1
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Choudhury R, Venkateswaran Venkatasubramani A, Hua J, Borsò M, Franconi C, Kinkley S, Forné I, Imhof A. The role of RNA in the maintenance of chromatin domains as revealed by antibody-mediated proximity labelling coupled to mass spectrometry. eLife 2024; 13:e95718. [PMID: 38717135 PMCID: PMC11147508 DOI: 10.7554/elife.95718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/26/2024] [Indexed: 06/04/2024] Open
Abstract
Eukaryotic chromatin is organized into functional domains, that are characterized by distinct proteomic compositions and specific nuclear positions. In contrast to cellular organelles surrounded by lipid membranes, the composition of distinct chromatin domains is rather ill described and highly dynamic. To gain molecular insight into these domains and explore their composition, we developed an antibody-based proximity biotinylation method targeting the RNA and proteins constituents. The method that we termed antibody-mediated proximity labelling coupled to mass spectrometry (AMPL-MS) does not require the expression of fusion proteins and therefore constitutes a versatile and very sensitive method to characterize the composition of chromatin domains based on specific signature proteins or histone modifications. To demonstrate the utility of our approach we used AMPL-MS to characterize the molecular features of the chromocenter as well as the chromosome territory containing the hyperactive X chromosome in Drosophila. This analysis identified a number of known RNA-binding proteins in proximity of the hyperactive X and the centromere, supporting the accuracy of our method. In addition, it enabled us to characterize the role of RNA in the formation of these nuclear bodies. Furthermore, our method identified a new set of RNA molecules associated with the Drosophila centromere. Characterization of these novel molecules suggested the formation of R-loops in centromeres, which we validated using a novel probe for R-loops in Drosophila. Taken together, AMPL-MS improves the selectivity and specificity of proximity ligation allowing for novel discoveries of weak protein-RNA interactions in biologically diverse domains.
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Affiliation(s)
- Rupam Choudhury
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
| | - Anuroop Venkateswaran Venkatasubramani
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Jie Hua
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
| | - Marco Borsò
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians, University (LMU) MunichPlanegg-MartinsriedGermany
| | - Celeste Franconi
- Chromatin Structure and Function group, Department of Computational Molecular Biology, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Sarah Kinkley
- Chromatin Structure and Function group, Department of Computational Molecular Biology, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians, University (LMU) MunichPlanegg-MartinsriedGermany
| | - Axel Imhof
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians, University (LMU) MunichPlanegg-MartinsriedGermany
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2
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Morderer D, Wren MC, Liu F, Kouri N, Maistrenko A, Khalil B, Pobitzer N, Salemi M, Phinney BS, Dickson DW, Murray ME, Rossoll W. Probe-dependent Proximity Profiling (ProPPr) Uncovers Similarities and Differences in Phospho-Tau-Associated Proteomes Between Tauopathies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.585597. [PMID: 38585836 PMCID: PMC10996607 DOI: 10.1101/2024.03.25.585597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Tauopathies represent a diverse group of neurodegenerative disorders characterized by the abnormal aggregation of the microtubule-associated protein tau. Despite extensive research, the precise mechanisms underlying the complexity of different types of tau pathology remain incompletely understood. Here we describe an approach for proteomic profiling of aggregate-associated proteomes on slides with formalin-fixed, paraffin-embedded (FFPE) tissue that utilizes proximity labelling upon high preservation of aggregate morphology, which permits the profiling of pathological aggregates regardless of their size. To comprehensively investigate the common and unique protein interactors associated with the variety of tau lesions present across different human tauopathies, Alzheimer's disease (AD), corticobasal degeneration (CBD), Pick's disease (PiD), and progressive supranuclear palsy (PSP), were selected to represent the major tauopathy diseases. Implementation of our widely applicable Probe-dependent Proximity Profiling (ProPPr) strategy, using the AT8 antibody, permitted identification and quantification of proteins associated with phospho-tau lesions in well-characterized human post-mortem tissue. The analysis revealed both common and disease-specific proteins associated with phospho-tau aggregates, highlighting potential targets for therapeutic intervention and biomarker development. Candidate validation through high-resolution co-immunofluorescence of distinct aggregates across disease and control cases, confirmed the association of retromer complex protein VPS35 with phospho-tau lesions across the studied tauopathies. Furthermore, we discovered disease-specific associations of proteins including ferritin light chain (FTL) and the neuropeptide precursor VGF within distinct pathological lesions. Notably, examination of FTL-positive microglia in CBD astrocytic plaques indicate a potential role for microglial involvement in the pathogenesis of these tau lesions. Our findings provide valuable insights into the proteomic landscape of tauopathies, shedding light on the molecular mechanisms underlying tau pathology. This first comprehensive characterization of tau-associated proteomes across different tauopathies enhances our understanding of disease heterogeneity and provides a resource for future functional investigation, as well as development of targeted therapies and diagnostic biomarkers.
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3
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Kotani N, Nakano T, Kuwahara R. Host cell membrane proteins located near SARS-CoV-2 spike protein attachment sites are identified using proximity labeling and proteomic analysis. J Biol Chem 2022; 298:102500. [PMID: 36152751 PMCID: PMC9492400 DOI: 10.1016/j.jbc.2022.102500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/31/2022] [Accepted: 09/08/2022] [Indexed: 11/19/2022] Open
Abstract
Coronavirus disease represents a real threat to the global population, and understanding the biological features of the causative virus, that is, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is imperative for mitigating this threat. Analyses of proteins such as primary receptors and coreceptors (cofactors), which are involved in the entry of SARS-CoV-2 into host cells, will provide important clues to help control the virus. Here, we identified host cell membrane protein candidates present in proximity to the attachment sites of SARS-CoV-2 spike proteins, using proximity labeling and proteomic analysis. The identified proteins represent key candidate factors that may be required for viral entry. We found SARS-CoV-2 host protein DPP4, cell adhesion protein Cadherin 17, and glycoprotein CD133 colocalized with cell membrane–bound SARS-CoV-2 spike proteins in Caco-2 cells and thus showed potential as candidate factors. Additionally, our analysis of the experimental infection of HEK293T cells with a SARS-CoV-2 pseudovirus indicated a 2-fold enhanced infectivity in the CD133-ACE2-coexpressing HEK293T cells compared to that in HEK293T cells expressing ACE-2 alone. The information and resources regarding these coreceptor labeling and analysis techniques could be utilized for the development of antiviral agents against SARS-CoV-2 and other emerging viruses.
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Affiliation(s)
- Norihiro Kotani
- Medical Research Center, Saitama Medical University, Moroyama-machi, Saitama, Japan; Department of Biochemistry, Saitama Medical University, Moroyama-machi, Saitama, Japan.
| | - Takanari Nakano
- Department of Biochemistry, Saitama Medical University, Moroyama-machi, Saitama, Japan
| | - Ryusuke Kuwahara
- Quantum Wave Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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4
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Kotani N, Araki T, Miyagawa-Yamaguchi A, Amimoto T, Nakano M, Honke K. Proximity Labeling and Proteomics: Get to Know Neighbors. Methods Enzymol 2022; 679:131-162. [PMID: 36682860 DOI: 10.1016/bs.mie.2022.07.031] [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: 01/25/2023]
Abstract
Protein-protein interactions are essential in biological reactions and fundamental to cell-cell communication (e.g., the binding of secreted proteins, such as hormones, to cell membrane receptors) and the subsequent intracellular signal transduction cascade. Several studies have been extensively carried out on protein-protein interactions because they have the potential to resolve various problems in molecular biology. Biochemical methods, such as chemical cross-linking and immunoprecipitation, have long been used to analyze which proteins interact with each other. However, there are some problems, such as unphysiological states and non-specific binding, that require the development of more useful experimental methods. This chapter discusses the "proximity labeling (Proteomics)" analysis technique, which has been attracting attention in protein-protein interaction analysis in recent years and is used in many biological studies. "Membrane proximity labeling (proteomics)," which analyzes the interaction of cell membrane proteins, and "intracellular proximity labeling (proteomics)" will be explained in-depth.
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Affiliation(s)
- Norihiro Kotani
- Medical Research Center, Saitama Medical University, Saitama, Japan; Department of Biochemistry, Saitama Medical University, Saitama, Japan.
| | - Tomoyuki Araki
- Department of Biochemistry, Saitama Medical University, Saitama, Japan
| | | | - Tomoko Amimoto
- Natural Science Center for Basic Research and Development, Hiroshima University, Higashi-Hiroshima, Japan
| | - Miyako Nakano
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Koichi Honke
- Department of Biochemistry, Kochi University Medical School, Nankoku, Japan
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5
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Oslund RC, Reyes-Robles T, White CH, Tomlinson JH, Crotty KA, Bowman EP, Chang D, Peterson VM, Li L, Frutos S, Vila-Perelló M, Vlerick D, Cromie K, Perlman DH, Ingale S, Hara SDO, Roberts LR, Piizzi G, Hett EC, Hazuda DJ, Fadeyi OO. Detection of cell-cell interactions via photocatalytic cell tagging. Nat Chem Biol 2022; 18:850-858. [PMID: 35654846 DOI: 10.1038/s41589-022-01044-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/22/2022] [Indexed: 02/07/2023]
Abstract
The growing appreciation of immune cell-cell interactions within disease environments has led to extensive efforts to develop immunotherapies. However, characterizing complex cell-cell interfaces in high resolution remains challenging. Thus, technologies leveraging therapeutic-based modalities to profile intercellular environments offer opportunities to study cell-cell interactions with molecular-level insight. We introduce photocatalytic cell tagging (PhoTag) for interrogating cell-cell interactions using single-domain antibodies (VHHs) conjugated to photoactivatable flavin-based cofactors. Following irradiation with visible light, the flavin photocatalyst generates phenoxy radical tags for targeted labeling. Using this technology, we demonstrate selective synaptic labeling across the PD-1/PD-L1 axis in antigen-presenting cell-T cell systems. In combination with multiomics single-cell sequencing, we monitored interactions between peripheral blood mononuclear cells and Raji PD-L1 B cells, revealing differences in transient interactions with specific T cell subtypes. The utility of PhoTag in capturing cell-cell interactions will enable detailed profiling of intercellular communication across different biological systems.
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Affiliation(s)
- Rob C Oslund
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA. .,InduPro, Cambridge, MA, USA.
| | | | - Cory H White
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Jake H Tomlinson
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Kelly A Crotty
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Edward P Bowman
- Discovery Research, Merck & Co., Inc., San Francisco, CA, USA
| | - Dan Chang
- Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA
| | | | - Lixia Li
- Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA
| | | | | | | | | | - David H Perlman
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Sampat Ingale
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | | | - Lee R Roberts
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Grazia Piizzi
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Erik C Hett
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Daria J Hazuda
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA.,Infectious Diseases and Vaccine Research, Merck & Co., Inc., West Point, PA, USA
| | - Olugbeminiyi O Fadeyi
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA. .,InduPro, Cambridge, MA, USA.
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6
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Furukawa K, Ohmi Y, Hamamura K, Kondo Y, Ohkawa Y, Kaneko K, Hashimoto N, Yesmin F, Bhuiyan RH, Tajima O, Furukawa K. Signaling domains of cancer-associated glycolipids. Glycoconj J 2022; 39:145-155. [PMID: 35315508 DOI: 10.1007/s10719-022-10051-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/06/2022] [Accepted: 02/15/2022] [Indexed: 12/16/2022]
Abstract
Immunotherapy of malignant cancers is now becoming one of representative approaches to overcome cancers. To construct strategies for immunotherapy, presence of tumor-specific antigens should be a major promise. A number of cancer specific- or cancer-associated antigens have been reported based on various experimental sets and various animal systems. The most reasonable strategy to define tumor-specific antigens might be "autologous typing" performed by Old's group, proposing three classes of tumor-antigens recognized by host immune systems of cancer patients. Namely, class 1, individual antigens that is present only in the patient's sample analyzed; class 2, shared antigens that can be found only in some group of cancers in some patients, but not in normal cells and tissues; class 3, universal antigens that are present in some cancers but also in normal cells and tissues with different densities. Sen Hakomori reported there were novel carbohydrates in cancers that could not be detected in normal cells mainly by biochemical approaches. Consequently, many of class 2 cancer-specific antigens have been revealed to be carbohydrate antigens, and been used for cancer diagnosis and treatment. Not only as cancer markers, but roles of those cancer-associated carbohydrates have also been recognized as functional molecules in cancer cells. In particular, roles of complex carbohydrates in the regulation of cell signaling on the cell surface microdomains, glycolipid-enriched microdomain (GEM)/rafts have been reported by Hakomori and many other researchers including us. The processes and present status of these studies on cancer-associated glycolipids were summarized.
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Affiliation(s)
- Koichi Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan. .,Department of Molecular and Cellular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Yuhsuke Ohmi
- Department of Clinical Engineering, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Kazunori Hamamura
- Department of Pharmacology, Aichi Gakuin University School of Dentistry, Nisshin, Japan
| | - Yuji Kondo
- Department of Molecular and Cellular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuki Ohkawa
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Institute, Osaka, Japan
| | - Kei Kaneko
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Noboru Hashimoto
- Department of Tissue Regeneration, Tokushima University Graduate School Institute of Biomedical Sciences, Tokushima, Japan
| | - Farhana Yesmin
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan.,Department of Molecular and Cellular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Robiul H Bhuiyan
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Orie Tajima
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Keiko Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
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7
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In situ proximity labeling identifies Lewy pathology molecular interactions in the human brain. Proc Natl Acad Sci U S A 2022; 119:2114405119. [PMID: 35082147 PMCID: PMC8812572 DOI: 10.1073/pnas.2114405119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2021] [Indexed: 12/16/2022] Open
Abstract
The intracellular misfolding and accumulation of alpha-synuclein into structures collectively called Lewy pathology (LP) is a central phenomenon for the pathogenesis of synucleinopathies, including Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Understanding the molecular architecture of LP is crucial for understanding synucleinopathy disease origins and progression. Here we used a technique called biotinylation by antibody recognition (BAR) to label total (BAR-SYN1) and pathological alpha-synuclein (BAR-PSER129) in situ for subsequent mass spectrometry analysis. Results showed superior immunohistochemical detection of LP following the BAR-PSER129 protocol, particularly for fibers and punctate pathology within the striatum and cortex. Mass spectrometry analysis of BAR-PSER129-labeled LP identified 261 significantly enriched proteins in the synucleinopathy brain when compared to nonsynucleinopathy brains. In contrast, BAR-SYN1 did not differentiate between disease and nonsynucleinopathy brains. Pathway analysis of BAR-PSER129-enriched proteins revealed enrichment for 718 pathways; notably, the most significant KEGG pathway was PD, and Gene Ontology (GO) cellular compartments were the vesicle, extracellular vesicle, extracellular exosome, and extracellular organelle. Pathway clustering revealed several superpathways, including metabolism, mitochondria, lysosome, and intracellular vesicle transport. Validation of the BAR-PSER129-identified protein hemoglobin beta (HBB) by immunohistochemistry confirmed the interaction of HBB with PSER129 Lewy neurites and Lewy bodies. In summary, BAR can be used to enrich for LP from formalin-fixed human primary tissues, which allowed the determination of molecular signatures of LP. This technique has broad potential to help understand the phenomenon of LP in primary human tissue and animal models.
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8
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Kushner JS, Liu G, Eisert RJ, Bradshaw GA, Pitt GS, Hinson JT, Kalocsay M, Marx SO. Detecting Cardiovascular Protein-Protein Interactions by Proximity Proteomics. Circ Res 2022; 130:273-287. [PMID: 35050691 PMCID: PMC8852690 DOI: 10.1161/circresaha.121.319810] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Rapidly changing and transient protein-protein interactions regulate dynamic cellular processes in the cardiovascular system. Traditional methods, including affinity purification and mass spectrometry, have revealed many macromolecular complexes in cardiomyocytes and the vasculature. Yet these methods often fail to identify in vivo or transient protein-protein interactions. To capture these interactions in living cells and animals with subsequent mass spectrometry identification, enzyme-catalyzed proximity labeling techniques have been developed in the past decade. Although the application of this methodology to cardiovascular research is still in its infancy, the field is developing rapidly, and the promise is substantial. In this review, we outline important concepts and discuss how proximity proteomics has been applied to study physiological and pathophysiological processes relevant to the cardiovascular system.
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Affiliation(s)
- Jared S. Kushner
- Division of Cardiology, Department of Medicine; Columbia University, Vagelos College of Physicians and Surgeons
| | - Guoxia Liu
- Division of Cardiology, Department of Medicine; Columbia University, Vagelos College of Physicians and Surgeons
| | - Robyn J. Eisert
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School
| | - Gary A. Bradshaw
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School
| | - Geoffrey S. Pitt
- Cardiovascular Research Institute, Weill Cornell Medical College
| | - J. Travis Hinson
- Cardiology Center, UConn Health, Farmington, CT
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Marian Kalocsay
- Department of Systems Biology, Laboratory of Systems Pharmacology, Harvard Medical School
| | - Steven O. Marx
- Division of Cardiology, Department of Medicine; Columbia University, Vagelos College of Physicians and Surgeons
- Department of Molecular Pharmacology and Therapeutics, Columbia University, Vagelos College of Physicians and Surgeons
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9
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Yesmin F, Bhuiyan RH, Ohmi Y, Yamamoto S, Kaneko K, Ohkawa Y, Zhang P, Hamamura K, Cheung NKV, Kotani N, Honke K, Okajima T, Kambe M, Tajima O, Furukawa K, Furukawa K. Ganglioside GD2 Enhances the Malignant Phenotypes of Melanoma Cells by Cooperating with Integrins. Int J Mol Sci 2021; 23:ijms23010423. [PMID: 35008849 PMCID: PMC8745508 DOI: 10.3390/ijms23010423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/12/2021] [Accepted: 12/28/2021] [Indexed: 11/16/2022] Open
Abstract
Gangliosides have been considered to modulate cell signals in the microdomain of the cell membrane, lipid/rafts, or glycolipid-enriched microdomain/rafts (GEM/rafts). In particular, cancer-associated gangliosides were reported to enhance the malignant properties of cancer cells. In fact, GD2-positive (GD2+) cells showed increased proliferation, invasion, and adhesion, compared with GD2-negative (GD2-) cells. However, the precise mechanisms by which gangliosides regulate cell signaling in GEM/rafts are not well understood. In order to analyze the roles of ganglioside GD2 in the malignant properties of melanoma cells, we searched for GD2-associating molecules on the cell membrane using the enzyme-mediated activation of radical sources combined with mass spectrometry, and integrin β1 was identified as a representative GD2-associating molecule. Then, we showed the physical association of GD2 and integrin β1 by immunoprecipitation/immunoblotting. Close localization was also shown by immuno-cytostaining and the proximity ligation assay. During cell adhesion, GD2+ cells showed multiple phospho-tyrosine bands, i.e., the epithelial growth factor receptor and focal adhesion kinase. The knockdown of integrin β1 revealed that the increased malignant phenotypes in GD2+ cells were clearly cancelled. Furthermore, the phosphor-tyrosine bands detected during the adhesion of GD2+ cells almost completely disappeared after the knockdown of integrin β1. Finally, immunoblotting to examine the intracellular distribution of integrins during cell adhesion revealed that large amounts of integrin β1 were localized in GEM/raft fractions in GD2+ cells before and just after cell adhesion, with the majority being localized in the non-raft fractions in GD2- cells. All these results suggest that GD2 and integrin β1 cooperate in GEM/rafts, leading to enhanced malignant phenotypes of melanomas.
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Affiliation(s)
- Farhana Yesmin
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai 487-8501, Japan; (F.Y.); (R.H.B.); (S.Y.); (K.K.); (Y.O.); (P.Z.); (M.K.); (O.T.); (K.F.)
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya 466-0065, Japan;
| | - Robiul H. Bhuiyan
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai 487-8501, Japan; (F.Y.); (R.H.B.); (S.Y.); (K.K.); (Y.O.); (P.Z.); (M.K.); (O.T.); (K.F.)
| | - Yuhsuke Ohmi
- Department of Medical Technology, Chubu University College of Life and Health Sciences, Kasugai 487-8501, Japan;
| | - Satoko Yamamoto
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai 487-8501, Japan; (F.Y.); (R.H.B.); (S.Y.); (K.K.); (Y.O.); (P.Z.); (M.K.); (O.T.); (K.F.)
| | - Kei Kaneko
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai 487-8501, Japan; (F.Y.); (R.H.B.); (S.Y.); (K.K.); (Y.O.); (P.Z.); (M.K.); (O.T.); (K.F.)
| | - Yuki Ohkawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai 487-8501, Japan; (F.Y.); (R.H.B.); (S.Y.); (K.K.); (Y.O.); (P.Z.); (M.K.); (O.T.); (K.F.)
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka 541-8567, Japan
| | - Pu Zhang
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai 487-8501, Japan; (F.Y.); (R.H.B.); (S.Y.); (K.K.); (Y.O.); (P.Z.); (M.K.); (O.T.); (K.F.)
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya 466-0065, Japan;
| | - Kazunori Hamamura
- Department of Pharmacology, Aichi Gakuin University School of Dentistry, Nagoya 464-8650, Japan;
| | | | - Norihiro Kotani
- Department of Biochemistry, Saitama Medical University, Saitama 350-0495, Japan;
| | - Koichi Honke
- Department of Biochemistry, Kochi University School of Medicine, Nangoku 783-8505, Japan;
| | - Tetsuya Okajima
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya 466-0065, Japan;
| | - Mariko Kambe
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai 487-8501, Japan; (F.Y.); (R.H.B.); (S.Y.); (K.K.); (Y.O.); (P.Z.); (M.K.); (O.T.); (K.F.)
| | - Orie Tajima
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai 487-8501, Japan; (F.Y.); (R.H.B.); (S.Y.); (K.K.); (Y.O.); (P.Z.); (M.K.); (O.T.); (K.F.)
| | - Keiko Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai 487-8501, Japan; (F.Y.); (R.H.B.); (S.Y.); (K.K.); (Y.O.); (P.Z.); (M.K.); (O.T.); (K.F.)
| | - Koichi Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai 487-8501, Japan; (F.Y.); (R.H.B.); (S.Y.); (K.K.); (Y.O.); (P.Z.); (M.K.); (O.T.); (K.F.)
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya 466-0065, Japan;
- Correspondence: ; Tel.: +81-568-51-9512
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10
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Kaneda H, Ida Y, Kuwahara R, Sato I, Nakano T, Tokuda H, Sato T, Murakoshi T, Honke K, Kotani N. Proximity Proteomics Has Potential for Extracellular Vesicle Identification. J Proteome Res 2021; 20:3519-3531. [PMID: 34115501 DOI: 10.1021/acs.jproteome.1c00149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Extracellular vesicles (EVs) are biomarkers and mediators of intercellular communication. In biological samples, EVs are secreted by various types of cells. The proteomic identification of proteins expressed in EVs has potential to contribute to research and clinical applications, particularly for cancer. In this study, the proximity-labeling method-based proteomic approach was used for EV identification, labeling membrane components proximal to a given molecule on the EV membrane surface. Due to the small labeling range, proteins on the surface of the same EVs are likely to be labeled by selecting a given EV surface antigen. The protein group of cancer cell-secreted EV (cEV), which abundantly expresses a close homologue of L1 (CHL1), was examined using a model mouse for lung cancer (LC). cEV-expressed proteins were identified by proteomic analysis of enzyme-mediated activation of radical sources by comparing serum EVs from wild-type and LC mice. SLC4A1 was found to be co-expressed in CHL1-expressing EVs, highlighting EVs expressing both CHL1 and SLC4A1 as candidates for cEVs. Serum EVs expressing both CHL1 and caspase 14 were significantly elevated in LC patients compared with healthy individuals. Thus, the combination of proximity labeling and proteomic analysis allows for effective EV identification.
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Affiliation(s)
- Hisako Kaneda
- Department of Biochemistry, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan.,Department of Oral and Maxillofacial Surgery, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Yui Ida
- Department of Biochemistry, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Ryusuke Kuwahara
- Quantum Wave Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Izumi Sato
- Department of Biochemistry, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Takanari Nakano
- Department of Biochemistry, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Haruhiko Tokuda
- Medical Genome Center Biobank, National Center for Geriatrics and Gerontology, 7-430 Morioka-cho, Obu, Aichi 474-8511, Japan
| | - Tsuyoshi Sato
- Department of Oral and Maxillofacial Surgery, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Takayuki Murakoshi
- Department of Biochemistry, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Koichi Honke
- Department of Biochemistry, Kochi University Medical School, Nankoku, Kochi 783-8505, Japan
| | - Norihiro Kotani
- Department of Biochemistry, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
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11
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Bosch JA, Chen CL, Perrimon N. Proximity-dependent labeling methods for proteomic profiling in living cells: An update. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 10:e392. [PMID: 32909689 DOI: 10.1002/wdev.392] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/11/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022]
Abstract
Characterizing the proteome composition of organelles and subcellular regions of living cells can facilitate the understanding of cellular organization as well as protein interactome networks. Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially restricted proteomes. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. The tagged endogenous proteins can then be isolated for further analysis by MS. To analyze protein-protein interactions or identify components that localize to discrete subcellular compartments, spatial expression is achieved by fusing the enzyme to specific proteins or signal peptides that target to particular subcellular regions. Although these technologies have only been introduced recently, they have already provided deep insights into a wide range of biological processes. Here, we provide an updated description and comparison of proximity labeling methods, as well as their applications and improvements. As each method has its own unique features, the goal of this review is to describe how different proximity labeling methods can be used to answer different biological questions. This article is categorized under: Technologies > Analysis of Proteins.
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Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Chiao-Lin Chen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Boston, Massachusetts, USA
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12
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Geri JB, Oakley JV, Reyes-Robles T, Wang T, McCarver SJ, White CH, Rodriguez-Rivera FP, Parker DL, Hett EC, Fadeyi OO, Oslund RC, MacMillan DWC. Microenvironment mapping via Dexter energy transfer on immune cells. Science 2020; 367:1091-1097. [PMID: 32139536 DOI: 10.1126/science.aay4106] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 11/13/2019] [Accepted: 02/06/2020] [Indexed: 12/20/2022]
Abstract
Many disease pathologies can be understood through the elucidation of localized biomolecular networks, or microenvironments. To this end, enzymatic proximity labeling platforms are broadly applied for mapping the wider spatial relationships in subcellular architectures. However, technologies that can map microenvironments with higher precision have long been sought. Here, we describe a microenvironment-mapping platform that exploits photocatalytic carbene generation to selectively identify protein-protein interactions on cell membranes, an approach we term MicroMap (μMap). By using a photocatalyst-antibody conjugate to spatially localize carbene generation, we demonstrate selective labeling of antibody binding targets and their microenvironment protein neighbors. This technique identified the constituent proteins of the programmed-death ligand 1 (PD-L1) microenvironment in live lymphocytes and selectively labeled within an immunosynaptic junction.
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Affiliation(s)
- Jacob B Geri
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544, USA
| | - James V Oakley
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544, USA
| | - Tamara Reyes-Robles
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA
| | - Tao Wang
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544, USA
| | - Stefan J McCarver
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544, USA
| | - Cory H White
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA
| | | | - Dann L Parker
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Erik C Hett
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA
| | | | - Rob C Oslund
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA.
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13
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Vilcaes AA, Garbarino-Pico E, Torres Demichelis V, Daniotti JL. Ganglioside Synthesis by Plasma Membrane-Associated Sialyltransferase in Macrophages. Int J Mol Sci 2020; 21:ijms21031063. [PMID: 32033474 PMCID: PMC7043224 DOI: 10.3390/ijms21031063] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/03/2020] [Accepted: 02/03/2020] [Indexed: 12/21/2022] Open
Abstract
Gangliosides are constituents of the mammalian cell membranes and participate in the inflammatory response. However, little is known about the presence and enzymatic activity of ganglioside sialyltransferases at the cell surface of macrophages, one of the most important immune cells involved in the innate inflammatory process. In the present study, using biochemical and fluorescent microscopy approaches, we found that endogenous ST8Sia-I is present at the plasma membrane (ecto-ST8Sia-I) of murine macrophage RAW264.7 cells. Moreover, ecto-ST8Sia-I can synthetize GD3 ganglioside at the cell surface in lipopolysaccharide (LPS)-stimulated macrophages even when LPS-stimulated macrophages reduced the total ST8Sia-I expression levels. Besides, cotreatment of LPS with an inhibitor of nitric oxide (NO) synthase recovered the ecto-ST8Sia-I expression, suggesting that NO production is involved in the reduction of ST8Sia-I expression. The diminution of ST8Sia-I expression in LPS-stimulated macrophages correlated with a reduction of GD3 and GM1 gangliosides and with an increment of GD1a. Taken together, the data supports the presence and activity of sialyltransferases at the plasma membrane of RAW264.7 cells. The variations of ecto-ST8Sia-I and ganglioside levels in stimulated macrophages constitutes a promissory pathway to further explore the physiological role of this and others ganglioside metabolism-related enzymes at the cell surface during the immune response.
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Affiliation(s)
- Aldo A. Vilcaes
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET. Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina; (E.G.-P.); (V.T.D.)
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
- Correspondence: (A.A.V.); (J.L.D.)
| | - Eduardo Garbarino-Pico
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET. Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina; (E.G.-P.); (V.T.D.)
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
| | - Vanina Torres Demichelis
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET. Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina; (E.G.-P.); (V.T.D.)
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
| | - Jose L. Daniotti
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET. Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina; (E.G.-P.); (V.T.D.)
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
- Correspondence: (A.A.V.); (J.L.D.)
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14
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Proteomic Analysis of Lipid Rafts from RBL-2H3 Mast Cells. Int J Mol Sci 2019; 20:ijms20163904. [PMID: 31405203 PMCID: PMC6720779 DOI: 10.3390/ijms20163904] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/01/2019] [Accepted: 08/08/2019] [Indexed: 12/15/2022] Open
Abstract
Lipid rafts are highly ordered membrane microdomains enriched in cholesterol, glycosphingolipids, and certain proteins. They are involved in the regulation of cellular processes in diverse cell types, including mast cells (MCs). The MC lipid raft protein composition was assessed using qualitative mass spectrometric characterization of the proteome from detergent-resistant membrane fractions from RBL-2H3 MCs. Using two different post-isolation treatment methods, a total of 949 lipid raft associated proteins were identified. The majority of these MC lipid raft proteins had already been described in the RaftProtV2 database and are among highest cited/experimentally validated lipid raft proteins. Additionally, more than half of the identified proteins had lipid modifications and/or transmembrane domains. Classification of identified proteins into functional categories showed that the proteins were associated with cellular membrane compartments, and with some biological and molecular functions, such as regulation, localization, binding, catalytic activity, and response to stimulus. Furthermore, functional enrichment analysis demonstrated an intimate involvement of identified proteins with various aspects of MC biological processes, especially those related to regulated secretion, organization/stabilization of macromolecules complexes, and signal transduction. This study represents the first comprehensive proteomic profile of MC lipid rafts and provides additional information to elucidate immunoregulatory functions coordinated by raft proteins in MCs.
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15
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Kotani N, Yamaguchi A, Ohnishi T, Kuwahara R, Nakano T, Nakano Y, Ida Y, Murakoshi T, Honke K. Proximity proteomics identifies cancer cell membrane cis-molecular complex as a potential cancer target. Cancer Sci 2019; 110:2607-2619. [PMID: 31228215 PMCID: PMC6676139 DOI: 10.1111/cas.14108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/10/2019] [Accepted: 06/15/2019] [Indexed: 12/22/2022] Open
Abstract
Cancer‐specific antigens expressed in the cell membrane have been used as targets for several molecular targeted strategies in the last 20 years with remarkable success. To develop more effective cancer treatments, novel targets and strategies for targeted therapies are needed. Here, we examined the cancer cell membrane‐resident “cis‐bimolecular complex” as a possible cancer target (cis‐bimolecular cancer target: BiCAT) using proximity proteomics, a technique that has attracted attention in the last 10 years. BiCAT were detected using a previously developed method termed the enzyme‐mediated activation of radical source (EMARS), to label the components proximal to a given cell membrane molecule. EMARS analysis identified some BiCAT, such as close homolog of L1 (CHL1), fibroblast growth factor 3 (FGFR3) and α2 integrin, which are commonly expressed in mouse primary lung cancer cells and human lung squamous cell carcinoma cells. Analysis of cancer specimens from 55 lung cancer patients revealed that CHL1 and α2 integrin were highly co–expressed in almost all cancer tissues compared with normal lung tissues. As an example of BiCAT application, in vitro simulation of effective drug combinations used for multiple drug treatment strategies was performed using reagents targeted to BiCAT molecules. The combination treatment based on BiCAT information moderately suppressed cancer cell proliferation compared with single administration, suggesting that the information about BiCAT in cancer cells is useful for the appropriate selection of the combination among molecular targeted reagents. Thus, BiCAT has the potential to contribute to several molecular targeted strategies in future.
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Affiliation(s)
- Norihiro Kotani
- Department of Biochemistry, Saitama Medical University, Saitama, Japan
| | - Arisa Yamaguchi
- Department of Biochemistry, Kochi University Medical School, Kochi, Japan
| | - Tomoko Ohnishi
- Department of Biochemistry, Kochi University Medical School, Kochi, Japan
| | - Ryusuke Kuwahara
- Quantum Wave Microscopy Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa, Japan
| | - Takanari Nakano
- Department of Biochemistry, Saitama Medical University, Saitama, Japan
| | - Yuka Nakano
- Department of Biochemistry, Saitama Medical University, Saitama, Japan
| | - Yui Ida
- Department of Biochemistry, Saitama Medical University, Saitama, Japan
| | | | - Koichi Honke
- Department of Biochemistry, Kochi University Medical School, Kochi, Japan
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16
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Furukawa K, Ohmi Y, Ohkawa Y, Bhuiyan RH, Zhang P, Tajima O, Hashimoto N, Hamamura K, Furukawa K. New era of research on cancer-associated glycosphingolipids. Cancer Sci 2019; 110:1544-1551. [PMID: 30895683 PMCID: PMC6501054 DOI: 10.1111/cas.14005] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/13/2019] [Accepted: 03/19/2019] [Indexed: 12/31/2022] Open
Abstract
Cancer‐associated glycosphingolipids have been used as markers for diagnosis and targets for immunotherapy of malignant tumors. Recent progress in the analysis of their implications in the malignant properties of cancer cells revealed that cancer‐associated glycosphingolipids are not only tumor markers, but also functional molecules regulating various signals introduced by membrane microdomains, lipid rafts. In particular, a novel approach, enzyme‐mediated activation of radical sources combined with mass spectrometry, has enabled us to clarify the mechanisms by which cancer‐associated glycosphingolipids regulate cell signals based on the interaction with membrane molecules and formation of molecular complexes on the cell surface. Novel findings obtained from these approaches are now providing us with insights into the development of new anticancer therapies targeting membrane molecular complexes consisting of cancer‐associated glycolipids and their associated membrane molecules. Thus, a new era of cancer‐associated glycosphingolipids has now begun.
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Affiliation(s)
- Koichi Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan.,Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuhsuke Ohmi
- Department of Medical Technology, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Yuki Ohkawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Robiul H Bhuiyan
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Pu Zhang
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan.,Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Orie Tajima
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Noboru Hashimoto
- Department of Molecular Biochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Anatomy, Faculty of Medical and Dental Sciences, Tokushima University, Tokushima, Japan
| | - Kazunori Hamamura
- Department of Pharmacology, School of Dentistry, Aichi-Gakuin University, Nagoya, Japan
| | - Keiko Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
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17
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Abstract
To understand cellular processes at molecular levels, elucidation of protein-protein interactions occurring at a specific location in living cells is required. We have developed a proximity labeling method mediated by the enzyme-mediated activation of radical source (EMARS) reaction, which features a radical formation from labeling reagents by horseradish peroxidase (HRP) set on a molecule of interest (probed molecule). Proximal molecules are covalently labeled with a tag conjugated with the labeling reagent. Here we describe protocols for preparation of a labeling reagent, labeling of neighboring proteins of the probed molecule in living cells, and identification of the labeled proteins.
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Affiliation(s)
- Koichi Honke
- Department of Biochemistry, Kochi University Medical School, Nankoku, Kochi, Japan.
- Center for Innovative and Translational Medicine, Kochi University Medical School, Nankoku, Kochi, Japan.
| | | | - Norihiro Kotani
- Department of Biochemistry, Saitama Medical University, Saitama, Japan
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18
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19
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Esaki N, Ohkawa Y, Hashimoto N, Tsuda Y, Ohmi Y, Bhuiyan RH, Kotani N, Honke K, Enomoto A, Takahashi M, Furukawa K, Furukawa K. ASC amino acid transporter 2, defined by enzyme-mediated activation of radical sources, enhances malignancy of GD2-positive small-cell lung cancer. Cancer Sci 2018; 109:141-153. [PMID: 29151270 PMCID: PMC5765286 DOI: 10.1111/cas.13448] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 10/31/2017] [Accepted: 11/12/2017] [Indexed: 12/20/2022] Open
Abstract
Ganglioside GD2 is specifically expressed in small‐cell lung cancer (SCLC) cells, leading to enhancement of malignant phenotypes, such as cell proliferation and migration. However, how GD2 promotes malignant phenotypes in SCLC cells is not well known. In this study, to reveal the mechanisms by which GD2 increases malignant phenotypes in SCLC cells, we used enzyme‐mediated activation of radical sources combined with mass spectrometry in GD2+SCLC cells. Consequently, we identified ASC amino acid transporter 2 (ASCT2), a major glutamine transporter, which coordinately works with GD2. We showed that ASCT2 was highly expressed in glycolipid‐enriched microdomain/rafts in GD2+SCLC cells, and colocalized with GD2 in both proximity ligation assay and immunocytostaining, and bound with GD2 in immunoprecipitation/TLC immunostaining. Malignant phenotypes of GD2+SCLC cells were enhanced by glutamine uptake, and were suppressed by L‐γ‐glutamyl‐p‐nitroanilide, a specific inhibitor of ASCT2, through reduced phosphorylation of p70 S6K1 and S6. These results suggested that ASCT2 enhances glutamine uptake in glycolipid‐enriched microdomain/rafts in GD2+SCLC cells, leading to the enhancement of cell proliferation and migration through increased phosphorylation of the mTOR complex 1 signaling axis.
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Affiliation(s)
- Nobutoshi Esaki
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan.,Departments of Biochemistry 2, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuki Ohkawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Noboru Hashimoto
- Departments of Biochemistry 2, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuhsuke Tsuda
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan.,Departments of Biochemistry 2, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuhsuke Ohmi
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Robiul H Bhuiyan
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Norihiro Kotani
- Department of Biochemistry, Saitama Medical University, Moroyama, Japan
| | - Koichi Honke
- Department of Biochemistry, Kochi University School of Medicine, Kochi, Japan
| | - Atsushi Enomoto
- Departments of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahide Takahashi
- Departments of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keiko Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
| | - Koichi Furukawa
- Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasugai, Japan
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20
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Honke K. Biological functions of sulfoglycolipids and the EMARS method for identification of co-clustered molecules in the membrane microdomains. J Biochem 2017; 163:253-263. [DOI: 10.1093/jb/mvx078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/03/2017] [Indexed: 01/24/2023] Open
Affiliation(s)
- Koichi Honke
- Department of Biochemistry, Kochi University Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783–8505, Japan
- Center for Innovative and Translational Medicine, Kochi University Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783–8505, Japan
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21
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Costantini F, Barbieri G. The HLA-DR mediated signalling increases the migration and invasion of melanoma cells, the expression and lipid raft recruitment of adhesion receptors, PD-L1 and signal transduction proteins. Cell Signal 2017; 36:189-203. [PMID: 28495591 DOI: 10.1016/j.cellsig.2017.05.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/25/2017] [Accepted: 05/06/2017] [Indexed: 02/04/2023]
Abstract
The constitutive expression of Major Histocompatibility Complex (MHC) class II molecules is restricted to professional Antigen-Presenting Cells (APCs), nevertheless almost 50% of melanomas express constitutively the MHC class II molecules. Therefore, in two MHC class II constitutive expressing melanoma cell lines we studied the signalling mediated by the HLA-DR molecules in the aim to understand the consequence of class II mediated signalling on metastatic dissemination of melanoma. In particular, we reported that the HLA-DR mediated signalling play a new role in melanoma progression, increasing the migration and invasion of melanoma cells. Furthermore, we showed that the HLA-DR mediated signalling increases the expression and the lipid raft localisation of class II molecules, PD-L1 receptor, Integrin and CAM adhesion receptors, FAK, AKT and STAT3 signalling proteins. We also showed that the HLA-DR mediated signalling increases the activation of FAK, AKT, ERK, PKC and STAT3 signalling proteins and the expression of ILK, PAX, BRAF, ERK and PKC. Indeed, the results showed suggest that the HLA-DR mediated signalling provides a platform useful to frustrate an effective anti-tumour response and to increase melanoma migration and metastatic dissemination of this cancer.
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Affiliation(s)
- Francesca Costantini
- Istituto di Biomedicina e Immunologia Molecolare "Alberto Monroy", Consiglio Nazionale delle Ricerche (CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy.
| | - Giovanna Barbieri
- Istituto di Biomedicina e Immunologia Molecolare "Alberto Monroy", Consiglio Nazionale delle Ricerche (CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy.
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22
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Li P, Li J, Wang L, Di LJ. Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Peipei Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Jingjing Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li Wang
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
- Metabolomics Core; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li-Jun Di
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
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23
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Chen CL, Perrimon N. Proximity-dependent labeling methods for proteomic profiling in living cells. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28387482 DOI: 10.1002/wdev.272] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/03/2017] [Accepted: 02/10/2017] [Indexed: 02/05/2023]
Abstract
Characterizing the proteome composition of organelles and subcellular regions of living cells can facilitate the understanding of cellular organization as well as protein interactome networks. Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially restricted proteomes. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins with biotin. The biotinylated endogenous proteins can then be isolated for further analysis by MS. To analyze protein-protein interactions or identify components that localize to discrete subcellular compartments, spatial expression is achieved by fusing the enzyme to specific proteins or signal peptides that target to particular subcellular regions. Although these technologies have only been introduced recently, they have already provided deep insights into a wide range of biological processes. Here, we describe and compare current methods of proximity labeling as well as their applications. As each method has its own unique features, the goal of this review is to describe how different proximity labeling methods can be used to answer different biological questions. WIREs Dev Biol 2017, 6:e272. doi: 10.1002/wdev.272 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Chiao-Lin Chen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA
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24
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Filling the Void: Proximity-Based Labeling of Proteins in Living Cells. Trends Cell Biol 2016; 26:804-817. [PMID: 27667171 DOI: 10.1016/j.tcb.2016.09.004] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 12/17/2022]
Abstract
There are inherent limitations with traditional methods to study protein behavior or to determine the constituency of proteins in discrete subcellular compartments. In response to these limitations, several methods have recently been developed that use proximity-dependent labeling. By fusing proteins to enzymes that generate reactive molecules, most commonly biotin, proximate proteins are covalently labeled to enable their isolation and identification. In this review we describe current methods for proximity-dependent labeling in living cells and discuss their applications and future use in the study of protein behavior.
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Kaneko K, Ohkawa Y, Hashimoto N, Ohmi Y, Kotani N, Honke K, Ogawa M, Okajima T, Furukawa K, Furukawa K. Neogenin, Defined as a GD3-associated Molecule by Enzyme-mediated Activation of Radical Sources, Confers Malignant Properties via Intracytoplasmic Domain in Melanoma Cells. J Biol Chem 2016; 291:16630-43. [PMID: 27288875 DOI: 10.1074/jbc.m115.708834] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Indexed: 11/06/2022] Open
Abstract
To investigate mechanisms for increased malignant properties in malignant melanomas by ganglioside GD3, enzyme-mediated activation of radical sources and subsequent mass spectrometry were performed using an anti-GD3 antibody and GD3-positive (GD3+) and GD3-negative (GD3-) melanoma cell lines. Neogenin, defined as a GD3-neighbored molecule, was largely localized in lipid/rafts in GD3+ cells. Silencing of neogenin resulted in the reduction of cell growth and invasion activity. Physical association between GD3 and neogenin was demonstrated by immunoblotting of the immunoprecipitates with anti-neogenin antibody from GD3+ cell lysates. The intracytoplasmic domain of neogenin (Ne-ICD) was detected in GD3+ cells at higher levels than in GD3- cells when cells were treated by a proteasome inhibitor but not when simultaneously treated with a γ-secretase inhibitor. Exogenous GD3 also induced increased Ne-ICD in GD3- cells. Overexpression of Ne-ICD in GD3- cells resulted in the increased cell growth and invasion activity, suggesting that Ne-ICD plays a role as a transcriptional factor to drive malignant properties of melanomas after cleavage with γ-secretase. γ-Secretase was found in lipid/rafts in GD3+ cells. Accordingly, immunocyto-staining revealed that GD3, neogenin, and γ-secretase were co-localized at the leading edge of GD3+ cells. All these results suggested that GD3 recruits γ-secretase to lipid/rafts, allowing efficient cleavage of neogenin. ChIP-sequencing was performed to identify candidates of target genes of Ne-ICD. Some of them actually showed increased expression after expression of Ne-ICD, probably exerting malignant phenotypes of melanomas under GD3 expression.
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Affiliation(s)
- Kei Kaneko
- From the Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya 466-0065
| | - Yuki Ohkawa
- Department of Life Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasuigai, Aichi 487-8501
| | - Noboru Hashimoto
- From the Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya 466-0065
| | - Yuhsuke Ohmi
- From the Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya 466-0065
| | - Norihiro Kotani
- Department of Biochemistry, Faculty of Medicine, Saitama Medical University, Moroyama-machi, Iruma-gun, Saitama 350-0495, and
| | - Koichi Honke
- Department of Biochemistry, Kochi University School of Medicine, Kochi 783-8505, Japan
| | - Mitsutaka Ogawa
- From the Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya 466-0065
| | - Tetsuya Okajima
- From the Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya 466-0065
| | - Keiko Furukawa
- Department of Life Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasuigai, Aichi 487-8501
| | - Koichi Furukawa
- From the Department of Biochemistry II, Nagoya University Graduate School of Medicine, Nagoya 466-0065, Department of Life Biomedical Sciences, Chubu University College of Life and Health Sciences, Kasuigai, Aichi 487-8501,
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26
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Abstract
Although the emergence of proteomics as an independent branch of science is fairly recent, within a short period of time it has contributed substantially in various disciplines. The tool of mass spectrometry has become indispensable in the analysis of complex biological samples. Clinical applications of proteomics include detection of predictive and diagnostic markers, understanding mechanism of action of drugs as well as resistance mechanisms against them and assessment of therapeutic efficacy and toxicity of drugs in patients. Here, we have summarized the major contributions of proteomics towards the study of melanoma, which is a deadly variety of skin cancer with a high mortality rate.
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Affiliation(s)
- Deepanwita Sengupta
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA; Department of Pathology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA
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27
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Iwamaru Y, Kitani H, Okada H, Takenouchi T, Shimizu Y, Imamura M, Miyazawa K, Murayama Y, Hoover EA, Yokoyama T. Proximity of SCG10 and prion protein in membrane rafts. J Neurochem 2015; 136:1204-1218. [PMID: 26663033 DOI: 10.1111/jnc.13488] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 11/23/2015] [Accepted: 11/24/2015] [Indexed: 12/14/2022]
Abstract
The conversion of normal cellular prion protein (PrPC) into its pathogenic isoform (PrPSc) is an essential event in prion pathogenesis. In culture models, membrane rafts are suggested to play a critical role in PrPSc formation. To identify the candidate molecules capable of interacting with PrPC and facilitating PrPSc formation in membrane rafts, we applied a novel biochemical labeling method termed enzyme-mediated activation of radical sources. Enzyme-mediated activation of radical sources was applied to the Lubrol WX insoluble detergent-resistant membrane fractions from mouse neuroblastoma (N2a) cells in which the surface PrPC was labeled with HRP-conjugated anti-PrP antibody. Two-dimensional western blots of these preparations revealed biotinylated spots of approximately 20 kDa with an isoelectric point of 8.0-9.0. Liquid chromatography-tandem mass spectrometry analysis resulted in the identification of peptides containing SCG10, the neuron-specific microtubule regulator. Proximity of SCG10 and PrPC was confirmed using proximity ligation assay and co-immunoprecipitation assay. Transfection of persistently 22L prion-infected N2a cells with SCG10 small interfering RNA reduced SCG10 expression, but did not prevent PrPSc accumulation, indicating that SCG10 appears to be unrelated to PrPSc formation of 22L prion. Immunofluorescence and western blot analyses showed reduced levels of SCG10 in the hippocampus of prion-infected mice, suggesting a possible association between SCG10 levels and the prion neuropathogenesis. By applying a novel biochemical labeling method against detergent-resistant membrane fractions from mouse neuroblastoma cells, the neuron-specific microtubule-destabilization protein, SCG10 was identified as a novel candidate that is proximate to normal prion protein (PrP) in membrane rafts. SCG10 seemed unrelated to disease-related PrP formation under certain conditions, while there is a possible association between SCG10 levels and prion neuropathogenesis. Cover Image for this issue: doi: 10.1111/jnc.13310.
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Affiliation(s)
- Yoshifumi Iwamaru
- Influenza and Prion Disease Research Center, National Institute of Animal Health, Tsukuba, Ibaraki, Japan.,Prion Research Center, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Hiroshi Kitani
- Animal Immune and Cell Biology Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Hiroyuki Okada
- Influenza and Prion Disease Research Center, National Institute of Animal Health, Tsukuba, Ibaraki, Japan
| | - Takato Takenouchi
- Animal Immune and Cell Biology Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Yoshihisa Shimizu
- Influenza and Prion Disease Research Center, National Institute of Animal Health, Tsukuba, Ibaraki, Japan
| | - Morikazu Imamura
- Influenza and Prion Disease Research Center, National Institute of Animal Health, Tsukuba, Ibaraki, Japan
| | - Kohtaro Miyazawa
- Influenza and Prion Disease Research Center, National Institute of Animal Health, Tsukuba, Ibaraki, Japan
| | - Yuichi Murayama
- Influenza and Prion Disease Research Center, National Institute of Animal Health, Tsukuba, Ibaraki, Japan
| | - Edward A Hoover
- Prion Research Center, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Takashi Yokoyama
- Influenza and Prion Disease Research Center, National Institute of Animal Health, Tsukuba, Ibaraki, Japan
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28
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Rees JS, Li XW, Perrett S, Lilley KS, Jackson AP. Protein Neighbors and Proximity Proteomics. Mol Cell Proteomics 2015; 14:2848-56. [PMID: 26355100 PMCID: PMC4638030 DOI: 10.1074/mcp.r115.052902] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Indexed: 12/31/2022] Open
Abstract
Within cells, proteins can co-assemble into functionally integrated and spatially restricted multicomponent complexes. Often, the affinities between individual proteins are relatively weak, and proteins within such clusters may interact only indirectly with many of their other protein neighbors. This makes proteomic characterization difficult using methods such as immunoprecipitation or cross-linking. Recently, several groups have described the use of enzyme-catalyzed proximity labeling reagents that covalently tag the neighbors of a targeted protein with a small molecule such as fluorescein or biotin. The modified proteins can then be isolated by standard pulldown methods and identified by mass spectrometry. Here we will describe the techniques as well as their similarities and differences. We discuss their applications both to study protein assemblies and to provide a new way for characterizing organelle proteomes. We stress the importance of proteomic quantitation and independent target validation in such experiments. Furthermore, we suggest that there are biophysical and cell-biological principles that dictate the appropriateness of enzyme-catalyzed proximity labeling methods to address particular biological questions of interest.
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Affiliation(s)
- Johanna S Rees
- From the ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QW, the §Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QR, and
| | - Xue-Wen Li
- the ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Sarah Perrett
- the ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Kathryn S Lilley
- the §Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QR, and
| | - Antony P Jackson
- From the ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QW,
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29
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Ohkawa Y, Momota H, Kato A, Hashimoto N, Tsuda Y, Kotani N, Honke K, Suzumura A, Furukawa K, Ohmi Y, Natsume A, Wakabayashi T, Furukawa K. Ganglioside GD3 Enhances Invasiveness of Gliomas by Forming a Complex with Platelet-derived Growth Factor Receptor α and Yes Kinase. J Biol Chem 2015; 290:16043-58. [PMID: 25940087 DOI: 10.1074/jbc.m114.635755] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Indexed: 11/06/2022] Open
Abstract
There have been a few studies on the ganglioside expression in human glioma tissues. However, the role of these gangliosides such as GD3 and GD2 has not been well understood. In this study we employed a genetically engineered mouse model of glioma to clarify the functions of GD3 in gliomas. Forced expression of platelet-derived growth factor B in cultured astrocytes derived from p53-deficient mice resulted in the expression of GD3 and GD2. GD3-positive astrocytes exhibited increased cell growth and invasion activities along with elevated phosphorylation of Akt and Yes kinase. By enzyme-mediated activation of radical sources reaction and mass spectrometry, we identified PDGF receptor α (PDGFRα) as a GD3-associated molecule. GD3-positive astrocytes showed a significant amount of PDGFRα in glycolipid-enriched microdomains/rafts compared with GD3-negative cells. Src kinase family Yes was co-precipitated with PDGFRα, and its pivotal role in the increased cell invasion of GD3-positive astrocytes was demonstrated by silencing with anti-Yes siRNA. Direct association between PDGFRα and GD3 was also shown, suggesting that GD3 forms ternary complex with PDGFRα and Yes. The fact that GD3, PDGFRα, and activated Yes were colocalized in lamellipodia and the edge of tumors in cultured cells and glioma tissues, respectively, suggests that GD3 induced by platelet-derived growth factor B enhances PDGF signals in glycolipid-enriched microdomain/rafts, leading to the promotion of malignant phenotypes such as cell proliferation and invasion in gliomas.
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Affiliation(s)
- Yuki Ohkawa
- From the Department of Biochemistry II, the Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-0065, Japan, the Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, 1200 Matsumoto-cho, Kasugai 487-8501, Japan
| | - Hiroyuki Momota
- the Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-0065, Japan
| | - Akira Kato
- the Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-0065, Japan
| | | | | | - Norihiro Kotani
- the Department of Biochemistry, Faculty of Medicine, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Koichi Honke
- the Department of Biochemistry, Kochi University Medical School, Kohasu, Okou-cho, Nankoku, Kochi 783-8505, Japan
| | - Akio Suzumura
- the Department of Neuroimmunology, Research Institute of Environmental Medicine, Nagoya University, Furou-cho, Chikusa-ku, Nagoya 464-8601, Japan, and
| | - Keiko Furukawa
- From the Department of Biochemistry II, the Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, 1200 Matsumoto-cho, Kasugai 487-8501, Japan
| | | | - Atsushi Natsume
- the Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-0065, Japan
| | - Toshihiko Wakabayashi
- the Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-0065, Japan
| | - Koichi Furukawa
- From the Department of Biochemistry II, the Department of Biomedical Sciences, Chubu University College of Life and Health Sciences, 1200 Matsumoto-cho, Kasugai 487-8501, Japan
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30
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Aureli M, Grassi S, Prioni S, Sonnino S, Prinetti A. Lipid membrane domains in the brain. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1851:1006-16. [PMID: 25677824 DOI: 10.1016/j.bbalip.2015.02.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 01/29/2015] [Accepted: 02/01/2015] [Indexed: 12/28/2022]
Abstract
The brain is characterized by the presence of cell types with very different functional specialization, but with the common trait of a very high complexity of structures originated by their plasma membranes. Brain cells bear evident membrane polarization with the creation of different morphological and functional subcompartments, whose formation, stabilization and function require a very high level of lateral order within the membrane. In other words, the membrane specialization of brain cells implies the presence of distinct membrane domains. The brain is the organ with the highest enrichment in lipids like cholesterol, glycosphingolipids, and the most recently discovered brain membrane lipid, phosphatidylglucoside, whose collective behavior strongly favors segregation within the membrane leading to the formation of lipid-driven membrane domains. Lipid-driven membrane domains function as dynamic platforms for signal transduction, protein processing, and membrane turnover. Essential events involved in the development and in the maintenance of the functional integrity of the brain depend on the organization of lipid-driven membrane domains, and alterations in lipid homeostasis, leading to deranged lipid-driven membrane organization, are common in several major brain diseases. In this review, we summarize the forces behind the formation of lipid membrane domains and their biological roles in different brain cells. This article is part of a Special Issue entitled Brain Lipids.
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Affiliation(s)
- Massimo Aureli
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Italy
| | - Sara Grassi
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Italy
| | - Simona Prioni
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Italy
| | - Sandro Sonnino
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Italy
| | - Alessandro Prinetti
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Italy.
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31
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Levin-Gromiko U, Koshelev V, Kushnir P, Fedida-Metula S, Voronov E, Fishman D. Amplified lipid rafts of malignant cells constitute a target for inhibition of aberrantly active NFAT and melanoma tumor growth by the aminobisphosphonate zoledronic acid. Carcinogenesis 2014; 35:2555-66. [DOI: 10.1093/carcin/bgu178] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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32
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Miyagawa-Yamaguchi A, Kotani N, Honke K. Expressed glycosylphosphatidylinositol-anchored horseradish peroxidase identifies co-clustering molecules in individual lipid raft domains. PLoS One 2014; 9:e93054. [PMID: 24671047 PMCID: PMC3966864 DOI: 10.1371/journal.pone.0093054] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 03/02/2014] [Indexed: 11/18/2022] Open
Abstract
Lipid rafts that are enriched in glycosylphosphatidylinositol (GPI)-anchored proteins serve as a platform for important biological events. To elucidate the molecular mechanisms of these events, identification of co-clustering molecules in individual raft domains is required. Here we describe an approach to this issue using the recently developed method termed enzyme-mediated activation of radical source (EMARS), by which molecules in the vicinity within 300 nm from horseradish peroxidase (HRP) set on the probed molecule are labeled. GPI-anchored HRP fusion proteins (HRP-GPIs), in which the GPI attachment signals derived from human decay accelerating factor and Thy-1 were separately connected to the C-terminus of HRP, were expressed in HeLa S3 cells, and the EMARS reaction was catalyzed by these expressed HRP-GPIs under a living condition. As a result, these different HRP-GPIs had differences in glycosylation and localization and formed distinct clusters. This novel approach distinguished molecular clusters associated with individual GPI-anchored proteins, suggesting that it can identify co-clustering molecules in individual raft domains.
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Affiliation(s)
- Arisa Miyagawa-Yamaguchi
- Kochi System Glycobiology Center, Kochi University Medical School, Nankoku, Kochi, Japan
- Center for Innovate and Translational Medicine, Kochi University Medical School, Nankoku, Kochi, Japan
| | - Norihiro Kotani
- Kochi System Glycobiology Center, Kochi University Medical School, Nankoku, Kochi, Japan
- Center for Innovate and Translational Medicine, Kochi University Medical School, Nankoku, Kochi, Japan
- Department of Biochemistry, Saitama Medical University, Iruma-gun, Saitama, Japan
| | - Koichi Honke
- Kochi System Glycobiology Center, Kochi University Medical School, Nankoku, Kochi, Japan
- Center for Innovate and Translational Medicine, Kochi University Medical School, Nankoku, Kochi, Japan
- Department of Biochemistry, Kochi University Medical School, Nankoku, Kochi, Japan
- * E-mail:
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33
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Miyagawa-Yamaguchi A, Kotani N, Honke K. Segregation of Lipid Rafts Revealed by the EMARS Method Using GPI-Anchored HRP Fusion Proteins. TRENDS GLYCOSCI GLYC 2014. [DOI: 10.4052/tigg.26.59] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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34
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Identification of cell-surface molecular interactions under living conditions by using the enzyme-mediated activation of radical sources (EMARS) method. SENSORS 2012; 12:16037-45. [PMID: 23443365 PMCID: PMC3571769 DOI: 10.3390/s121216037] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 11/12/2012] [Accepted: 11/12/2012] [Indexed: 11/24/2022]
Abstract
Important biological events associated with plasma membranes, such as signal transduction, cell adhesion, and protein trafficking, are mediated through the membrane microdomains. We have developed a novel method termed enzyme-mediated activation of radical sources (EMARS) to identify coclustering molecules on the cell surface under living conditions, which features a radical formation from an aryl azide reagent by horseradish peroxidase (HRP). For identification of molecules labeled by the EMARS reaction, antibody array system and mass spectrometry-based proteomics approaches are available. Spatio- temporally-regulated interaction between β1 integrin and ErbB4 involved in fibronectin-dependent cell migration and therapeutic antibody-stimulated interaction between FGFR3 and CD20 were discovered using the EMARS method.
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