1
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Garapati K, Ding H, Charlesworth MC, Kim Y, Zenka R, Saraswat M, Mun DG, Chavan S, Shingade A, Lucien F, Zhong J, Kandasamy RK, Pandey A. sBioSITe enables sensitive identification of the cell surface proteome through direct enrichment of biotinylated peptides. Clin Proteomics 2023; 20:56. [PMID: 38053024 PMCID: PMC10696767 DOI: 10.1186/s12014-023-09445-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Cell surface proteins perform critical functions related to immune response, signal transduction, cell-cell interactions, and cell migration. Expression of specific cell surface proteins can determine cell-type identity, and can be altered in diseases including infections, cancer and genetic disorders. Identification of the cell surface proteome remains a challenge despite several enrichment methods exploiting their biochemical and biophysical properties. METHODS Here, we report a novel method for enrichment of proteins localized to cell surface. We developed this new approach designated surface Biotinylation Site Identification Technology (sBioSITe) by adapting our previously published method for direct identification of biotinylated peptides. In this strategy, the primary amine groups of lysines on proteins on the surface of live cells are first labeled with biotin, and subsequently, biotinylated peptides are enriched by anti-biotin antibodies and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS By direct detection of biotinylated lysines from PC-3, a prostate cancer cell line, using sBioSITe, we identified 5851 peptides biotinylated on the cell surface that were derived from 1409 proteins. Of these proteins, 533 were previously shown or predicted to be localized to the cell surface or secreted extracellularly. Several of the identified cell surface markers have known associations with prostate cancer and metastasis including CD59, 4F2 cell-surface antigen heavy chain (SLC3A2) and adhesion G protein-coupled receptor E5 (CD97). Importantly, we identified several biotinylated peptides derived from plectin and nucleolin, both of which are not annotated in surface proteome databases but have been shown to have aberrant surface localization in certain cancers highlighting the utility of this method. CONCLUSIONS Detection of biotinylation sites on cell surface proteins using sBioSITe provides a reliable method for identifying cell surface proteins. This strategy complements existing methods for detection of cell surface expressed proteins especially in discovery-based proteomics approaches.
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Affiliation(s)
- Kishore Garapati
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Husheng Ding
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Yohan Kim
- Department of Urology, Mayo Clinic, Rochester, MN, USA
| | - Roman Zenka
- Proteomics Core, Mayo Clinic, Rochester, MN, USA
| | - Mayank Saraswat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Dong-Gi Mun
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Sandip Chavan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Ashish Shingade
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Fabrice Lucien
- Department of Urology, Mayo Clinic, Rochester, MN, USA
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Jun Zhong
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Richard K Kandasamy
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
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2
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Almeida-Pinto J, Lagarto MR, Lavrador P, Mano JF, Gaspar VM. Cell Surface Engineering Tools for Programming Living Assemblies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304040. [PMID: 37823678 DOI: 10.1002/advs.202304040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/10/2023] [Indexed: 10/13/2023]
Abstract
Breakthroughs in precision cell surface engineering tools are supporting the rapid development of programmable living assemblies with valuable features for tackling complex biological problems. Herein, the authors overview the most recent technological advances in chemically- and biologically-driven toolboxes for engineering mammalian cell surfaces and triggering their assembly into living architectures. A particular focus is given to surface engineering technologies for enabling biomimetic cell-cell social interactions and multicellular cell-sorting events. Further advancements in cell surface modification technologies may expand the currently available bioengineering toolset and unlock a new generation of personalized cell therapeutics with clinically relevant biofunctionalities. The combination of state-of-the-art cell surface modifications with advanced biofabrication technologies is envisioned to contribute toward generating living materials with increasing tissue/organ-mimetic bioactivities and therapeutic potential.
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Affiliation(s)
- José Almeida-Pinto
- Department of Chemistry, CICECO-Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Matilde R Lagarto
- Department of Chemistry, CICECO-Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Pedro Lavrador
- Department of Chemistry, CICECO-Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - João F Mano
- Department of Chemistry, CICECO-Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
| | - Vítor M Gaspar
- Department of Chemistry, CICECO-Aveiro Institute of Materials University of Aveiro Campus Universitário de Santiago, Aveiro, 3810-193, Portugal
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3
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Application of plasma membrane proteomics to identify cancer biomarkers. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00008-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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4
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Wojdyla K, Collier AJ, Fabian C, Nisi PS, Biggins L, Oxley D, Rugg-Gunn PJ. Cell-Surface Proteomics Identifies Differences in Signaling and Adhesion Protein Expression between Naive and Primed Human Pluripotent Stem Cells. Stem Cell Reports 2020; 14:972-988. [PMID: 32302559 PMCID: PMC7220956 DOI: 10.1016/j.stemcr.2020.03.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 12/19/2022] Open
Abstract
Naive and primed human pluripotent stem cells (hPSC) provide valuable models to study cellular and molecular developmental processes. The lack of detailed information about cell-surface protein expression in these two pluripotent cell types prevents an understanding of how the cells communicate and interact with their microenvironments. Here, we used plasma membrane profiling to directly measure cell-surface protein expression in naive and primed hPSC. This unbiased approach quantified over 1,700 plasma membrane proteins, including those involved in cell adhesion, signaling, and cell interactions. Notably, multiple cytokine receptors upstream of JAK-STAT signaling were more abundant in naive hPSC. In addition, functional experiments showed that FOLR1 and SUSD2 proteins are highly expressed at the cell surface in naive hPSC but are not required to establish human naive pluripotency. This study provides a comprehensive stem cell proteomic resource that uncovers differences in signaling pathway activity and has identified new markers to define human pluripotent states.
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Affiliation(s)
- Katarzyna Wojdyla
- Epigenetics Programme, The Babraham Institute, Cambridge, UK; Mass Spectrometry Facility, The Babraham Institute, Cambridge, UK
| | | | - Charlene Fabian
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Paola S Nisi
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Laura Biggins
- Bioinformatics Group, The Babraham Institute, Cambridge, UK
| | - David Oxley
- Mass Spectrometry Facility, The Babraham Institute, Cambridge, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge, UK; Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
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5
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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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6
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CiliaCarta: An integrated and validated compendium of ciliary genes. PLoS One 2019; 14:e0216705. [PMID: 31095607 PMCID: PMC6522010 DOI: 10.1371/journal.pone.0216705] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/26/2019] [Indexed: 12/25/2022] Open
Abstract
The cilium is an essential organelle at the surface of mammalian cells whose dysfunction causes a wide range of genetic diseases collectively called ciliopathies. The current rate at which new ciliopathy genes are identified suggests that many ciliary components remain undiscovered. We generated and rigorously analyzed genomic, proteomic, transcriptomic and evolutionary data and systematically integrated these using Bayesian statistics into a predictive score for ciliary function. This resulted in 285 candidate ciliary genes. We generated independent experimental evidence of ciliary associations for 24 out of 36 analyzed candidate proteins using multiple cell and animal model systems (mouse, zebrafish and nematode) and techniques. For example, we show that OSCP1, which has previously been implicated in two distinct non-ciliary processes, causes ciliogenic and ciliopathy-associated tissue phenotypes when depleted in zebrafish. The candidate list forms the basis of CiliaCarta, a comprehensive ciliary compendium covering 956 genes. The resource can be used to objectively prioritize candidate genes in whole exome or genome sequencing of ciliopathy patients and can be accessed at http://bioinformatics.bio.uu.nl/john/syscilia/ciliacarta/.
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7
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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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8
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Wang X, Liang S. Gel Absorption-Based Sample Preparation Method for Shotgun Analysis of Membrane Proteome. Methods Mol Biol 2019; 1855:483-490. [PMID: 30426442 DOI: 10.1007/978-1-4939-8793-1_41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Membrane proteins solubilized in a starting buffer containing high concentration of SDS are directly entrapped and immobilized into gel matrix when the membrane protein solution is absorbed by the vacuum-dried polyacrylamide gel. After the detergent and other salts are removed by washing, the proteins are subjected to in-gel digestion, and the tryptic peptides are extracted and analyzed by CapLC-MS/MS. The newly developed method not only avoids protein loss and the adverse protein modifications during gel-embedment but also improves the subsequent in-gel digestion and the recovery of tryptic peptides, particularly hydrophobic peptides. Thus, this method facilitates the identification of membrane proteins, especially integral membrane proteins.
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Affiliation(s)
- Xianchun Wang
- College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, China.
| | - Songping Liang
- College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, China
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9
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Taleb RSZ, Moez P, Younan D, Eisenacher M, Tenbusch M, Sitek B, Bracht T. Protein Biomarker Discovery Using Human Blood Plasma Microparticles. Methods Mol Biol 2019; 1959:51-64. [PMID: 30852815 DOI: 10.1007/978-1-4939-9164-8_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cells shed into the extracellular space a population of membranous vesicles of plasma membrane origin called microparticles (MP). Given the fact that MP are abundantly present in body fluids including plasma, rich in cell-type or disease-specific proteins and formed in conditions of stress and injury, they have been extensively investigated as biomarkers in various diseases. With the advancement in the mass spectrometry-based proteome analysis, the knowledge of the protein composition of plasma MP (PMP) has been intensively expanded, which aids the discovery of novel diagnostic target proteins. However, the lack of standardized and accurate protocols for PMP isolation limits the implementation of PMP as biomarkers in clinical settings. Here, we describe in detail a robust protocol for PMP isolation from human blood plasma via ultracentrifugation followed by label-free quantitative proteome analysis of PMP.
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Affiliation(s)
- Raghda Saad Zaghloul Taleb
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
- Clinical and Chemical Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Pacint Moez
- Clinical and Chemical Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Doreen Younan
- Clinical and Chemical Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Matthias Tenbusch
- Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Barbara Sitek
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Thilo Bracht
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
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10
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Wang D, Ba H, Li C, Zhao Q, Li C. Proteomic Analysis of Plasma Membrane Proteins of Antler Stem Cells Using Label-Free LC⁻MS/MS. Int J Mol Sci 2018; 19:E3477. [PMID: 30400663 PMCID: PMC6275008 DOI: 10.3390/ijms19113477] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/31/2018] [Accepted: 11/03/2018] [Indexed: 12/16/2022] Open
Abstract
Deer antlers are unusual mammalian organs that can fully regenerate after annual shedding. Stem cells resident in the pedicle periosteum (PPCs) provide the main cell source for antler regeneration. Central to various cellular processes are plasma membrane proteins, but the expression of these proteins has not been well documented in antler regeneration. In the present study, plasma membrane proteins of PPCs and facial periosteal cells (FPCs) were analyzed using label-free liquid chromatography⁻mass spetrometry (LC⁻MS/MS). A total of 1739 proteins were identified. Of these proteins, 53 were found solely in the PPCs, 100 solely in the FPCs, and 1576 co-existed in both PPCs and FPCs; and 39 were significantly up-regulated in PPCs and 49 up-regulated in FPCs. In total, 226 gene ontology (GO) terms were significantly enriched from the differentially expressed proteins (DEPs). Five clusters of biological processes from these GO terms comprised responses to external stimuli, signal transduction, membrane transport, regulation of tissue regeneration, and protein modification processes. Further studies are required to demonstrate the relevancy of these DEPs in antler stem cell biology and antler regeneration.
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Affiliation(s)
- Datao Wang
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
| | - Hengxing Ba
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
| | - Chenguang Li
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China.
| | - Quanmin Zhao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China.
| | - Chunyi Li
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
- Department of Biology, Changchun Sci-Tech University, Changchun 130600, China.
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11
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Moreira RF, Matos MNC, Alves JG, do Valle RV, Eloy AMX, Pinto TMF, Machado SP, Costa CRR, de Lima JL, Lima JPMS, da Cunha RMS. Diversity of ejaculated sperm proteins in Moxotó bucks ( Capra hircus ) evaluated by multiple extraction methods. Anim Reprod 2018; 15:84-92. [PMID: 33365100 PMCID: PMC7746222 DOI: 10.21451/1984-3143-2017-ar966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
This study aimed to develop protocols for the extraction of sperm proteins from Moxotó
goats (Capra hircus) and to compare the resulting proteomic maps. The
sperm proteins were isolated using an extraction buffer containing 7 M urea and 2 M thiourea,
20 mM DTT, and one of the following detergents: 1% or 4% CHAPS; 1% or 4% SDS; 1% or 4% Triton X-100;
or a combination of CHAPS and SDS. The 1-DE and 2-DE profiles of the isolated proteins revealed
that the various isolation methods were efficient. Qualitative and quantitative differences
in the 1-DE and 2-DE profiles were observed. 2-DE maps indicated that the amount and diversity
of proteins visualized depended on the detergent that was used. Furthermore, this work revealed
that the combination of detergents increased the resolution of some spots and retained the
characteristics of the individual detergents, depending on their concentrations.
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Affiliation(s)
- Raulzito Fernandes Moreira
- Departamento de Biotecnologia, Universidade Federal do Ceará (UFC), programa de pós-graduação em biotecnologia (PPGB), Sobral, CE, .,Núcleo de Biotecnologia de Sobral (NUBIS), Universidade Estadual Vale do Acaraú (UVA), Sobral, Ceará,
| | - Maria Nágila Carneiro Matos
- Departamento de Biotecnologia, Universidade Federal do Ceará (UFC), programa de pós-graduação em biotecnologia (PPGB), Sobral, CE, .,Núcleo de Biotecnologia de Sobral (NUBIS), Universidade Estadual Vale do Acaraú (UVA), Sobral, Ceará,
| | - João Garcia Alves
- Núcleo de Biotecnologia de Sobral (NUBIS), Universidade Estadual Vale do Acaraú (UVA), Sobral, Ceará,
| | - Roberta Vianna do Valle
- Departamento de Zootecnia, Universidade Estadual Vale do Acaraú (UVA), Programa de Pós-Graduação em Zootecnia (PPGZ), Sobral, CE
| | - Angela Maria Xavier Eloy
- Departamento de Zootecnia, Universidade Estadual Vale do Acaraú (UVA), Programa de Pós-Graduação em Zootecnia (PPGZ), Sobral, CE.,Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA Caprinos e Ovinos), Sobral, CE,
| | - Tatiana Maria Farias Pinto
- Departamento de Zootecnia, Universidade Estadual Vale do Acaraú (UVA), Programa de Pós-Graduação em Zootecnia (PPGZ), Sobral, CE.,Núcleo de Biotecnologia de Sobral (NUBIS), Universidade Estadual Vale do Acaraú (UVA), Sobral, Ceará,
| | | | | | - José Luiz de Lima
- Laboratório de imunopatologia keizo Asami (LIKA), Departamento de Bioquímica, , ,
| | - João Paulo Matos Santos Lima
- Departamento de Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, Brasil. Endereço: Campus Universitário Lagoa Nova, ,
| | - Rodrigo Maranguape Silva da Cunha
- Departamento de Biotecnologia, Universidade Federal do Ceará (UFC), programa de pós-graduação em biotecnologia (PPGB), Sobral, CE, .,Núcleo de Biotecnologia de Sobral (NUBIS), Universidade Estadual Vale do Acaraú (UVA), Sobral, Ceará,
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12
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Yang# Y, Yu# J, Esfahani AM, Seiffert-Sinha K, Xi N, Lee I, Sinha AA, Chen L, Sun Z, Yang R, Dong L. Single-cell membrane drug delivery using porous pen nanodeposition. NANOSCALE 2018; 10:12704-12712. [PMID: 29946596 PMCID: PMC6528655 DOI: 10.1039/c8nr02600a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Delivering molecules onto the plasma membrane of single cells is still a challenging task in profiling cell signaling pathways with single cell resolution. We demonstrated that a large quantity of molecules could be targeted and released onto the membrane of individual cells to trigger signaling responses. This is achieved by a porous pen nanodeposition (PPN) method, in which a multilayer porous structure, serving as a reservoir for a large amount of molecules, is formed on an atomic force microscope (AFM) tip using layer-by-layer assembly and post processing. To demonstrate its capability for single cell membrane drug delivery, PPN was employed to induce a calcium flux triggered by the binding of released antibodies to membrane antigens in an autoimmune skin disease model. This calcium signal propagates from the target cell to its neighbors in a matter of seconds, proving the theory of intercellular communication through cell-cell junctions. Collectively, these results demonstrated the effectiveness of PPN in membrane drug delivery for single cells; to the best of our knowledge, this is the first technique that can perform the targeted transport and delivery in single cell resolution, paving the way for probing complex signaling interactions in multicellular settings.
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Affiliation(s)
- Yongliang Yang#
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA,
| | - Jing Yu#
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA
| | - Amir Monemian Esfahani
- Department of Mechanical and Materials Engineering, University of Nebraska -Lincoln, Lincoln, NE 68588, USA
| | | | - Ning Xi
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Ilsoon Lee
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA
| | - Animesh A. Sinha
- Department of Dermatology, University at Buffalo, Buffalo, New York 14203, USA
| | - Liangliang Chen
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Zhiyong Sun
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Ruiguo Yang
- Department of Mechanical and Materials Engineering, University of Nebraska -Lincoln, Lincoln, NE 68588, USA,
| | - Lixin Dong
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA,
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13
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Andjelković U, Josić D. Mass spectrometry based proteomics as foodomics tool in research and assurance of food quality and safety. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2018.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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14
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Martinović T, Šrajer Gajdošik M, Josić D. Sample preparation in foodomic analyses. Electrophoresis 2018; 39:1527-1542. [DOI: 10.1002/elps.201800029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/12/2018] [Accepted: 03/27/2018] [Indexed: 12/30/2022]
Affiliation(s)
| | | | - Djuro Josić
- Department of Biotechnology; University of Rijeka; Rijeka Croatia
- Department of Medicine; Brown Medical School; Brown University; Providence RI USA
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15
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Lin Q, Peng S, Yang Y. Inhibition of CD9 expression reduces the metastatic capacity of human hepatocellular carcinoma cell line MHCC97-H. Int J Oncol 2018; 53:266-274. [PMID: 29749468 DOI: 10.3892/ijo.2018.4381] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 04/17/2018] [Indexed: 11/06/2022] Open
Abstract
Metastasis is a characteristic of malignant tumors and may be a fatal clinical factor for many patients with cancer. Hepatocellular carcinoma (HCC) cells are highly metastatic; the mechanism of metastasis is complicated and may be influenced by a number of factors. Membrane proteins may block receptors or inhibit important enzymes, thus inhibiting tumor progression, and may be potential therapeutic targets for tumor prognosis and treatment. The present study aimed to use proteomics to analyze the dynamic changes of membrane proteins in HCC cells, to improve our understanding of membrane protein functions and to clarify the important components of the mechanisms of HCC metastasis. The present study used the highly metastatic MHCC97-H and the lowly metastatic MHCC97-L HCC cell lines, and the isobaric tags for relative and absolute quantitation (iTRAQ) approach was used for high-throughput screening of metastasis-related membrane proteins. A total of 22 membrane proteins were identified as differentially expressed between the MHCC97-H and MHCC97-L cell lines; these results were verified by reverse transcription-quantitative polymerase chain reaction and western blotting. A number of the identified proteins were revealed to be related to tumor metastasis, including the tetraspan in transmembrane protein CD9. CD9 was demonstrated to be highly expressed in MHCC97-H cells compared with MHCC97-L cells. The functional role of CD9 was characterized by inhibiting its expression using a small interfering RNAs, which demonstrated that reduced CD9 expression inhibited cell migration and metastasis, as determined by wound-healing and invasion assays. Results from the present study demonstrated that CD9 was highly expressed in the highly metastatic HCC cells and promoted HCC cell migration. This protein may be a novel target for regulating the invasive phenotype in HCC.
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Affiliation(s)
- Qing Lin
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, P.R. China
| | - Shifang Peng
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yixuan Yang
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, P.R. China
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16
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Yoon C, Song H, Yin T, Bausch-Fluck D, Frei AP, Kattman S, Dubois N, Witty AD, Hewel JA, Guo H, Emili A, Wollscheid B, Keller G, Zandstra PW. FZD4 Marks Lateral Plate Mesoderm and Signals with NORRIN to Increase Cardiomyocyte Induction from Pluripotent Stem Cell-Derived Cardiac Progenitors. Stem Cell Reports 2017; 10:87-100. [PMID: 29249665 PMCID: PMC5768897 DOI: 10.1016/j.stemcr.2017.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 01/14/2023] Open
Abstract
The identification of cell surface proteins on stem cells or stem cell derivatives is a key strategy for the functional characterization, isolation, and understanding of stem cell population dynamics. Here, using an integrated mass spectrometry- and microarray-based approach, we analyzed the surface proteome and transcriptome of cardiac progenitor cells (CPCs) generated from the stage-specific differentiation of mouse and human pluripotent stem cells. Through bioinformatics analysis, we have identified and characterized FZD4 as a marker for lateral plate mesoderm. Additionally, we utilized FZD4, in conjunction with FLK1 and PDGFRA, to further purify CPCs and increase cardiomyocyte (CM) enrichment in both mouse and human systems. Moreover, we have shown that NORRIN presented to FZD4 further increases CM output via proliferation through the canonical WNT pathway. Taken together, these findings demonstrate a role for FZD4 in mammalian cardiac development. Identified and characterized FZD4 as a new marker for lateral plate mesoderm FZD4, in conjunction with FLK1 and PDGFRA, increases cardiomyocyte enrichment FZD4 is expressed in the human system and shows enrichment in cardiomyocytes NORRIN addition shows increase in cardiomyocyte output from FZD4 progenitor cells
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Affiliation(s)
- Charles Yoon
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Hannah Song
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Ting Yin
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Damaris Bausch-Fluck
- Institute of Molecular Systems Biology at the Department of Health Sciences and Technology, Zurich 8092, Switzerland
| | - Andreas P Frei
- Institute of Molecular Systems Biology at the Department of Health Sciences and Technology, Zurich 8092, Switzerland
| | - Steven Kattman
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Nicole Dubois
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Alec D Witty
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Johannes A Hewel
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hongbo Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andrew Emili
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Bernd Wollscheid
- Institute of Molecular Systems Biology at the Department of Health Sciences and Technology, Zurich 8092, Switzerland
| | - Gordon Keller
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Centre for Commercialization of Regenerative Medicine, Toronto, ON M5G 1M1, Canada; Medicine by Design: A Canada First Research Excellence Fund Program, University of Toronto, Toronto, ON M5G 1M1, Canada.
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17
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Üretmen Kagıalı ZC, Şentürk A, Özkan Küçük NE, Qureshi MH, Özlü N. Proteomics in Cell Division. Proteomics 2017; 17. [PMID: 28548456 DOI: 10.1002/pmic.201600100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/07/2017] [Indexed: 11/08/2022]
Abstract
Cell division requires a coordinated action of the cell cycle machinery, cytoskeletal elements, chromosomes, and membranes. Cell division studies have greatly benefitted from the mass spectrometry (MS)-based proteomic approaches for probing the biochemistry of highly dynamic complexes and their coordination with each other as a cell progresses into division. In this review, the authors first summarize a wide-range of proteomic studies that focus on the identification of sub-cellular components/protein complexes of the cell division machinery including kinetochores, mitotic spindle, midzone, and centrosomes. The authors also highlight MS-based large-scale analyses of the cellular components that are largely understudied during cell division such as the cell surface and lipids. Then, the authors focus on posttranslational modification analyses, especially phosphorylation and the resulting crosstalk with other modifications as a cell undergoes cell division. Combining proteomic approaches that probe the biochemistry of cell division components with functional genomic assays will lead to breakthroughs toward a systems-level understanding of cell division.
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Affiliation(s)
| | - Aydanur Şentürk
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | | | - Mohammad Haroon Qureshi
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey.,Biomedical Sciences and Engineering, Koç University, Istanbul, Turkey
| | - Nurhan Özlü
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
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18
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Andjelković U, Šrajer Gajdošik M, Gašo-Sokač D, Martinović T, Josić D. Foodomics and Food Safety: Where We Are. Food Technol Biotechnol 2017; 55:290-307. [PMID: 29089845 PMCID: PMC5654429 DOI: 10.17113/ftb.55.03.17.5044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 05/31/2017] [Indexed: 12/21/2022] Open
Abstract
The power of foodomics as a discipline that is now broadly used for quality assurance of food products and adulteration identification, as well as for determining the safety of food, is presented. Concerning sample preparation and application, maintenance of highly sophisticated instruments for both high-performance and high-throughput techniques, and analysis and data interpretation, special attention has to be paid to the development of skilled analysts. The obtained data shall be integrated under a strong bioinformatics environment. Modern mass spectrometry is an extremely powerful analytical tool since it can provide direct qualitative and quantitative information about a molecule of interest from only a minute amount of sample. Quality of this information is influenced by the sample preparation procedure, the type of mass spectrometer used and the analyst's skills. Technical advances are bringing new instruments of increased sensitivity, resolution and speed to the market. Other methods presented here give additional information and can be used as complementary tools to mass spectrometry or for validation of obtained results. Genomics and transcriptomics, as well as affinity-based methods, still have a broad use in food analysis. Serious drawbacks of some of them, especially the affinity-based methods, are the cross-reactivity between similar molecules and the influence of complex food matrices. However, these techniques can be used for pre-screening in order to reduce the large number of samples. Great progress has been made in the application of bioinformatics in foodomics. These developments enabled processing of large amounts of generated data for both identification and quantification, and for corresponding modeling.
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Affiliation(s)
- Uroš Andjelković
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, RS-11000 Belgrade, Serbia
| | - Martina Šrajer Gajdošik
- Department of Chemistry, J. J. Strossmayer University of Osijek, Cara Hadrijana 8/A, HR-31000 Osijek, Croatia
| | - Dajana Gašo-Sokač
- Faculty of Food Technology, J. J. Strossmayer University of Osijek, Franje Kuhača 20, HR-31000 Osijek, Croatia
| | - Tamara Martinović
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
| | - Djuro Josić
- Department of Biotechnology, University of Rijeka, Radmile Matejčić 2, HR-51000 Rijeka, Croatia
- Warren Alpert Medical School, Brown University, 222 Richmond St, Providence, RI 02903, USA
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19
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Müller MM, Lehmann R, Klassert TE, Reifenstein S, Conrad T, Moore C, Kuhn A, Behnert A, Guthke R, Driesch D, Slevogt H. Global analysis of glycoproteins identifies markers of endotoxin tolerant monocytes and GPR84 as a modulator of TNFα expression. Sci Rep 2017; 7:838. [PMID: 28404994 PMCID: PMC5429802 DOI: 10.1038/s41598-017-00828-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/14/2017] [Indexed: 12/12/2022] Open
Abstract
Exposure of human monocytes to lipopolysaccharide (LPS) induces a temporary insensitivity to subsequent LPS challenges, a cellular state called endotoxin tolerance. In this study, we investigated the LPS-induced global glycoprotein expression changes of tolerant human monocytes and THP-1 cells to identify markers and glycoprotein targets capable to modulate the immunosuppressive state. Using hydrazide chemistry and LC-MS/MS analysis, we analyzed glycoprotein expression changes during a 48 h LPS time course. The cellular snapshots at different time points identified 1491 glycoproteins expressed by monocytes and THP-1 cells. Label-free quantitative analysis revealed transient or long-lasting LPS-induced expression changes of secreted or membrane-anchored glycoproteins derived from intracellular membrane coated organelles or from the plasma membrane. Monocytes and THP-1 cells demonstrated marked differences in glycoproteins differentially expressed in the tolerant state. Among the shared differentially expressed glycoproteins G protein-coupled receptor 84 (GPR84) was identified as being capable of modulating pro-inflammatory TNFα mRNA expression in the tolerant cell state when activated with its ligand Decanoic acid.
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Affiliation(s)
- Mario M Müller
- Septomics Research Center, Jena University Hospital, Jena, Germany.,Jena University Hospital, Integrated Research and Treatment Center - Center for Sepsis Control and Care (CSCC), Jena, Germany
| | - Roland Lehmann
- Septomics Research Center, Jena University Hospital, Jena, Germany
| | | | | | - Theresia Conrad
- Septomics Research Center, Jena University Hospital, Jena, Germany.,Leibnitz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institut, Jena, Germany
| | - Christoph Moore
- Septomics Research Center, Jena University Hospital, Jena, Germany
| | - Anna Kuhn
- Septomics Research Center, Jena University Hospital, Jena, Germany.,Leibnitz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institut, Jena, Germany
| | - Andrea Behnert
- Jena University Hospital, Integrated Research and Treatment Center - Center for Sepsis Control and Care (CSCC), Jena, Germany
| | - Reinhard Guthke
- Leibnitz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institut, Jena, Germany
| | | | - Hortense Slevogt
- Septomics Research Center, Jena University Hospital, Jena, Germany.
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20
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Podergajs N, Motaln H, Rajčević U, Verbovšek U, Koršič M, Obad N, Espedal H, Vittori M, Herold-Mende C, Miletic H, Bjerkvig R, Turnšek TL. Transmembrane protein CD9 is glioblastoma biomarker, relevant for maintenance of glioblastoma stem cells. Oncotarget 2016; 7:593-609. [PMID: 26573230 PMCID: PMC4808020 DOI: 10.18632/oncotarget.5477] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 10/31/2015] [Indexed: 12/20/2022] Open
Abstract
The cancer stem cell model suggests that glioblastomas contain a subpopulation of stem-like tumor cells that reproduce themselves to sustain tumor growth. Targeting these cells thus represents a novel treatment strategy and therefore more specific markers that characterize glioblastoma stem cells need to be identified. In the present study, we performed transcriptomic analysis of glioblastoma tissues compared to normal brain tissues revealing sensible up-regulation of CD9 gene. CD9 encodes the transmembrane protein tetraspanin which is involved in tumor cell invasion, apoptosis and resistance to chemotherapy. Using the public REMBRANDT database for brain tumors, we confirmed the prognostic value of CD9, whereby a more than two fold up-regulation correlates with shorter patient survival. We validated CD9 gene and protein expression showing selective up-regulation in glioblastoma stem cells isolated from primary biopsies and in primary organotypic glioblastoma spheroids as well as in U87-MG and U373 glioblastoma cell lines. In contrast, no or low CD9 gene expression was observed in normal human astrocytes, normal brain tissue and neural stem cells. CD9 silencing in three CD133+ glioblastoma cell lines (NCH644, NCH421k and NCH660h) led to decreased cell proliferation, survival, invasion, and self-renewal ability, and altered expression of the stem-cell markers CD133, nestin and SOX2. Moreover, CD9-silenced glioblastoma stem cells showed altered activation patterns of the Akt, MapK and Stat3 signaling transducers. Orthotopic xenotransplantation of CD9-silenced glioblastoma stem cells into nude rats promoted prolonged survival. Therefore, CD9 should be further evaluated as a target for glioblastoma treatment.
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Affiliation(s)
- Neža Podergajs
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Helena Motaln
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Uroš Rajčević
- Department of Biochemistry, Blood Transfusion Centre of Slovenia, 1000 Ljubljana, Slovenia
| | - Urška Verbovšek
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Marjan Koršič
- Department of Neurosurgery, University Medical Centre, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Nina Obad
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Heidi Espedal
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Miloš Vittori
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Christel Herold-Mende
- Division of Neurosurgical Research, Department of Neurosurgery, University of Heidelberg, 69120 Heidelberg, Germany
| | - Hrvoje Miletic
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Rolf Bjerkvig
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway.,NorLux Neuro-Oncology Laboratory, Centre de Recherche Public de la Santé, 1526 Luxembourg, Luxembourg
| | - Tamara Lah Turnšek
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, 1000 Ljubljana, Slovenia.,Department of Biochemistry, Faculty of Chemistry and Chemical Engineering, University of Ljubljana, 1000 Ljubljana, Slovenia
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21
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Thimiri Govinda Raj DB, Khan NA. Designer nanoparticle: nanobiotechnology tool for cell biology. NANO CONVERGENCE 2016; 3:22. [PMID: 28191432 PMCID: PMC5271163 DOI: 10.1186/s40580-016-0082-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/29/2016] [Indexed: 05/17/2023]
Abstract
This article discusses the use of nanotechnology for subcellular compartment isolation and its application towards subcellular omics. This technology review significantly contributes to our understanding on use of nanotechnology for subcellular systems biology. Here we elaborate nanobiotechnology approach of using superparamagnetic nanoparticles (SPMNPs) optimized with different surface coatings for subcellular organelle isolation. Using pulse-chase approach, we review that SPMNPs interacted differently with the cell depending on its surface functionalization. The article focuses on the use of functionalized-SPMNPs as a nanobiotechnology tool to isolate high quality (both purity and yield) plasma membranes and endosomes or lysosomes. Such nanobiotechnology tool can be applied in generating subcellular compartment inventories. As a future perspective, this strategy could be applied in areas such as immunology, cancer and stem cell research.
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Affiliation(s)
- Deepak B. Thimiri Govinda Raj
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation and Unit of Virus Host-Cell Interactions (UVHCI), UJF-EMBL-CNRS, UMR 5233 Grenoble, France
- Envirotransgene Bio-solutions Global, Chennai, India
- Biotechnology Centre for Oslo, Centre for Molecular Medicine Norway (NCMM), P.O. Box 1137, Blindern, 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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22
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Pavić T, Gudelj I, Keser T, Pučić-Baković M, Gornik O. Enrichment of hydrophobic membrane proteins using Triton X-114 and subsequent analysis of their N-glycosylation. Biochim Biophys Acta Gen Subj 2015; 1860:1710-5. [PMID: 26746104 DOI: 10.1016/j.bbagen.2015.12.025] [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: 10/26/2015] [Revised: 12/21/2015] [Accepted: 12/27/2015] [Indexed: 01/28/2023]
Abstract
BACKGROUND Numerous proteins depend on correct glycosylation for their proper function and nearly all membrane, as well as secreted, proteins are glycosylated. Glycosylation of membrane proteins plays a crucial role in many processes including the intercellular recognition and intermolecular interactions on the cell surface. The composition of N-glycans attached to membrane proteins has not been sufficiently studied due to the lack of efficient and reproducible analytical methods. METHODS The aim of this study was to optimise cloud-point extraction (CPE) of membrane proteins with the non-ionic detergent Triton X-114 and analyse their N-glycosylation using hydrophilic interaction liquid chromatography (HILIC-UPLC). Purification of isolated proteins from the excess of detergent proved to be the key step. Therefore, several purification procedures were tested to efficiently remove detergent, while retaining maximum protein recoveries. RESULTS CPE showed to be an efficient method to simultaneously extract membrane and soluble proteins, which subsequently resulted in different N-glycan profiles of the aforementioned protein groups. The resulting protocol showed satisfactory reproducibility and potential for N-glycan analysis of both membrane and intracellular (soluble) proteins from different kinds of biological material. CONCLUSIONS This method can be used as a new analytical tool for reliable detection and quantification of oligomannose and complex type N-glycans attached to membrane proteins, thus serving to distinguish between differences in cell types and states. GENERAL SIGNIFICANCE The simple method was successfully optimised to generate reliable HILIC-UPLC profiles of N-glycans released from membrane proteins. This article is part of a Special Issue entitled "Glycans in personalised medicine" Guest Editor: Professor Gordan Lauc.
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Affiliation(s)
- Tamara Pavić
- Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10 000 Zagreb, Croatia
| | - Ivan Gudelj
- Glycobiology Department, Genos Ltd., Hondlova 2, 10 000 Zagreb, Croatia
| | - Toma Keser
- Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10 000 Zagreb, Croatia
| | | | - Olga Gornik
- Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10 000 Zagreb, Croatia.
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23
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Li J, Gao J, Jiang M, Chen J, Liu Z, Chen P, Liang S. Rat liver sinusoidal surface N-linked glycoproteomic analysis by affinity enrichment and mass spectrometric identification. BIOCHEMISTRY (MOSCOW) 2015; 80:260-75. [PMID: 25761681 DOI: 10.1134/s0006297915030025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Glycosylation in liver is one of the most biologically important protein modifications. It plays critical roles in many physiological and pathological processes by virtue of its unique location at the blood-tissue interface, including angiogenesis, liver cancer, cirrhosis, and fibrosis. To analyze glycosylation of plasma membrane proteins in liver sinusoidal endothelial cells (LSEC), N-glycopeptides of the LSEC surface were enriched using a filter-assisted sample preparation-based lectin affinity capture method and subsequently identified with mass spectrometry. In total, 225 unique N-glycosylation sites on 152 glycoproteins were identified, of which 119 (53%) sites had not previously been determined experimentally. Among the glycoproteins, 53% were classified as plasma membrane proteins and 47 (31%) as signaling proteins and receptors. Moreover, 23 cluster of differentiation antigens with 49 glycopeptides were detected within the membrane glycoproteins of the liver sinusoidal surface. Furthermore, bioinformatics analysis revealed that the majority of identified glycoproteins have an impact on processes of LSEC. Therefore, N-glycoproteomic analysis of the liver sinusoidal surface may provide useful information on liver regeneration and facilitate liver disease diagnosis.
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Affiliation(s)
- Jianglin Li
- Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha, 410081, P. R. China.
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24
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Yasueda Y, Tamura T, Kuwara K, Takaoka Y, Hamachi I. Biomembrane-embedded Catalysts for Membrane-associated Protein Labeling on Red Blood Cells. CHEM LETT 2015. [DOI: 10.1246/cl.150797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yuki Yasueda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Keiko Kuwara
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University
| | | | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency
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25
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Shetty D, Khedkar JK, Park KM, Kim K. Can we beat the biotin-avidin pair?: cucurbit[7]uril-based ultrahigh affinity host-guest complexes and their applications. Chem Soc Rev 2015; 44:8747-61. [PMID: 26434388 DOI: 10.1039/c5cs00631g] [Citation(s) in RCA: 291] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The design of synthetic, monovalent host-guest molecular recognition pairs is still challenging and of particular interest to inquire into the limits of the affinity that can be achieved with designed systems. In this regard, cucurbit[7]uril (CB[7]), an important member of the host family cucurbit[n]uril (CB[n], n = 5-8, 10, 14), has attracted much attention because of its ability to form ultra-stable complexes with multiple guests. The strong hydrophobic effect between the host cavity and guests, ion-dipole and dipole-dipole interactions of guests with CB portals helps in cooperative and multiple noncovalent interactions that are essential for realizing such strong complexations. These highly selective, strong yet dynamic interactions can be exploited in many applications including affinity chromatography, biomolecule immobilization, protein isolation, biological catalysis, and sensor technologies. In this review, we summarize the progress in the development of high affinity guests for CB[7], factors affecting the stability of complexes, theoretical insights, and the utility of these high affinity pairs in different challenging applications.
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Affiliation(s)
- Dinesh Shetty
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang 37673, Republic of Korea.
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26
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Yan Q, Tang S, Tan Z, Han X, Zhou C, Kang J, Wang M. Proteomic Analysis of Isolated Plasma Membrane Fractions from the Mammary Gland in Lactating Cows. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:7388-7398. [PMID: 26237224 DOI: 10.1021/acs.jafc.5b02231] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The mammary gland of dairy cows is a formidable lipid-synthesizing machine for lactation. This unique function depends on the activities of plasma membrane (PM) proteins in mammary cells. Little information is known about the expression profiles of PM proteins and their functions during the lactating process. This study investigated the proteome map of PM fractions of mammary gland in lactating cows using 1D-Gel-LC-MS/MS and identified 872 nonredundant proteins with 141 unknown proteins, wherein 215 were PM-associated proteins. Most of the PM-associated proteins were binding, transport, and catalytic proteins such as annexin proteins, heat shock proteins, integrins, RAS oncogene family members, and S100 calcium binding proteins. The PM-associated pathways such as caveolae-mediated endocytosis, leukocyte extravasation, aldosterone signaling in epithelial cells, and remodeling of epithelial adherens junctions were also significantly over-represented. Proteomic analysis revealed the characteristics and predicted functions of PM proteins isolated from the lactating bovine mammary gland. These results further provide experimental evidence for the presence of many proteins predicted in the annotated bovine genome. The data generated here also provide a reference for the PM-related functional research in the mammary gland of lactating cows.
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Affiliation(s)
- Qiongxian Yan
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Research Center of Livestock & Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences , Changsha, Hunan 410125, People's Republic of China
| | - Shaoxun Tang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Research Center of Livestock & Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences , Changsha, Hunan 410125, People's Republic of China
| | - Zhiliang Tan
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Research Center of Livestock & Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences , Changsha, Hunan 410125, People's Republic of China
| | - Xuefeng Han
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Research Center of Livestock & Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences , Changsha, Hunan 410125, People's Republic of China
| | - Chuanshe Zhou
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Research Center of Livestock & Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences , Changsha, Hunan 410125, People's Republic of China
| | - Jinhe Kang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Research Center of Livestock & Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences , Changsha, Hunan 410125, People's Republic of China
| | - Min Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Hunan Research Center of Livestock & Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, The Chinese Academy of Sciences , Changsha, Hunan 410125, People's Republic of China
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27
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Myerson JW, Brenner JS, Greineder CF, Muzykantov VR. Systems approaches to design of targeted therapeutic delivery. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:253-65. [PMID: 25946066 PMCID: PMC4713047 DOI: 10.1002/wsbm.1304] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/15/2015] [Accepted: 04/17/2015] [Indexed: 02/06/2023]
Abstract
Targeted drug delivery aims to improve therapeutic effects and enable mechanisms that are not feasible for untargeted agents (e.g., due to impermeable biological barriers). To achieve targeting, a drug or its carrier should possess properties providing specific accumulation from circulation at the desired site. There are several examples of systems-inspired approaches that have been applied to achieve this goal. First, proteomics analysis of plasma membrane fraction of the vascular endothelium has identified a series of target molecules and their ligands (e.g., antibodies) that deliver conjugated cargoes to well-defined vascular cells and subcellular compartments. Second, selection of ligands binding to cells of interest using phage display libraries in vitro and in vivo has provided peptides and polypeptides that bind to normal and pathologically altered cells. Finally, large-scale high-throughput combinatorial synthesis and selection of lipid- and polymer-based nanocarriers varying their chemical components has yielded a series of carriers accumulating in diverse organs and delivering RNA interference agents to diverse cells. Together, these approaches offer a basis for systems-based design and selection of targets, targeting molecules, and targeting vehicles. Current studies focus on expanding the arsenal of these and alternative targeting strategies, devising drug delivery systems capitalizing on these strategies and evaluation of their benefit/risk ratio in adequate animal models of human diseases. These efforts, combined with better understanding of mechanisms and unintended consequences of these targeted interventions, need to be ultimately translated into industrial development and the clinical domain.
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Affiliation(s)
- Jacob W Myerson
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacob S Brenner
- Pulmonary and Critical Care Division, University of Pennsylvania, Philadelphia, PA, USA
| | - Colin F Greineder
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA, USA
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28
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Bausch-Fluck D, Hofmann A, Bock T, Frei AP, Cerciello F, Jacobs A, Moest H, Omasits U, Gundry RL, Yoon C, Schiess R, Schmidt A, Mirkowska P, Härtlová A, Van Eyk JE, Bourquin JP, Aebersold R, Boheler KR, Zandstra P, Wollscheid B. A mass spectrometric-derived cell surface protein atlas. PLoS One 2015; 10:e0121314. [PMID: 25894527 PMCID: PMC4404347 DOI: 10.1371/journal.pone.0121314] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 01/30/2015] [Indexed: 01/08/2023] Open
Abstract
Cell surface proteins are major targets of biomedical research due to their utility as cellular markers and their extracellular accessibility for pharmacological intervention. However, information about the cell surface protein repertoire (the surfaceome) of individual cells is only sparsely available. Here, we applied the Cell Surface Capture (CSC) technology to 41 human and 31 mouse cell types to generate a mass-spectrometry derived Cell Surface Protein Atlas (CSPA) providing cellular surfaceome snapshots at high resolution. The CSPA is presented in form of an easy-to-navigate interactive database, a downloadable data matrix and with tools for targeted surfaceome rediscovery (http://wlab.ethz.ch/cspa). The cellular surfaceome snapshots of different cell types, including cancer cells, resulted in a combined dataset of 1492 human and 1296 mouse cell surface glycoproteins, providing experimental evidence for their cell surface expression on different cell types, including 136 G-protein coupled receptors and 75 membrane receptor tyrosine-protein kinases. Integrated analysis of the CSPA reveals that the concerted biological function of individual cell types is mainly guided by quantitative rather than qualitative surfaceome differences. The CSPA will be useful for the evaluation of drug targets, for the improved classification of cell types and for a better understanding of the surfaceome and its concerted biological functions in complex signaling microenvironments.
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Affiliation(s)
- Damaris Bausch-Fluck
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Health Sciences and Technology, BMPP, ETH Zurich, Zurich, Switzerland
| | - Andreas Hofmann
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Thomas Bock
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Andreas P. Frei
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ferdinando Cerciello
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Molecular Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Andrea Jacobs
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Hansjoerg Moest
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ulrich Omasits
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Health Sciences and Technology, BMPP, ETH Zurich, Zurich, Switzerland
| | - Rebekah L. Gundry
- Department of Biochemistry, Medical College of Wisconsin, Wisconsin, Milwaukee, United States of America
| | - Charles Yoon
- Institute for Biomaterials & Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Ralph Schiess
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Alexander Schmidt
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Paulina Mirkowska
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Oncology Research Laboratory, University Children Hospital Zurich, Zurich, Switzerland
| | - Anetta Härtlová
- Centre of Advanced Studies, Faculty of Military Health Sciences, University of Defense, Hradec Kralove, Czech Republic
| | - Jennifer E. Van Eyk
- Department of Medicine, Biological Chemistry and Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jean-Pierre Bourquin
- Oncology Research Laboratory, University Children Hospital Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Kenneth R. Boheler
- SCRMC, LKS Faculty of Medicine, Hong Kong University, Hong Kong, Hong Kong SAR
- Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Peter Zandstra
- Institute for Biomaterials & Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Bernd Wollscheid
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Health Sciences and Technology, BMPP, ETH Zurich, Zurich, Switzerland
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29
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Gunnarsson A, Snijder A, Hicks J, Gunnarsson J, Höök F, Geschwindner S. Drug Discovery at the Single Molecule Level: Inhibition-in-Solution Assay of Membrane-Reconstituted β-Secretase Using Single-Molecule Imaging. Anal Chem 2015; 87:4100-3. [DOI: 10.1021/acs.analchem.5b00740] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anders Gunnarsson
- Discovery Sciences, AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden
| | - Arjan Snijder
- Discovery Sciences, AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden
| | - Jennifer Hicks
- Discovery Sciences, AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden
| | - Jenny Gunnarsson
- Discovery Sciences, AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden
| | - Fredrik Höök
- Department
of Applied Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
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30
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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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31
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Yang H, Yuan B, Zhang X, Scherman OA. Supramolecular chemistry at interfaces: host-guest interactions for fabricating multifunctional biointerfaces. Acc Chem Res 2014; 47:2106-15. [PMID: 24766328 DOI: 10.1021/ar500105t] [Citation(s) in RCA: 341] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
CONSPECTUS: Host-guest chemistry can greatly improve the selectivity of biomolecule-ligand binding on account of recognition-directed interactions. In addition, functional structures and the actuation of supramolecular assemblies in molecular systems can be controlled efficiently through various host-guest chemistry. Together, these highly selective, strong yet dynamic interactions can be exploited as an alternative methodology for applications in the field of programmable and controllable engineering of supramolecular soft materials through the reversible binding between complementary components. Many processes in living systems such as biotransformation, transportation of matter, and energy transduction begin with interfacial molecular recognition, which is greatly influenced by various external stimuli at biointerfaces. Detailed investigations about the molecular recognition at interfaces can result in a better understanding of life science, and further guide us in developing new biomaterials and medicines. In order to mimic complicated molecular-recognition systems observed in nature that adapt to changes in their environment, combining host-guest chemistry and surface science is critical for fabricating the next generation of multifunctional biointerfaces with efficient stimuli-responsiveness and good biocompatibility. In this Account, we will summarize some recent progress on multifunctional stimuli-responsive biointerfaces and biosurfaces fabricated by cyclodextrin- or cucurbituril-based host-guest chemistry and highlight their potential applications including drug delivery, bioelectrocatalysis, and reversible adsorption and resistance of peptides, proteins, and cells. In addition, these biointerfaces and biosurfaces demonstrate efficient response toward various external stimuli, such as UV light, pH, redox chemistry, and competitive guests. All of these external stimuli can aid in mimicking the biological stimuli evident in complex biological environments. We begin by reviewing the current state of stimuli-responsive supramolecular assemblies formed by host-guest interactions, discussing how to transfer host-guest chemistry from solution onto surfaces required for fabricating multifunctional biosurfaces and biointerfaces. Then, we present different stimuli-responsive biosurfaces and biointerfaces, which have been prepared through a combination of cyclodextrin- or cucurbituril-based host-guest chemistry and various surface technologies such as self-assembled monolayers or layer-by-layer assembly. Moreover, we discuss the applications of these biointerfaces and biosurfaces in the fields of drug release, reversible adsorption and release of some organic molecules, peptides, proteins, and cells, and photoswitchable bioelectrocatalysis. In addition, we summarize the merits and current limitations of these methods for fabricating multifunctional stimuli-responsive biointerfaces in a dynamic noncovalent manner. Finally, we present possible strategies for future designs of stimuli-responsive multifunctional biointerfaces and biosurfaces by combining host-guest chemistry with surface science, which will lead to further critical development of supramolecular chemistry at interfaces.
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Affiliation(s)
- Hui Yang
- The Key Lab of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Bin Yuan
- The Key Lab of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xi Zhang
- The Key Lab of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Oren A. Scherman
- Melville Laboratory for Polymer
Synthesis, Department of Chemistry, University of Cambridge, Cambridge CB21EW, United Kingdom
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32
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An iron-regulated and glycosylation-dependent proteasomal degradation pathway for the plasma membrane metal transporter ZIP14. Proc Natl Acad Sci U S A 2014; 111:9175-80. [PMID: 24927598 DOI: 10.1073/pnas.1405355111] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Protein degradation is instrumental in regulating cellular function. Plasma membrane proteins targeted for degradation are internalized and sorted to multivesicular bodies, which fuse with lysosomes, where they are degraded. ZIP14 is a newly identified iron transporter with multitransmembrane domains. In an attempt to dissect the molecular mechanisms by which iron regulates ZIP14 levels, we found that ZIP14 is endocytosed, extracted from membranes, deglycosylated, and degraded by proteasomes. This pathway did not depend on the retrograde trafficking to the endoplasmic reticulum and thus did not involve the well-defined endoplasmic reticulum-associated protein degradation pathway. Iron inhibited membrane extraction of internalized ZIP14, resulting in higher steady-state levels of ZIP14. Asparagine-linked (N-linked) glycosylation of ZIP14, particularly the glycosylation at N102, was required for efficient membrane extraction of ZIP14 and therefore is necessary for its iron sensitivity. These findings highlight the importance of proteasomes in the degradation of endocytosed plasma membrane proteins.
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33
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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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34
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Kume H, Muraoka S, Kuga T, Adachi J, Narumi R, Watanabe S, Kuwano M, Kodera Y, Matsushita K, Fukuoka J, Masuda T, Ishihama Y, Matsubara H, Nomura F, Tomonaga T. Discovery of colorectal cancer biomarker candidates by membrane proteomic analysis and subsequent verification using selected reaction monitoring (SRM) and tissue microarray (TMA) analysis. Mol Cell Proteomics 2014; 13:1471-84. [PMID: 24687888 DOI: 10.1074/mcp.m113.037093] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent advances in quantitative proteomic technology have enabled the large-scale validation of biomarkers. We here performed a quantitative proteomic analysis of membrane fractions from colorectal cancer tissue to discover biomarker candidates, and then extensively validated the candidate proteins identified. A total of 5566 proteins were identified in six tissue samples, each of which was obtained from polyps and cancer with and without metastasis. GO cellular component analysis predicted that 3087 of these proteins were membrane proteins, whereas TMHMM algorithm predicted that 1567 proteins had a transmembrane domain. Differences were observed in the expression of 159 membrane proteins and 55 extracellular proteins between polyps and cancer without metastasis, while the expression of 32 membrane proteins and 17 extracellular proteins differed between cancer with and without metastasis. A total of 105 of these biomarker candidates were quantitated using selected (or multiple) reaction monitoring (SRM/MRM) with stable synthetic isotope-labeled peptides as an internal control. The results obtained revealed differences in the expression of 69 of these proteins, and this was subsequently verified in an independent set of patient samples (polyps (n = 10), cancer without metastasis (n = 10), cancer with metastasis (n = 10)). Significant differences were observed in the expression of 44 of these proteins, including ITGA5, GPRC5A, PDGFRB, and TFRC, which have already been shown to be overexpressed in colorectal cancer, as well as proteins with unknown function, such as C8orf55. The expression of C8orf55 was also shown to be high not only in colorectal cancer, but also in several cancer tissues using a multicancer tissue microarray, which included 1150 cores from 14 cancer tissues. This is the largest verification study of biomarker candidate membrane proteins to date; our methods for biomarker discovery and subsequent validation using SRM/MRM will contribute to the identification of useful biomarker candidates for various cancers. Data are available via ProteomeXchange with identifier PXD000851.
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Affiliation(s)
- Hideaki Kume
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Satoshi Muraoka
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Takahisa Kuga
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Jun Adachi
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Ryohei Narumi
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Shio Watanabe
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Masayoshi Kuwano
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Yoshio Kodera
- §Laboratory of Biomolecular Dynamics, Department of Physics, Kitasato University School of Science, Kanagawa, Japan
| | - Kazuyuki Matsushita
- ¶Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan; ‖Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
| | - Junya Fukuoka
- **Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takeshi Masuda
- ‡‡Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Yasushi Ishihama
- §§Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Hisahiro Matsubara
- ¶¶Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Fumio Nomura
- ¶Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan; ‖Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
| | - Takeshi Tomonaga
- From the ‡Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan;
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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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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
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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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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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38
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Pozzi D, Caracciolo G, Capriotti AL, Cavaliere C, Piovesana S, Colapicchioni V, Palchetti S, Riccioli A, Laganà A. A proteomics-based methodology to investigate the protein corona effect for targeted drug delivery. ACTA ACUST UNITED AC 2014; 10:2815-9. [DOI: 10.1039/c4mb00292j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we introduce a proteomics methodology based on nanoliquid-chromatography tandem mass spectrometry (nanoLC/MS-MS) to investigate the “protein corona effect for targeted drug delivery”.
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Affiliation(s)
- D. Pozzi
- Department of Molecular Medicine
- “Sapienza” University of Rome
- 00161 Rome, Italy
| | - G. Caracciolo
- Department of Molecular Medicine
- “Sapienza” University of Rome
- 00161 Rome, Italy
| | - A. L. Capriotti
- Department of Chemistry
- “Sapienza” University of Rome
- 00185 Rome, Italy
| | - C. Cavaliere
- Department of Chemistry
- “Sapienza” University of Rome
- 00185 Rome, Italy
| | - S. Piovesana
- Department of Chemistry
- “Sapienza” University of Rome
- 00185 Rome, Italy
| | - V. Colapicchioni
- Istituto Italiano di Tecnologia
- Center for Life Nano Science@Sapienza
- Rome, Italy
| | - S. Palchetti
- Department of Anatomy
- Histology
- Forensic Medicine and Orthopaedics
- Section of Histology and Medical Embryology
- “Sapienza” University of Rome
| | - A. Riccioli
- Department of Anatomy
- Histology
- Forensic Medicine and Orthopaedics
- Section of Histology and Medical Embryology
- “Sapienza” University of Rome
| | - A. Laganà
- Department of Chemistry
- “Sapienza” University of Rome
- 00185 Rome, Italy
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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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Srivastava V, Malm E, Sundqvist G, Bulone V. Quantitative proteomics reveals that plasma membrane microdomains from poplar cell suspension cultures are enriched in markers of signal transduction, molecular transport, and callose biosynthesis. Mol Cell Proteomics 2013; 12:3874-85. [PMID: 24051156 DOI: 10.1074/mcp.m113.029033] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The plasma membrane (PM) is a highly dynamic interface that contains detergent-resistant microdomains (DRMs). The aim of this work was to determine the main functions of such microdomains in poplar through a proteomic analysis using gel-based and solution (iTRAQ) approaches. A total of 80 proteins from a limited number of functional classes were found to be significantly enriched in DRM relative to PM. The enriched proteins are markers of signal transduction, molecular transport at the PM, or cell wall biosynthesis. Their intrinsic properties are presented and discussed together with the biological significance of their enrichment in DRM. Of particular importance is the significant and specific enrichment of several callose [(1 → 3)-β-glucan] synthase isoforms, whose catalytic activity represents a final response to stress, leading to the deposition of callose plugs at the surface of the PM. An integrated functional model that connects all DRM-enriched proteins identified is proposed. This report is the only quantitative analysis available to date of the protein composition of membrane microdomains from a tree species.
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Affiliation(s)
- Vaibhav Srivastava
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden
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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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42
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Tsuchida S, Satoh M, Kawashima Y, Sogawa K, Kado S, Sawai S, Nishimura M, Ogita M, Takeuchi Y, Kobyashi H, Aoki A, Kodera Y, Matsushita K, Izumi Y, Nomura F. Application of quantitative proteomic analysis using tandem mass tags for discovery and identification of novel biomarkers in periodontal disease. Proteomics 2013; 13:2339-50. [PMID: 23696425 DOI: 10.1002/pmic.201200510] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 03/25/2013] [Accepted: 04/15/2013] [Indexed: 01/06/2023]
Abstract
Periodontal disease is a bacterial infection that destroys the gingiva and surrounding tissues of the oral cavity. Gingival crevicular fluid (GCF) is extracted from the gingival sulcus and pocket. Analysis of biochemical markers in GCF, which predict the progression of periodontal disease, may facilitate disease diagnosis. However, no useful GCF biochemical markers with high sensitivity for detecting periodontal disease have been identified. Thus, the search for biochemical markers of periodontal disease is of continued interest in experimental and clinical periodontal disease research. Using tandem mass tag (TMT) labeling, we analyzed GCF samples from healthy subjects and patients with periodontal disease, and identified a total of 619 GCF proteins based on proteomic analysis. Of these, we focused on two proteins, matrix metalloproteinase (MMP)-9 and neutrophil gelatinase-associated lipocalin (LCN2), which are involved in the progression of periodontal disease. Western blot analysis revealed that the levels of MMP-9 and LCN2 were significantly higher in patients with periodontal disease than in healthy subjects. In addition, ELISA also detected significantly higher levels of LCN2 in patients with periodontal disease than in healthy subjects. Thus, LC-MS/MS analyses of GCF using TMT labeling led to the identification of LCN2, which may be a promising GCF biomarker for the detection of periodontal disease.
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Affiliation(s)
- Sachio Tsuchida
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
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Milovancev M, Hilgart-Martiszus I, McNamara MJ, Goodall CP, Seguin B, Bracha S, Wickramasekara SI. Comparative analysis of the surface exposed proteome of two canine osteosarcoma cell lines and normal canine osteoblasts. BMC Vet Res 2013; 9:116. [PMID: 23758893 PMCID: PMC3684535 DOI: 10.1186/1746-6148-9-116] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 06/05/2013] [Indexed: 11/10/2022] Open
Abstract
Background Osteosarcoma (OSA) is the most common primary bone tumor of dogs and carries a poor prognosis despite aggressive treatment. An improved understanding of the biology of OSA is critically needed to allow for development of novel diagnostic, prognostic, and therapeutic tools. The surface-exposed proteome (SEP) of a cancerous cell includes a multifarious array of proteins critical to cellular processes such as proliferation, migration, adhesion, and inter-cellular communication. The specific aim of this study was to define a SEP profile of two validated canine OSA cell lines and a normal canine osteoblast cell line utilizing a biotinylation/streptavidin system to selectively label, purify, and identify surface-exposed proteins by mass spectrometry (MS) analysis. Additionally, we sought to validate a subset of our MS-based observations via quantitative real-time PCR, Western blot and semi-quantitative immunocytochemistry. Our hypothesis was that MS would detect differences in the SEP composition between the OSA and the normal osteoblast cells. Results Shotgun MS identified 133 putative surface proteins when output from all samples were combined, with good consistency between biological replicates. Eleven of the MS-detected proteins underwent analysis of gene expression by PCR, all of which were actively transcribed, but varied in expression level. Western blot of whole cell lysates from all three cell lines was effective for Thrombospondin-1, CYR61 and CD44, and indicated that all three proteins were present in each cell line. Semi-quantitative immunofluorescence indicated that CD44 was expressed at much higher levels on the surface of the OSA than the normal osteoblast cell lines. Conclusions The results of the present study identified numerous differences, and similarities, in the SEP of canine OSA cell lines and normal canine osteoblasts. The PCR, Western blot, and immunocytochemistry results, for the subset of proteins evaluated, were generally supportive of the mass spectrometry data. These methods may be applied to other cell lines, or other biological materials, to highlight unique and previously unrecognized differences between samples. While this study yielded data that may prove useful for OSA researchers and clinicians, further refinements of the described techniques are expected to yield greater accuracy and produce a more thorough SEP analysis.
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Affiliation(s)
- Milan Milovancev
- Department of Clinical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA.
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van Dam TJ, Wheway G, Slaats GG, Huynen MA, Giles RH. The SYSCILIA gold standard (SCGSv1) of known ciliary components and its applications within a systems biology consortium. Cilia 2013; 2:7. [PMID: 23725226 PMCID: PMC3674929 DOI: 10.1186/2046-2530-2-7] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 05/28/2013] [Indexed: 12/21/2022] Open
Abstract
The multinational SYSCILIA consortium aims to gain a mechanistic understanding of the cilium. We utilize multiple parallel high-throughput (HTP) initiatives to develop predictive models of relationships between complex genotypes and variable phenotypes of ciliopathies. The models generated are only as good as the wet laboratory data fed into them. It is therefore essential to orchestrate a well-annotated and high-confidence dataset to be able to assess the quality of any HTP dataset. Here, we present the inaugural SYSCILIA gold standard of known ciliary components as a public resource.
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Affiliation(s)
- Teunis Jp van Dam
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands.
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45
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Kadakkuzha BM, Puthanveettil SV. Genomics and proteomics in solving brain complexity. MOLECULAR BIOSYSTEMS 2013; 9:1807-21. [PMID: 23615871 DOI: 10.1039/c3mb25391k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The human brain is extraordinarily complex, composed of billions of neurons and trillions of synaptic connections. Neurons are organized into circuit assemblies that are modulated by specific interneurons and non-neuronal cells, such as glia and astrocytes. Data on human genome sequences predicts that each of these cells in the human brain has the potential of expressing ∼20 000 protein coding genes and tens of thousands of noncoding RNAs. A major challenge in neuroscience is to determine (1) how individual neurons and circuitry utilize this potential during development and maturation of the nervous system, and for higher brain functions such as cognition, and (2) how this potential is altered in neurological and psychiatric disorders. In this review, we will discuss how recent advances in next generation sequencing, proteomics and bioinformatics have transformed our understanding of gene expression and the functions of neural circuitry, memory storage, and disorders of cognition.
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Affiliation(s)
- Beena M Kadakkuzha
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida 130 Scripps Way, Jupiter, FL 33458, USA
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46
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Kim GH, Park EC, Yun SH, Hong Y, Lee DG, Shin EY, Jung J, Kim YH, Lee KB, Jang IS, Lee ZW, Chung YH, Choi JS, Cheong C, Kim S, Kim SI. Proteomic and bioinformatic analysis of membrane proteome in type 2 diabetic mouse liver. Proteomics 2013; 13:1164-79. [PMID: 23349036 DOI: 10.1002/pmic.201200210] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 12/27/2012] [Accepted: 01/07/2013] [Indexed: 12/16/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is the most prevalent and serious metabolic disease affecting people worldwide. T2DM results from insulin resistance of the liver, muscle, and adipose tissue. In this study, we used proteomic and bioinformatic methodologies to identify novel hepatic membrane proteins that are related to the development of hepatic insulin resistance, steatosis, and T2DM. Using FT-ICR MS, we identified 95 significantly differentially expressed proteins in the membrane fraction of normal and T2DM db/db mouse liver. These proteins are primarily involved in energy metabolism pathways, molecular transport, and cellular signaling, and many of them have not previously been reported in diabetic studies. Bioinformatic analysis revealed that 16 proteins may be related to the regulation of insulin signaling in the liver. In addition, six proteins are associated with energy stress-induced, nine proteins with inflammatory stress-induced, and 14 proteins with endoplasmic reticulum stress-induced hepatic insulin resistance. Moreover, we identified 19 proteins that may regulate hepatic insulin resistance in a c-Jun amino-terminal kinase-dependent manner. In addition, three proteins, 14-3-3 protein beta (YWHAB), Slc2a4 (GLUT4), and Dlg4 (PSD-95), are discovered by comprehensive bioinformatic analysis, which have correlations with several proteins identified by proteomics approach. The newly identified proteins in T2DM should provide additional insight into the development and pathophysiology of hepatic steatosis and insulin resistance, and they may serve as useful diagnostic markers and/or therapeutic targets for these diseases.
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Affiliation(s)
- Gun-Hwa Kim
- Division of Life Science, Korea Basic Science Institute, Daejeon, Republic of Korea
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Increased expression of LDL receptor-related protein 1 during human cytomegalovirus infection reduces virion cholesterol and infectivity. Cell Host Microbe 2013; 12:86-96. [PMID: 22817990 DOI: 10.1016/j.chom.2012.05.012] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 03/16/2012] [Accepted: 05/04/2012] [Indexed: 12/22/2022]
Abstract
In response to virus infection, cells can alter protein expression to modify cellular functions and limit viral replication. To examine host protein expression during infection with human cytomegalovirus (HCMV), an enveloped DNA virus, we performed a semiquantitative, temporal analysis of the cell surface proteome in infected fibroblasts. We determined that resident low density lipoprotein related receptor 1 (LRP1), a plasma membrane receptor that regulates lipid metabolism, is elevated early after HCMV infection, resulting in decreased intracellular cholesterol. siRNA knockdown or antibody-mediated inhibition of LRP1 increased intracellular cholesterol and concomitantly increased the infectious virus yield. Virions produced under these conditions contained elevated cholesterol, resulting in increased infectivity. Depleting cholesterol from virions reduced their infectivity by blocking fusion of the virion envelope with the cell membrane. Thus, LRP1 restricts HCMV infectivity by controlling the availability of cholesterol for the virion envelope, and increased LRP1 expression is likely a defense response to infection.
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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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Swadzba ME, Hauck SM, Naim HY, Amann B, Deeg CA. Retinal glycoprotein enrichment by concanavalin a enabled identification of novel membrane autoantigen synaptotagmin-1 in equine recurrent uveitis. PLoS One 2012; 7:e50929. [PMID: 23236410 PMCID: PMC3517615 DOI: 10.1371/journal.pone.0050929] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 10/26/2012] [Indexed: 12/11/2022] Open
Abstract
Complete knowledge of autoantigen spectra is crucial for understanding pathomechanisms of autoimmune diseases like equine recurrent uveitis (ERU), a spontaneous model for human autoimmune uveitis. While several ERU autoantigens were identified previously, no membrane protein was found so far. As there is a great overlap between glycoproteins and membrane proteins, the aim of this study was to test whether pre-enrichment of retinal glycoproteins by ConA affinity is an effective tool to detect autoantigen candidates among membrane proteins. In 1D Western blots, the glycoprotein preparation allowed detection of IgG reactions to low abundant proteins in sera of ERU patients. Synaptotagmin-1, a Ca2+-sensing protein in synaptic vesicles, was identified as autoantigen candidate from the pre-enriched glycoprotein fraction by mass spectrometry and was validated as a highly prevalent autoantigen by enzyme-linked immunosorbent assay. Analysis of Syt1 expression in retinas of ERU cases showed a downregulation in the majority of ERU affected retinas to 24%. Results pointed to a dysregulation of retinal neurotransmitter release in ERU. Identification of synaptotagmin-1, the first cell membrane associated autoantigen in this spontaneous autoimmune disease, demonstrated that examination of tissue fractions can lead to the discovery of previously undetected novel autoantigens. Further experiments will address its role in ERU pathology.
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Affiliation(s)
- Margarete E. Swadzba
- Institute of Animal Physiology, Department of Veterinary Sciences, Ludwig-Maximilians University, München, Germany
| | - Stefanie M. Hauck
- Research Unit for Protein Science, Helmholtz Zentrum München–German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Hassan Y. Naim
- Department of Physiological Chemistry, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Barbara Amann
- Institute of Animal Physiology, Department of Veterinary Sciences, Ludwig-Maximilians University, München, Germany
| | - Cornelia A. Deeg
- Institute of Animal Physiology, Department of Veterinary Sciences, Ludwig-Maximilians University, München, Germany
- * E-mail:
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50
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Lin Y, Jiang H, Yan Y, Peng B, Chen J, Lin H, Liu Z. Shotgun analysis of membrane proteomes by an improved SDS-assisted sample preparation method coupled with liquid chromatography–tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 911:6-14. [DOI: 10.1016/j.jchromb.2012.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 10/14/2012] [Accepted: 10/15/2012] [Indexed: 10/27/2022]
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