chapel Hill NC USA
| | - Steven A. Soper
- Department of Chemistry; Louisiana State University; Baton Rouge LA USA
- Department of Chemistry; University of North Carolina; Chapel Hill NC USA
- Department of Biomedical Engineering; University of North Carolina; Chapel Hill NC USA
- BioFluidica, LLC, c/o Carolina Kick-Start; Chapel Hill NC USA
- School of Nano-Bioscience and Chemical Engineering; Ulsan National Institute of Science and Technology; Ulsan Korea
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35
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Battle KN, Jackson JM, Witek MA, Hupert ML, Hunsucker SA, Armistead PM, Soper SA. Solid-phase extraction and purification of membrane proteins using a UV-modified PMMA microfluidic bioaffinity μSPE device. Analyst 2014; 139:1355-63. [PMID: 24487280 PMCID: PMC3970079 DOI: 10.1039/c3an02400h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We present a novel microfluidic solid-phase extraction (μSPE) device for the affinity enrichment of biotinylated membrane proteins from whole cell lysates. The device offers features that address challenges currently associated with the extraction and purification of membrane proteins from whole cell lysates, including the ability to release the enriched membrane protein fraction from the extraction surface so that they are available for downstream processing. The extraction bed was fabricated in PMMA using hot embossing and was comprised of 3600 micropillars. Activation of the PMMA micropillars by UV/O3 treatment permitted generation of surface-confined carboxylic acid groups and the covalent attachment of NeutrAvidin onto the μSPE device surfaces, which was used to affinity select biotinylated MCF-7 membrane proteins directly from whole cell lysates. The inclusion of a disulfide linker within the biotin moiety permitted release of the isolated membrane proteins via DTT incubation. Very low levels (∼20 fmol) of membrane proteins could be isolated and recovered with ∼89% efficiency with a bed capacity of 1.7 pmol. Western blotting indicated no traces of cytosolic proteins in the membrane protein fraction as compared to significant contamination using a commercial detergent-based method. We highlight future avenues for enhanced extraction efficiency and increased dynamic range of the μSPE device using computational simulations of different micropillar geometries to guide future device designs.
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Affiliation(s)
- Katrina N. Battle
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803-1804, USA
| | - Joshua M. Jackson
- Department of Chemistry, University of North Carolina, Campus Box 3290, Chapel Hill, NC 27599-3290, USA
| | - Małgorzata A. Witek
- Department of Biomedical Engineering, University of North Carolina,152 MacNider Hall Campus Box 7575 Chapel Hill, NC 27599-7575, USA
| | - Mateusz L. Hupert
- Department of Biomedical Engineering, University of North Carolina,152 MacNider Hall Campus Box 7575 Chapel Hill, NC 27599-7575, USA
- BioFluidica, LLC, c/o Carolina Kick-Start, 321 Bondurant Hall, Chapel Hill, NC, 27599
| | - Sally A. Hunsucker
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Paul M. Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Steven A. Soper
- Department of Chemistry, University of North Carolina, Campus Box 3290, Chapel Hill, NC 27599-3290, USA
- Department of Biomedical Engineering, University of North Carolina,152 MacNider Hall Campus Box 7575 Chapel Hill, NC 27599-7575, USA
- BioFluidica, LLC, c/o Carolina Kick-Start, 321 Bondurant Hall, Chapel Hill, NC, 27599
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
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36
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Liu T, Chen JA, Wang W, Simon M, Wu F, Hu W, Chen JB, Zheng H. A combined proteomic and transcriptomic analysis on sulfur metabolism pathways of Arabidopsis thaliana under simulated acid rain. PLoS One 2014; 9:e90120. [PMID: 24595051 PMCID: PMC3940841 DOI: 10.1371/journal.pone.0090120] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 01/27/2014] [Indexed: 11/30/2022] Open
Abstract
With rapid economic development, most regions in southern China have suffered acid rain (AR) pollution. In our study, we analyzed the changes in sulfur metabolism in Arabidopsis under simulated AR stress which provide one of the first case studies, in which the systematic responses in sulfur metabolism were characterized by high-throughput methods at different levels including proteomic, genomic and physiological approaches. Generally, we found that all of the processes related to sulfur metabolism responded to AR stress, including sulfur uptake, activation and also synthesis of sulfur-containing amino acid and other secondary metabolites. Finally, we provided a catalogue of the detected sulfur metabolic changes and reconstructed the coordinating network of their mutual influences. This study can help us to understand the mechanisms of plants to adapt to AR stress.
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Affiliation(s)
- Tingwu Liu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, P. R. China
- Department of Biology, Huaiyin Normal University, Huaian, Jiangsu, P. R. China
| | - Juan A. Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, P. R. China
| | - Wenhua Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, P. R. China
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Martin Simon
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, P. R. China
| | - Feihua Wu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, P. R. China
| | - Wenjun Hu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, P. R. China
| | - Juan B. Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, P. R. China
| | - Hailei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, P. R. China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, P. R. China
- * E-mail:
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37
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Waas M, Bhattacharya S, Chuppa S, Wu X, Jensen DR, Omasits U, Wollscheid B, Volkman BF, Noon KR, Gundry RL. Combine and conquer: surfactants, solvents, and chaotropes for robust mass spectrometry based analyses of membrane proteins. Anal Chem 2014; 86:1551-9. [PMID: 24392666 PMCID: PMC4007983 DOI: 10.1021/ac403185a] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Mass spectrometry
(MS) based proteomic technologies enable the identification and quantification
of membrane proteins as well as their post-translational modifications.
A prerequisite for their quantitative and reliable MS-based bottom-up
analysis is the efficient digestion into peptides by proteases, though
digestion of membrane proteins is typically challenging due to their
inherent properties such as hydrophobicity. Here, we investigated
the effect of eight commercially available MS-compatible surfactants,
two organic solvents, and two chaotropes on the enzymatic digestion
efficiency of membrane protein-enriched complex mixtures in a multiphase
study using a gelfree approach. Multiple parameters, including the
number of peptides and proteins identified, total protein sequence
coverage, and digestion specificity were used to evaluate transmembrane
protein digestion performance. A new open-source software tool was
developed to allow for the specific assessment of transmembrane domain
sequence coverage. Results demonstrate that while Progenta anionic
surfactants outperform other surfactants when tested alone, combinations
of guanidine and acetonitrile improve performance of all surfactants
to near similar levels as well as enhance trypsin specificity to >90%,
which has critical implications for future quantitative and qualitative
proteomic studies.
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Affiliation(s)
- Matthew Waas
- Milwaukee School of Engineering , Milwaukee, Wisconsin 53202, United States
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38
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Liu R, Wang K, Yuan K, Wei Y, Huang C. Integrative oncoproteomics strategies for anticancer drug discovery. Expert Rev Proteomics 2014; 7:411-29. [DOI: 10.1586/epr.10.14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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39
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Tian R. Exploring intercellular signaling by proteomic approaches. Proteomics 2013; 14:498-512. [DOI: 10.1002/pmic.201300259] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/15/2013] [Accepted: 08/28/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Ruijun Tian
- Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; Toronto ON Canada
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40
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Ishihara T, Kakiya K, Takahashi K, Miwa H, Rokushima M, Yoshinaga T, Tanaka Y, Ito T, Togame H, Takemoto H, Amano M, Iwasaki N, Minami A, Nishimura SI. Discovery of novel differentiation markers in the early stage of chondrogenesis by glycoform-focused reverse proteomics and genomics. Biochim Biophys Acta Gen Subj 2013; 1840:645-55. [PMID: 24161698 DOI: 10.1016/j.bbagen.2013.10.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/20/2013] [Accepted: 10/16/2013] [Indexed: 12/18/2022]
Abstract
BACKGROUND Osteoarthritis (OA) is one of the most common chronic diseases among adults, especially the elderly, which is characterized by destruction of the articular cartilage. Despite affecting more than 100 million individuals all over the world, therapy is currently limited to treating pain, which is a principal symptom of OA. New approaches to the treatment of OA that induce regeneration and repair of cartilage are strongly needed. METHODS To discover potent markers for chondrogenic differentiation, glycoform-focused reverse proteomics and genomics were performed on the basis of glycoblotting-based comprehensive approach. RESULTS Expression levels of high-mannose type N-glycans were up-regulated significantly at the late stage of differentiation of the mouse chondroprogenitor cells. Among 246 glycoproteins carrying this glycotype identified by ConA affinity chromatography and LC/MS, it was demonstrated that 52% are classified as cell surface glycoproteins. Gene expression levels indicated that mRNAs for 15 glycoproteins increased distinctly in the earlier stages during differentiation compared with Type II collagen. The feasibility of mouse chondrocyte markers in human chondrogenesis model was demonstrated by testing gene expression levels of these 15 glycoproteins during differentiation in human mesenchymal stem cells. CONCLUSION The results showed clearly an evidence of up-regulation of 5 genes, ectonucleotide pyrophosphatase/phosphodiesterase family member 1, collagen alpha-1(III) chain, collagen alpha-1(XI) chain, aquaporin-1, and netrin receptor UNC5B, in the early stages of differentiation. GENERAL SIGNIFICANCE These cell surface 5 glycoproteins become highly sensitive differentiation markers of human chondrocytes that contribute to regenerative therapies, and development of novel therapeutic reagents.
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Affiliation(s)
- Takeshi Ishihara
- Shionogi Innovation Center for Drug Discovery, Shionogi & Co. Ltd., Kita-ku, Sapporo 001-0021, Japan
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41
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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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Kim SK, Choksawangkarn W, Rose R, Fenselau C, Lee SB. Nanowire pellicles for eukaryotic cells: nanowire coating and interaction with cells. Nanomedicine (Lond) 2013; 9:1171-80. [PMID: 23901782 DOI: 10.2217/nnm.13.96] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
AIM To construct a new robust nanowire-based pellicle for eukaryotic cells, to investigate the interactions between nanowires (NWs) and cell surfaces and the internalization of nanowires, and to demonstrate for isolation of the plasma membrane with improved enrichment of transmembrane proteins. MATERIALS & METHODS Silica NWs were coated with alumina to give positive charges on their surface. Multiple myeloma cells were coated with the positively charged NWs by dropping the cells into a buffered suspension of NWs. After the NW-coated cells were lysed, plasma membrane fragments were enriched by differential centrifugation for proteomic studies. RESULTS Here we demonstrate complete cell coating with positively charged, alumina-coated silica NWs via nonspecific electrostatic interactions, and characterize a robust pellicle and little/no uptake of NWs. CONCLUSION Robust pellicles provide a new platform for therapeutic, diagnostic and biochemical interactions of nanostructures with eukaryotic cells.
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Affiliation(s)
- Sung-Kyoung Kim
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742, USA
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43
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Mun JY, Lee KJ, Seo H, Sung MS, Cho YS, Lee SG, Kwon O, Oh DB. Efficient Adhesion-Based Plasma Membrane Isolation for Cell Surface N-Glycan Analysis. Anal Chem 2013; 85:7462-70. [DOI: 10.1021/ac401431u] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - Min-Sun Sung
- Biosystems and
Bioengineering
Program, University of Science and Technology (UST), Daejeon 305-350, South Korea
| | | | - Seung-Goo Lee
- Biosystems and
Bioengineering
Program, University of Science and Technology (UST), Daejeon 305-350, South Korea
| | - Ohsuk Kwon
- Biosystems and
Bioengineering
Program, University of Science and Technology (UST), Daejeon 305-350, South Korea
| | - Doo-Byoung Oh
- Biosystems and
Bioengineering
Program, University of Science and Technology (UST), Daejeon 305-350, South Korea
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44
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Kalli A, Smith GT, Sweredoski MJ, Hess S. Evaluation and optimization of mass spectrometric settings during data-dependent acquisition mode: focus on LTQ-Orbitrap mass analyzers. J Proteome Res 2013; 12:3071-86. [PMID: 23642296 DOI: 10.1021/pr3011588] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass-spectrometry-based proteomics has evolved as the preferred method for the analysis of complex proteomes. Undoubtedly, recent advances in mass spectrometry instrumentation have greatly enhanced proteomic analysis. A popular instrument platform in proteomics research is the LTQ-Orbitrap mass analyzer. In this tutorial, we discuss the significance of evaluating and optimizing mass spectrometric settings on the LTQ-Orbitrap during CID data-dependent acquisition (DDA) mode to improve protein and peptide identification rates. We focus on those MS and MS/MS parameters that have been systematically examined and evaluated by several researchers and are commonly used during DDA. More specifically, we discuss the effect of mass resolving power, preview mode for FTMS scan, monoisotopic precursor selection, signal threshold for triggering MS/MS events, number of microscans per MS/MS scan, number of MS/MS events, automatic gain control target value (ion population) for MS and MS/MS, maximum ion injection time for MS/MS, rapid and normal scan rate, and prediction of ion injection time. We furthermore present data from the latest generation LTQ-Orbitrap system, the Orbitrap Elite, along with recommended MS and MS/MS parameters. The Orbitrap Elite outperforms the Orbitrap Classic in terms of scan speed, sensitivity, dynamic range, and resolving power and results in higher identification rates. Several of the optimized MS parameters determined on the LTQ-Orbitrap Classic and XL were easily transferable to the Orbitrap Elite, whereas others needed to be reevaluated. Finally, the Q Exactive and HCD are briefly discussed, as well as sample preparation, LC-optimization, and bioinformatics analysis. We hope this tutorial will serve as guidance for researchers new to the field of proteomics and assist in achieving optimal results.
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Affiliation(s)
- Anastasia Kalli
- Proteome Exploration Laboratory, Division of Biology, Beckman Institute, California Institute of Technology, Pasadena, California 91125, USA
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Renes J, Mariman E. Application of proteomics technology in adipocyte biology. MOLECULAR BIOSYSTEMS 2013; 9:1076-91. [PMID: 23629546 DOI: 10.1039/c3mb25596d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Obesity and its associated complications have reached epidemic proportions in Western-type societies. Concomitantly, the obesity incidence in developing countries is increasing. One hallmark of obesity is the differentiation of pre-adipocytes into mature triglyceride-loaded adipocytes present in subcutaneous and visceral adipose tissue depots. This may ultimately lead to dysfunctional adipose tissue together with detrimental changes in the profiles of (pre-)adipocyte-secreted proteins, known as adipokines. Obesity-induced alterations in adipokine profiles contribute to the development of obesity-associated disorders. Consequently, the interest in the molecular events responsible for adipose tissue modifications during weight gain and weight loss as well as in the aetiology of obesity-associated disorders is growing. Molecular mechanisms involved in pre-adipocyte differentiation and alterations in adipokine profiles have been examined at the gene and protein level by high-throughput technologies. Independent proteomics studies have contributed significantly to further insight into adipocyte biology, particularly with respect to adipokine profiling. In this review novel findings obtained with adipo-proteomics studies are highlighted and the relevance of proteomics technologies to further understand molecular aspects of adipocyte biology is discussed.
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Affiliation(s)
- Johan Renes
- Department of Human Biology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
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46
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Liddy KA, White MY, Cordwell SJ. Functional decorations: post-translational modifications and heart disease delineated by targeted proteomics. Genome Med 2013; 5:20. [PMID: 23445784 PMCID: PMC3706772 DOI: 10.1186/gm424] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The more than 300 currently identified post-translational modifications (PTMs) provides great scope for subtle or dramatic alteration of protein structure and function. Furthermore, the rapid and transient nature of many PTMs allows efficient signal transmission in response to internal and environmental stimuli. PTMs are predominantly added by enzymes, and the enzymes responsible (such as kinases) are thus attractive targets for therapeutic interventions. Modifications can be grouped according to their stability or transience (reversible versus irreversible): irreversible types (such as irreversible redox modifications or protein deamidation) are often associated with aging or tissue injury, whereas transient modifications are associated with signal propagation and regulation. This is particularly important in the setting of heart disease, which comprises a diverse range of acute (such as ischemia/reperfusion), chronic (such as heart failure, dilated cardiomyopathy) and genetic (such as hypertrophic cardiomyopathy) disease states, all of which have been associated with protein PTM. Recently the interplay between diverse PTMs has been suggested to also influence cellular function, with cooperation or competition for sites of modification possible. Here we discuss the utility of proteomics for examining PTMs in the context of the molecular mechanisms of heart disease.
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Affiliation(s)
- Kiersten A Liddy
- School of Molecular Bioscience, The University of Sydney, 2006 Sydney, Australia
| | - Melanie Y White
- School of Molecular Bioscience, The University of Sydney, 2006 Sydney, Australia ; Discipline of Pathology, School of Medical Sciences, The University of Sydney, 2006 Sydney, Australia
| | - Stuart J Cordwell
- School of Molecular Bioscience, The University of Sydney, 2006 Sydney, Australia ; Discipline of Pathology, School of Medical Sciences, The University of Sydney, 2006 Sydney, Australia
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47
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Lai X, Wang L, Witzmann FA. Issues and applications in label-free quantitative mass spectrometry. INTERNATIONAL JOURNAL OF PROTEOMICS 2013; 2013:756039. [PMID: 23401775 PMCID: PMC3562690 DOI: 10.1155/2013/756039] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 10/17/2012] [Accepted: 10/31/2012] [Indexed: 11/17/2022]
Abstract
To address the challenges associated with differential expression proteomics, label-free mass spectrometric protein quantification methods have been developed as alternatives to array-based, gel-based, and stable isotope tag or label-based approaches. In this paper, we focus on the issues associated with label-free methods that rely on quantitation based on peptide ion peak area measurement. These issues include chromatographic alignment, peptide qualification for quantitation, and normalization. In addressing these issues, we present various approaches, assembled in a recently developed label-free quantitative mass spectrometry platform, that overcome these difficulties and enable comprehensive, accurate, and reproducible protein quantitation in highly complex protein mixtures from experiments with many sample groups. As examples of the utility of this approach, we present a variety of cases where the platform was applied successfully to assess differential protein expression or abundance in body fluids, in vitro nanotoxicology models, tissue proteomics in genetic knock-in mice, and cell membrane proteomics.
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Affiliation(s)
- Xianyin Lai
- Department of Cellular & Integrative Physiology, Biotechnology Research & Training Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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48
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Scheffer KD, Popa-Wagner R, Florin L. Isolation and characterization of pathogen-bearing endosomes enable analysis of endosomal escape and identification of new cellular cofactors of infection. Methods Mol Biol 2013; 1064:101-13. [PMID: 23996252 DOI: 10.1007/978-1-62703-601-6_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Many pathogens, including viruses, bacteria, as well as bacterial toxins, enter their target cells by endocytosis leading to accumulation of pathogenic and cellular proteins in endosomes. Here, we present detailed experimental instructions on isolation of endosomes after virus infection and their subsequent biomolecular characterization. The isolation of endosomes is based on discontinuous sucrose gradient centrifugation, where different endosomal compartments accumulate at a specific sucrose interface. This enables the enrichment and separation of the virus-interacting and co-internalized cell-surface receptors and membrane-associated proteins. The endosomal fractions can be further analyzed by Western blot or quantitative real-time PCR, which reveals changes in the viral protein or DNA content during the processes of endocytosis and endosomal escape. In addition, comparative quantitative mass spectrometry enables the identification of unknown host-cell factors required for infection.
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Affiliation(s)
- Konstanze D Scheffer
- Department of Medical Microbiology and Hygiene, Johannes Gutenberg University Mainz, Mainz, Germany
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Won KJ, Lee KP, Kim DK, Jung SH, Lee CK, Lee DH, Yu SY, Park SH, Lee HM, Kim B. Monoclonal Antibody against a-Actinin 4 from Human Umbilical Vein Endothelial Cells Inhibits Endothelium-Dependent Vasorelaxation. J Vasc Res 2013; 50:210-20. [DOI: 10.1159/000350588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 03/06/2013] [Indexed: 11/19/2022] Open
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50
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Kohnke PL, Mactier S, Almazi JG, Crossett B, Christopherson RI. Fludarabine and Cladribine Induce Changes in Surface Proteins on Human B-Lymphoid Cell Lines Involved with Apoptosis, Cell Survival, and Antitumor Immunity. J Proteome Res 2012; 11:4436-48. [DOI: 10.1021/pr300079c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Philippa L. Kohnke
- School of
Molecular Bioscience, University of Sydney,
Sydney, NSW 2006, Australia
| | - Swetlana Mactier
- School of
Molecular Bioscience, University of Sydney,
Sydney, NSW 2006, Australia
| | - Juhura G. Almazi
- School of
Molecular Bioscience, University of Sydney,
Sydney, NSW 2006, Australia
| | - Ben Crossett
- School of
Molecular Bioscience, University of Sydney,
Sydney, NSW 2006, Australia
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