1
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Xie H, Ding X. The Intriguing Landscape of Single-Cell Protein Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105932. [PMID: 35199955 PMCID: PMC9036017 DOI: 10.1002/advs.202105932] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Indexed: 05/15/2023]
Abstract
Profiling protein expression at single-cell resolution is essential for fundamental biological research (such as cell differentiation and tumor microenvironmental examination) and clinical precision medicine where only a limited number of primary cells are permitted. With the recent advances in engineering, chemistry, and biology, single-cell protein analysis methods are developed rapidly, which enable high-throughput and multiplexed protein measurements in thousands of individual cells. In combination with single cell RNA sequencing and mass spectrometry, single-cell multi-omics analysis can simultaneously measure multiple modalities including mRNAs, proteins, and metabolites in single cells, and obtain a more comprehensive exploration of cellular signaling processes, such as DNA modifications, chromatin accessibility, protein abundance, and gene perturbation. Here, the recent progress and applications of single-cell protein analysis technologies in the last decade are summarized. Current limitations, challenges, and possible future directions in this field are also discussed.
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Affiliation(s)
- Haiyang Xie
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
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2
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Lombard-Banek C, Schiel JE. Mass Spectrometry Advances and Perspectives for the Characterization of Emerging Adoptive Cell Therapies. Molecules 2020; 25:E1396. [PMID: 32204371 PMCID: PMC7144572 DOI: 10.3390/molecules25061396] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 12/12/2022] Open
Abstract
Adoptive cell therapy is an emerging anti-cancer modality, whereby the patient's own immune cells are engineered to express T-cell receptor (TCR) or chimeric antigen receptor (CAR). CAR-T cell therapies have advanced the furthest, with recent approvals of two treatments by the Food and Drug Administration of Kymriah (trisagenlecleucel) and Yescarta (axicabtagene ciloleucel). Recent developments in proteomic analysis by mass spectrometry (MS) make this technology uniquely suited to enable the comprehensive identification and quantification of the relevant biochemical architecture of CAR-T cell therapies and fulfill current unmet needs for CAR-T product knowledge. These advances include improved sample preparation methods, enhanced separation technologies, and extension of MS-based proteomic to single cells. Innovative technologies such as proteomic analysis of raw material quality attributes (MQA) and final product quality attributes (PQA) may provide insights that could ultimately fuel development strategies and lead to broad implementation.
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Affiliation(s)
- Camille Lombard-Banek
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA;
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - John E. Schiel
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA;
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
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3
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Griss J, Bauer W, Wagner C, Simon M, Chen M, Grabmeier-Pfistershammer K, Maurer-Granofszky M, Roka F, Penz T, Bock C, Zhang G, Herlyn M, Glatz K, Läubli H, Mertz KD, Petzelbauer P, Wiesner T, Hartl M, Pickl WF, Somasundaram R, Steinberger P, Wagner SN. B cells sustain inflammation and predict response to immune checkpoint blockade in human melanoma. Nat Commun 2019; 10:4186. [PMID: 31519915 PMCID: PMC6744450 DOI: 10.1038/s41467-019-12160-2] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 08/22/2019] [Indexed: 01/01/2023] Open
Abstract
Tumor associated inflammation predicts response to immune checkpoint blockade in human melanoma. Current theories on regulation of inflammation center on anti-tumor T cell responses. Here we show that tumor associated B cells are vital to melanoma associated inflammation. Human B cells express pro- and anti-inflammatory factors and differentiate into plasmablast-like cells when exposed to autologous melanoma secretomes in vitro. This plasmablast-like phenotype can be reconciled in human melanomas where plasmablast-like cells also express T cell-recruiting chemokines CCL3, CCL4, CCL5. Depletion of B cells in melanoma patients by anti-CD20 immunotherapy decreases tumor associated inflammation and CD8+ T cell numbers. Plasmablast-like cells also increase PD-1+ T cell activation through anti-PD-1 blockade in vitro and their frequency in pretherapy melanomas predicts response and survival to immune checkpoint blockade. Tumor associated B cells therefore orchestrate and sustain melanoma inflammation and may represent a predictor for survival and response to immune checkpoint blockade therapy.
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Affiliation(s)
- Johannes Griss
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria.
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD Hinxton, Cambridge, UK.
| | - Wolfgang Bauer
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
| | - Christine Wagner
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
| | - Martin Simon
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
| | - Minyi Chen
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
| | - Katharina Grabmeier-Pfistershammer
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090, Vienna, Austria
| | - Margarita Maurer-Granofszky
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
- Children's Cancer Research Institute, 1090, Vienna, Austria
| | - Florian Roka
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090, Vienna, Austria
| | - Gao Zhang
- Molecular & Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, 19104-4265, USA
- Department of Neurosurgery & The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Meenhard Herlyn
- Molecular & Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, 19104-4265, USA
| | - Katharina Glatz
- Institute of Pathology, University Hospital Basel, 4031, Basel, Switzerland
| | - Heinz Läubli
- Division of Medical Oncology, University Hospital Basel, 4031, Basel, Switzerland
| | - Kirsten D Mertz
- Institute of Pathology, Cantonal Hospital Baselland, 4410, Liestal, Switzerland
| | - Peter Petzelbauer
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
| | - Thomas Wiesner
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria
| | - Markus Hartl
- Mass Spectrometry Facility, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Winfried F Pickl
- Division of Cellular Immunology and Immunohematology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090, Vienna, Austria
| | - Rajasekharan Somasundaram
- Molecular & Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, 19104-4265, USA
| | - Peter Steinberger
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090, Vienna, Austria
| | - Stephan N Wagner
- Department of Dermatology, Medical University of Vienna, 1090, Vienna, Austria.
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4
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Lee SE, Song J, Bösl K, Müller AC, Vitko D, Bennett KL, Superti-Furga G, Pandey A, Kandasamy RK, Kim MS. Proteogenomic Analysis to Identify Missing Proteins from Haploid Cell Lines. Proteomics 2018; 18:e1700386. [DOI: 10.1002/pmic.201700386] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/14/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Seung-Eun Lee
- Department of Applied Chemistry College of Applied Science; Kyung Hee University; Yongin-si Republic of Korea
- Department of Biomedical Science and TechnologyKyung Hee Medical Science Research Institute; Kyung Hee University; Yongin-si Republic of Korea
| | - JongKeon Song
- Department of Applied Chemistry College of Applied Science; Kyung Hee University; Yongin-si Republic of Korea
| | - Korbinian Bösl
- Centre of Molecular Inflammation Research (SFF-CEMIR), and Department of Clinical and Molecular Medicine (IKOM); Norwegian University of Science and Technology; Trondheim Norway
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | - Dijana Vitko
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
- Center for Physiology and Pharmacology; Medical University of Vienna; Vienna Austria
| | - Akhilesh Pandey
- Department of Applied Chemistry College of Applied Science; Kyung Hee University; Yongin-si Republic of Korea
- Department of Biological Chemistry; Johns Hopkins University School of Medicine; Baltimore MD USA
| | - Richard K. Kandasamy
- Centre of Molecular Inflammation Research (SFF-CEMIR), and Department of Clinical and Molecular Medicine (IKOM); Norwegian University of Science and Technology; Trondheim Norway
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences; Vienna Austria
- Centre for Molecular Medicine Norway (NCMM) Nordic EMBL Partnership; University of Oslo and Oslo University Hospital; Oslo Norway
| | - Min-Sik Kim
- Department of Applied Chemistry College of Applied Science; Kyung Hee University; Yongin-si Republic of Korea
- Department of Biomedical Science and TechnologyKyung Hee Medical Science Research Institute; Kyung Hee University; Yongin-si Republic of Korea
- Global Center for Pharmaceutical Ingredient Materials; Kyung Hee University; Yongin-si Republic of Korea
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5
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Brown M, Johnson LA, Leone DA, Majek P, Vaahtomeri K, Senfter D, Bukosza N, Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong YK, Bennett KL, Kain R, Detmar M, Sixt M, Jackson DG, Kerjaschki D. Lymphatic exosomes promote dendritic cell migration along guidance cues. J Cell Biol 2018; 217:2205-2221. [PMID: 29650776 PMCID: PMC5987709 DOI: 10.1083/jcb.201612051] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 01/16/2018] [Accepted: 03/20/2018] [Indexed: 01/08/2023] Open
Abstract
Inflammation stimulates lymphatic endothelial cells to release exosomes, which accumulate in the perivascular stroma. Brown et al. show that these exosomes promote the directional migration of dendritic cells along guidance cues in complex environments by enhancing dynamic cellular protrusions in a CX3CL1-dependent manner. Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified >1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments.
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Affiliation(s)
- Markus Brown
- Clinical Department of Pathology, Medical University of Vienna, Vienna, Austria.,Institute of Science and Technology, Klosterneuburg, Austria
| | - Louise A Johnson
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, England, UK
| | - Dario A Leone
- Clinical Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Peter Majek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kari Vaahtomeri
- Institute of Science and Technology, Klosterneuburg, Austria
| | - Daniel Senfter
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Nora Bukosza
- Clinical Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Helga Schachner
- Clinical Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Gabriele Asfour
- Clinical Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Brigitte Langer
- Clinical Department of Pathology, Medical University of Vienna, Vienna, Austria
| | | | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Young-Kwon Hong
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Renate Kain
- Clinical Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Michael Detmar
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Michael Sixt
- Institute of Science and Technology, Klosterneuburg, Austria
| | - David G Jackson
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, England, UK
| | - Dontscho Kerjaschki
- Clinical Department of Pathology, Medical University of Vienna, Vienna, Austria
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6
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Li ZY, Huang M, Wang XK, Zhu Y, Li JS, Wong CCL, Fang Q. Nanoliter-Scale Oil-Air-Droplet Chip-Based Single Cell Proteomic Analysis. Anal Chem 2018; 90:5430-5438. [PMID: 29551058 DOI: 10.1021/acs.analchem.8b00661] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single cell proteomic analysis provides crucial information on cellular heterogeneity in biological systems. Herein, we describe a nanoliter-scale oil-air-droplet (OAD) chip for achieving multistep complex sample pretreatment and injection for single cell proteomic analysis in the shotgun mode. By using miniaturized stationary droplet microreaction and manipulation techniques, our system allows all sample pretreatment and injection procedures to be performed in a nanoliter-scale droplet with minimum sample loss and a high sample injection efficiency (>99%), thus substantially increasing the analytical sensitivity for single cell samples. We applied the present system in the proteomic analysis of 100 ± 10, 50 ± 5, 10, and 1 HeLa cell(s), and protein IDs of 1360, 612, 192, and 51 were identified, respectively. The OAD chip-based system was further applied in single mouse oocyte analysis, with 355 protein IDs identified at the single oocyte level, which demonstrated its special advantages of high enrichment of sequence coverage, hydrophobic proteins, and enzymatic digestion efficiency over the traditional in-tube system.
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Affiliation(s)
- Zi-Yi Li
- Institute of Microanalytical Systems, Chemistry Department and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
| | - Min Huang
- National Center for Protein Science (Shanghai), Institute of Biochemistry and Cell Biology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , 200031 , China
| | - Xiu-Kun Wang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science , Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai , 200031 , China
| | - Ying Zhu
- Institute of Microanalytical Systems, Chemistry Department and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
| | - Jin-Song Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science , Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai , 200031 , China
| | - Catherine C L Wong
- Center for Precision Medicine Multi-Omics Research , Peking University Health Science Center , Beijing , 100191 , China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , Beijing , 100191 , China.,National Center for Protein Science (Shanghai), Institute of Biochemistry and Cell Biology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , 200031 , China
| | - Qun Fang
- Institute of Microanalytical Systems, Chemistry Department and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
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7
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Perego M, Maurer M, Wang JX, Shaffer S, Müller AC, Parapatics K, Li L, Hristova D, Shin S, Keeney F, Liu S, Xu X, Raj A, Jensen JK, Bennett KL, Wagner SN, Somasundaram R, Herlyn M. A slow-cycling subpopulation of melanoma cells with highly invasive properties. Oncogene 2018; 37:302-312. [PMID: 28925403 PMCID: PMC5799768 DOI: 10.1038/onc.2017.341] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/02/2017] [Accepted: 08/12/2017] [Indexed: 12/16/2022]
Abstract
Melanoma is a heterogeneous tumor with different subpopulations showing different proliferation rates. Slow-cycling cells were previously identified in melanoma, but not fully biologically characterized. Using the label-retention method, we identified a subpopulation of slow-cycling cells, defined as label-retaining cells (LRC), with strong invasive properties. We demonstrate through live imaging that LRC are leaving the primary tumor mass at a very early stage and disseminate to peripheral organs. Through global proteome analyses, we identified the secreted protein SerpinE2/protease nexin-1 as causative for the highly invasive potential of LRC in melanomas.
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Affiliation(s)
- M Perego
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - M Maurer
- Division of Immunology, Allergy and Infectious Diseases, Medical University of Vienna, Vienna, Austria
| | - J X Wang
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - S Shaffer
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - A C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - K Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - L Li
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - D Hristova
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - S Shin
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - F Keeney
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - S Liu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - X Xu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - A Raj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - J K Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - K L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - S N Wagner
- Division of Immunology, Allergy and Infectious Diseases, Medical University of Vienna, Vienna, Austria
| | - R Somasundaram
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - M Herlyn
- Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
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8
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Ramirez MI, Amorim MG, Gadelha C, Milic I, Welsh JA, Freitas VM, Nawaz M, Akbar N, Couch Y, Makin L, Cooke F, Vettore AL, Batista PX, Freezor R, Pezuk JA, Rosa-Fernandes L, Carreira ACO, Devitt A, Jacobs L, Silva IT, Coakley G, Nunes DN, Carter D, Palmisano G, Dias-Neto E. Technical challenges of working with extracellular vesicles. NANOSCALE 2018; 10:881-906. [PMID: 29265147 DOI: 10.1039/c7nr08360b] [Citation(s) in RCA: 324] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Extracellular Vesicles (EVs) are gaining interest as central players in liquid biopsies, with potential applications in diagnosis, prognosis and therapeutic guidance in most pathological conditions. These nanosized particles transmit signals determined by their protein, lipid, nucleic acid and sugar content, and the unique molecular pattern of EVs dictates the type of signal to be transmitted to recipient cells. However, their small sizes and the limited quantities that can usually be obtained from patient-derived samples pose a number of challenges to their isolation, study and characterization. These challenges and some possible options to overcome them are discussed in this review.
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Affiliation(s)
- Marcel I Ramirez
- Fundação Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brazil and Universidade Federal do Paraná, Curitiba, PR, Brazil
| | | | - Catarina Gadelha
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Ivana Milic
- School of Life and Health Sciences, Aston University, England, UK
| | | | | | - Muhammad Nawaz
- Universidade de São Paulo, São Paulo, SP, Brazil and University of Gothenburg, Sweden
| | - Naveed Akbar
- Division of Cardiovascular Medicine, University of Oxford, Oxford, England, UK
| | - Yvonne Couch
- Acute Stroke Programme, RDM-Investigative Medicine, University of Oxford, Oxford, England, UK
| | - Laura Makin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, England, UK
| | - Fiona Cooke
- University of St Andrews, St Andrews, Fife, Scotland, UK
| | - Andre L Vettore
- Federal University of São Paulo campus Diadema, Diadema, Brazil
| | | | | | - Julia A Pezuk
- Universidade Anhanguera de São Paulo, São Paulo, Brazil
| | - Lívia Rosa-Fernandes
- Universidade de São Paulo, São Paulo, SP, Brazil and University of Southern Denmark, Odense, Denmark
| | | | - Andrew Devitt
- School of Life and Health Sciences, Aston University, England, UK
| | | | | | - Gillian Coakley
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, Scotland, UK
| | - Diana N Nunes
- CIPE, A.C.Camargo Cancer Center, São Paulo, SP, Brazil.
| | - Dave Carter
- Oxford Brookes University, Oxford, England, UK
| | - Giuseppe Palmisano
- Universidade de São Paulo, São Paulo, SP, Brazil and IRCCS, Fondazione Santa Lucia, Rome, Italy
| | - Emmanuel Dias-Neto
- CIPE, A.C.Camargo Cancer Center, São Paulo, SP, Brazil. and Universidade de São Paulo, São Paulo, SP, Brazil
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9
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Rosa-Fernandes L, Rocha VB, Carregari VC, Urbani A, Palmisano G. A Perspective on Extracellular Vesicles Proteomics. Front Chem 2017; 5:102. [PMID: 29209607 PMCID: PMC5702361 DOI: 10.3389/fchem.2017.00102] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/03/2017] [Indexed: 12/15/2022] Open
Abstract
Increasing attention has been given to secreted extracellular vesicles (EVs) in the past decades, especially in the portrayal of their molecular cargo and role as messengers in both homeostasis and pathophysiological conditions. This review presents the state-of-the-art proteomic technologies to identify and quantify EVs proteins along with their PTMs, interacting partners and structural details. The rapid growth of mass spectrometry-based analytical strategies for protein sequencing, PTMs and structural characterization has improved the level of molecular details that can be achieved from limited amount of EVs isolated from different biological sources. Here we will provide a perspective view on the achievements and challenges on EVs proteome characterization using mass spectrometry. A detailed bioinformatics approach will help us to picture the molecular fingerprint of EVs and understand better their pathophysiological function.
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Affiliation(s)
- Livia Rosa-Fernandes
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Victória Bombarda Rocha
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Andrea Urbani
- Proteomic and Metabonomic Laboratory, Fondazione Santa Lucia, Rome, Italy.,Institute of Biochemistry and Biochemical Clinic, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Proteomic and Metabonomic Laboratory, Fondazione Santa Lucia, Rome, Italy
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10
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Sielaff M, Kuharev J, Bohn T, Hahlbrock J, Bopp T, Tenzer S, Distler U. Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range. J Proteome Res 2017; 16:4060-4072. [DOI: 10.1021/acs.jproteome.7b00433] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Malte Sielaff
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Jörg Kuharev
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Toszka Bohn
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Jennifer Hahlbrock
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Tobias Bopp
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Stefan Tenzer
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Ute Distler
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
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11
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Purification and Quantification of Kunitz Trypsin Inhibitor in Soybean Using Two-Dimensional Liquid Chromatography. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-0902-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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13
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Radic-Sarikas B, Tsafou KP, Emdal KB, Papamarkou T, Huber KVM, Mutz C, Toretsky JA, Bennett KL, Olsen JV, Brunak S, Kovar H, Superti-Furga G. Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities. Mol Cancer Ther 2017; 16:88-101. [PMID: 28062706 DOI: 10.1158/1535-7163.mct-16-0235] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 10/27/2016] [Accepted: 11/03/2016] [Indexed: 11/16/2022]
Abstract
Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any associated adverse side effects through reduced dosing, which is particularly important in childhood tumors. Using a parallel phenotypic combinatorial screening approach of cells derived from three pediatric tumor types, we identified Ewing sarcoma-specific interactions of a diverse set of targeted agents including approved drugs. We were able to retrieve highly synergistic drug combinations specific for Ewing sarcoma and identified signaling processes important for Ewing sarcoma cell proliferation determined by EWS-FLI1 We generated a molecular target profile of PKC412, a multikinase inhibitor with strong synergistic propensity in Ewing sarcoma, revealing its targets in critical Ewing sarcoma signaling routes. Using a multilevel experimental approach including quantitative phosphoproteomics, we analyzed the molecular rationale behind the disease-specific synergistic effect of simultaneous application of PKC412 and IGF1R inhibitors. The mechanism of the drug synergy between these inhibitors is different from the sum of the mechanisms of the single agents. The combination effectively inhibited pathway crosstalk and averted feedback loop repression, in EWS-FLI1-dependent manner. Mol Cancer Ther; 16(1); 88-101. ©2016 AACR.
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MESH Headings
- Animals
- Antigens, CD
- Antineoplastic Agents/pharmacology
- Cell Line, Tumor
- Computational Biology/methods
- Disease Models, Animal
- Drug Discovery
- Drug Evaluation, Preclinical
- Drug Interactions
- Drug Screening Assays, Antitumor
- Humans
- Molecular Targeted Therapy
- Oncogene Proteins, Fusion/antagonists & inhibitors
- Phosphorylation
- Protein Kinase Inhibitors/pharmacology
- Proteomics/methods
- Proto-Oncogene Protein c-fli-1/antagonists & inhibitors
- RNA-Binding Protein EWS/antagonists & inhibitors
- Receptor, IGF Type 1
- Receptor, Insulin/antagonists & inhibitors
- Receptors, Somatomedin/antagonists & inhibitors
- Sarcoma, Ewing/drug therapy
- Sarcoma, Ewing/genetics
- Sarcoma, Ewing/metabolism
- Sarcoma, Ewing/pathology
- Signal Transduction/drug effects
- Staurosporine/analogs & derivatives
- Staurosporine/pharmacology
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Branka Radic-Sarikas
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kalliopi P Tsafou
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- Department of Oncology, Georgetown University Medical Center, Washington, DC
| | - Kristina B Emdal
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Theodore Papamarkou
- School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Kilian V M Huber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Cornelia Mutz
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Jeffrey A Toretsky
- Department of Oncology, Georgetown University Medical Center, Washington, DC
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Heinrich Kovar
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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14
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Li J, Casteels T, Frogne T, Ingvorsen C, Honoré C, Courtney M, Huber KVM, Schmitner N, Kimmel RA, Romanov RA, Sturtzel C, Lardeau CH, Klughammer J, Farlik M, Sdelci S, Vieira A, Avolio F, Briand F, Baburin I, Májek P, Pauler FM, Penz T, Stukalov A, Gridling M, Parapatics K, Barbieux C, Berishvili E, Spittler A, Colinge J, Bennett KL, Hering S, Sulpice T, Bock C, Distel M, Harkany T, Meyer D, Superti-Furga G, Collombat P, Hecksher-Sørensen J, Kubicek S. Artemisinins Target GABA A Receptor Signaling and Impair α Cell Identity. Cell 2016; 168:86-100.e15. [PMID: 27916275 PMCID: PMC5236063 DOI: 10.1016/j.cell.2016.11.010] [Citation(s) in RCA: 273] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 08/04/2016] [Accepted: 11/03/2016] [Indexed: 12/12/2022]
Abstract
Type 1 diabetes is characterized by the destruction of pancreatic β cells, and generating new insulin-producing cells from other cell types is a major aim of regenerative medicine. One promising approach is transdifferentiation of developmentally related pancreatic cell types, including glucagon-producing α cells. In a genetic model, loss of the master regulatory transcription factor Arx is sufficient to induce the conversion of α cells to functional β-like cells. Here, we identify artemisinins as small molecules that functionally repress Arx by causing its translocation to the cytoplasm. We show that the protein gephyrin is the mammalian target of these antimalarial drugs and that the mechanism of action of these molecules depends on the enhancement of GABAA receptor signaling. Our results in zebrafish, rodents, and primary human pancreatic islets identify gephyrin as a druggable target for the regeneration of pancreatic β cell mass from α cells. Artemisinins inhibit ARX function and impair α cell identity Compounds act by stabilizing gephyrin, thus enhancing GABAA receptor signaling Artemisinins increase β cell mass in zebrafish and rodent models Functional and transcriptional data indicate a conserved phenotype in human islets
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Affiliation(s)
- Jin Li
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria
| | - Tamara Casteels
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria
| | - Thomas Frogne
- Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | | | | | - Monica Courtney
- Université Côte d'Azur, INSERM, CNRS, iBV, 06108 Nice, France
| | - Kilian V M Huber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria
| | - Nicole Schmitner
- Institute of Molecular Biology, Leopold-Franzens-University Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Robin A Kimmel
- Institute of Molecular Biology, Leopold-Franzens-University Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Roman A Romanov
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, 1090 Vienna, Austria; Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Caterina Sturtzel
- Children's Cancer Research Institute, Innovative Cancer Models, Zimmermannplatz 10, 1090 Vienna, Austria
| | - Charles-Hugues Lardeau
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria; Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Johanna Klughammer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria
| | - Sara Sdelci
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria
| | - Andhira Vieira
- Université Côte d'Azur, INSERM, CNRS, iBV, 06108 Nice, France
| | - Fabio Avolio
- Université Côte d'Azur, INSERM, CNRS, iBV, 06108 Nice, France
| | - François Briand
- Physiogenex S.A.S., Prologue Biotech, 516, rue Pierre et Marie Curie, 31670 Labege, France
| | - Igor Baburin
- Institute of Pharmacology and Toxicology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Peter Májek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria
| | - Florian M Pauler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria
| | - Alexey Stukalov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria
| | - Manuela Gridling
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria
| | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria
| | - Charlotte Barbieux
- Cell Isolation and Transplantation Center, Department of Surgery, Geneva University Hospitals and University of Geneva, 1211 Geneva, Switzerland
| | - Ekaterine Berishvili
- Cell Isolation and Transplantation Center, Department of Surgery, Geneva University Hospitals and University of Geneva, 1211 Geneva, Switzerland; Institute of Medical Research, Ilia State University, Tbilisi 0162, Georgia
| | - Andreas Spittler
- Core Facility Flow Cytometry and Department of Surgery, Research Laboratories, Medical University of Vienna, 1090 Vienna, Austria
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria
| | - Steffen Hering
- Institute of Pharmacology and Toxicology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Thierry Sulpice
- Physiogenex S.A.S., Prologue Biotech, 516, rue Pierre et Marie Curie, 31670 Labege, France
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Martin Distel
- Children's Cancer Research Institute, Innovative Cancer Models, Zimmermannplatz 10, 1090 Vienna, Austria
| | - Tibor Harkany
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, 1090 Vienna, Austria; Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Dirk Meyer
- Institute of Molecular Biology, Leopold-Franzens-University Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | | | | | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Lazarettgasse 14, 1090 Vienna, Austria; Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria.
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15
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Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nat Immunol 2016; 17:1361-1372. [PMID: 27798618 DOI: 10.1038/ni.3590] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/28/2016] [Indexed: 12/15/2022]
Abstract
Hemolysis drives susceptibility to bacterial infections and predicts poor outcome from sepsis. These detrimental effects are commonly considered to be a consequence of heme-iron serving as a nutrient for bacteria. We employed a Gram-negative sepsis model and found that elevated heme levels impaired the control of bacterial proliferation independently of heme-iron acquisition by pathogens. Heme strongly inhibited phagocytosis and the migration of human and mouse phagocytes by disrupting actin cytoskeletal dynamics via activation of the GTP-binding Rho family protein Cdc42 by the guanine nucleotide exchange factor DOCK8. A chemical screening approach revealed that quinine effectively prevented heme effects on the cytoskeleton, restored phagocytosis and improved survival in sepsis. These mechanistic insights provide potential therapeutic targets for patients with sepsis or hemolytic disorders.
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16
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Chen W, Wang S, Adhikari S, Deng Z, Wang L, Chen L, Ke M, Yang P, Tian R. Simple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling. Anal Chem 2016; 88:4864-71. [PMID: 27062885 DOI: 10.1021/acs.analchem.6b00631] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Great efforts have been taken for developing high-sensitive mass spectrometry (MS)-based proteomic technologies, among which sample preparation is one of the major focus. Here, a simple and integrated spintip-based proteomics technology (SISPROT) consisting of strong cation exchange beads and C18 disk in one pipet tip was developed. Both proteomics sample preparation steps, including protein preconcentration, reduction, alkylation, and digestion, and reversed phase (RP)-based desalting and high-pH RP-based peptide fractionation can be achieved in a fully integrated manner for the first time. This easy-to-use technology achieved high sensitivity with negligible sample loss. Proteomic analysis of 2000 HEK 293 cells readily identified 1270 proteins within 1.4 h of MS time, while 7826 proteins were identified when 100000 cells were processed and analyzed within only 22 h of MS time. More importantly, the SISPROT can be easily multiplexed on a standard centrifuge with good reproducibility (Pearson correlation coefficient > 0.98) for both single-shot analysis and deep proteome profiling with five-step high-pH RP fractionation. The SISPROT was exemplified by the triplicate analysis of 100000 stem cells from human exfoliated deciduous teeth (SHED). This led to the identification of 9078 proteins containing 3771 annotated membrane proteins, which was the largest proteome data set for dental stem cells reported to date. We expect that the SISPROT will be well suited for deep proteome profiling for fewer than 100000 cells and applied for translational studies where multiplexed technology with good label-free quantification precision is required.
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Affiliation(s)
- Wendong Chen
- Department of Chemistry, Fudan University , Shanghai 200433, China
| | - Shuai Wang
- ENT Institute of Shenzhen University, Shenzhen Longgang ENT Hospital , Shenzhen 518172, China
| | | | - Zuhui Deng
- ENT Institute of Shenzhen University, Shenzhen Longgang ENT Hospital , Shenzhen 518172, China
| | | | | | | | - Pengyuan Yang
- Department of Chemistry, Fudan University , Shanghai 200433, China
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17
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Zhao Q, Fang F, Wu C, Wu Q, Liang Y, Liang Z, Zhang L, Zhang Y. imFASP: An integrated approach combining in-situ filter-aided sample pretreatment with microwave-assisted protein digestion for fast and efficient proteome sample preparation. Anal Chim Acta 2016; 912:58-64. [DOI: 10.1016/j.aca.2016.01.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/21/2016] [Accepted: 01/27/2016] [Indexed: 01/02/2023]
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18
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Shao S, Guo T, Koh CC, Gillessen S, Joerger M, Jochum W, Aebersold R. Minimal sample requirement for highly multiplexed protein quantification in cell lines and tissues by PCT-SWATH mass spectrometry. Proteomics 2015; 15:3711-21. [DOI: 10.1002/pmic.201500161] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 07/13/2015] [Accepted: 08/12/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Shiying Shao
- Division of Endocrinology, Tongji Hospital; Huazhong University of Science & Technology; Wuhan P. R. China
- Department of Biology, Institute of Molecular Systems Biology; Eidgenössische Technische Hochschule (ETH); Zurich Switzerland
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology; Eidgenössische Technische Hochschule (ETH); Zurich Switzerland
| | - Chiek Ching Koh
- Department of Biology, Institute of Molecular Systems Biology; Eidgenössische Technische Hochschule (ETH); Zurich Switzerland
| | - Silke Gillessen
- Department of Oncology/Hematology; Kantonsspital St. Gallen; St. Gallen Switzerland
| | - Markus Joerger
- Department of Oncology/Hematology; Kantonsspital St. Gallen; St. Gallen Switzerland
| | - Wolfram Jochum
- Institute of Pathology; Kantonsspital St. Gallen; St. Gallen Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology; Eidgenössische Technische Hochschule (ETH); Zurich Switzerland
- Faculty of Science; University of Zurich; Zurich Switzerland
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19
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Chen Q, Yan G, Zhang X. Applying multiple proteases to direct digestion of hundred-scale cell samples for proteome analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1389-1394. [PMID: 26147478 DOI: 10.1002/rcm.7230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 04/16/2015] [Accepted: 05/19/2015] [Indexed: 06/04/2023]
Abstract
RATIONALE Analyzing the proteome on the scale of only several hundred cells with mass spectrometry has great significance for applications with limited sample amounts. We applied multiple proteases to the direct digestion of cells and compared the identified proteins both qualitatively and quantitatively. METHODS Three hundred cells were directly digested by trypsin, chymotrypsin, or the combination of trypsin and chymotrypsin. The peptides were identified using a LTQ-Orbitrap XL, and data were analyzed using MaxQuant software. RESULTS Different proteases produced different identified protein numbers. Trypsin proved to be the best choice for generating the largest protein number, while other proteases complemented the identification results of trypsin by increasing protein sequence coverage. Concerning the quantitative perspective, using trypsin would produce the biggest number of proteins quantifiable by intensity-based absolute quantification (iBAQ). CONCLUSIONS When hundred-scale cell samples are analyzed, an optimum choice of proteases should be made to realize different analytical objectives.
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Affiliation(s)
- Qi Chen
- Department of Chemistry, Fudan University, No. 220 Handan Rd., Shanghai, 200433, China
| | - Guoquan Yan
- Department of Chemistry, Fudan University, No. 220 Handan Rd., Shanghai, 200433, China
| | - Xiangmin Zhang
- Department of Chemistry, Fudan University, No. 220 Handan Rd., Shanghai, 200433, China
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20
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Integrated SDS removal and protein digestion by hollow fiber membrane based device for SDS-assisted proteome analysis. Talanta 2015; 141:235-8. [DOI: 10.1016/j.talanta.2015.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 03/30/2015] [Accepted: 04/05/2015] [Indexed: 11/18/2022]
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21
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Chen Q, Yan G, Gao M, Zhang X. Ultrasensitive Proteome Profiling for 100 Living Cells by Direct Cell Injection, Online Digestion and Nano-LC-MS/MS Analysis. Anal Chem 2015; 87:6674-80. [PMID: 26061007 DOI: 10.1021/acs.analchem.5b00808] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Single-cell proteome analysis has always been an exciting goal because it provides crucial information about cellular heterogeneity and dynamic change. Here we presented an integrated proteome analysis device (iPAD) for 100 living cells (iPAD-100) that might be suitable for single-cell analysis. Once cells were cultured, the iPAD-100 could be applied to inject 100 living cells, to transform the living cells into peptides, and to produce protein identification results with total automation. Due to the major obstacle for detection limit of mass spectrometry, we applied the iPAD-100 to analyze the proteome of 100 cells. In total, 813 proteins were identified in a DLD-cell proteome by three duplicate runs. Gene Ontology analysis revealed that proteins from different cellular compartments were well-represented, including membrane proteins. The iPAD-100 greatly simplified the sampling process, reduced sample loss, and prevented contamination. As a result, proteins whose copy numbers were lower than 1000 were identified from 100-cell samples with the iPAD-100, showing that a detection limit of 200 zmol was achieved. With increased sensitivity of mass spectrometry, the iPAD-100 may be able to reveal bountiful proteome information from a single cell in the near future.
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Affiliation(s)
- Qi Chen
- Collaborative Innovation Center of Chemistry for Life Sciences, Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Guoquan Yan
- Collaborative Innovation Center of Chemistry for Life Sciences, Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Mingxia Gao
- Collaborative Innovation Center of Chemistry for Life Sciences, Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Xiangmin Zhang
- Collaborative Innovation Center of Chemistry for Life Sciences, Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
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22
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Ghafari M, Keihan Falsafi S, Höger H, Bennett KL, Lubec G. Identification of new phosphorylation sites of AMPA receptors in the rat hippocampus--A resource for neuroscience research. Proteomics Clin Appl 2015; 9:808-16. [PMID: 25656447 DOI: 10.1002/prca.201400057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 10/16/2014] [Accepted: 02/03/2015] [Indexed: 12/14/2022]
Abstract
PURPOSE AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptors (AMPARs) are glutamate-gated ion channels that mediate the majority of fast excitatory synaptic transmissions in the mammalian brain. A series of phosphorylation sites have been predicted or identified and knowledge on phosphorylations is mandatory for understanding receptor biology and functions. EXPERIMENTAL DESIGN Immunoprecipitation from extracted hippocampal rat proteins was carried out using an antibody against the AMPAR GluA1 subunit, followed by identification of GluA1 and binding partners by MS. Bands from SDS-PAGE were picked, peptides were generated by trypsin and chymotrypsin digestion and identified by MS/MS (LTQ Orbitrap Velos). RESULTS Using Mascot as a search engine, phosphorylation sites S506, S645, S720, S849, S863, S895, T858, Y228, Y419, and T734 were found on GluA1; S357, S513, S656, S727, T243, T420, T741, Y 143, Y301,Y426 on GluA2; S301, S516, S657, S732, T222, and T746 were observed on GluA3; and S514, S653 was phosphorylated on GluA4. CONCLUSIONS AND CLINICAL RELEVANCE A series of additional protein modifications were observed and in particular, tyrosine and tryptophan nitrations on GluA1 were detected that may raise questions on additional regulation mechanisms for AMPARs in addition to phosphorylations. The findings are relevant for interpretation of previous work and design of future studies using AMPAR serving as a resource for neuroscience research and indeed, phosphorylations and PTMs per se would have to be respected when neuropathological and neurological disorders are being studied.
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Affiliation(s)
- Maryam Ghafari
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | | | - Harald Höger
- Core Unit of Biomedical Research, Division of Laboratory Animal Science and Genetics, Medical University of Vienna, Himberg, Austria
| | - Keiryn L Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gert Lubec
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
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23
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Li S, Plouffe BD, Belov AM, Ray S, Wang X, Murthy SK, Karger BL, Ivanov AR. An Integrated Platform for Isolation, Processing, and Mass Spectrometry-based Proteomic Profiling of Rare Cells in Whole Blood. Mol Cell Proteomics 2015; 14:1672-83. [PMID: 25755294 DOI: 10.1074/mcp.m114.045724] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Indexed: 12/29/2022] Open
Abstract
Isolation and molecular characterization of rare cells (e.g. circulating tumor and stem cells) within biological fluids and tissues has significant potential in clinical diagnostics and personalized medicine. The present work describes an integrated platform of sample procurement, preparation, and analysis for deep proteomic profiling of rare cells in blood. Microfluidic magnetophoretic isolation of target cells spiked into 1 ml of blood at the level of 1000-2000 cells/ml, followed by focused acoustics-assisted sample preparation has been coupled with one-dimensional PLOT-LC-MS methodology. The resulting zeptomole detection sensitivity enabled identification of ∼4000 proteins with injection of the equivalent of only 100-200 cells per analysis. The characterization of rare cells in limited volumes of physiological fluids is shown by the isolation and quantitative proteomic profiling of first MCF-7 cells spiked into whole blood as a model system and then two CD133+ endothelial progenitor and hematopoietic cells in whole blood from volunteers.
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Affiliation(s)
- Siyang Li
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts; §Department of Chemical Engineering, Northeastern University, Boston, Massachusetts
| | - Brian D Plouffe
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts; ¶Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Arseniy M Belov
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts; §Department of Chemical Engineering, Northeastern University, Boston, Massachusetts
| | - Somak Ray
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts
| | - Xianzhe Wang
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts; §Department of Chemical Engineering, Northeastern University, Boston, Massachusetts
| | - Shashi K Murthy
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts; ¶Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Barry L Karger
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts; §Department of Chemical Engineering, Northeastern University, Boston, Massachusetts
| | - Alexander R Ivanov
- From the ‡Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts; §Department of Chemical Engineering, Northeastern University, Boston, Massachusetts
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24
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Liu J, Wang F, Mao J, Zhang Z, Liu Z, Huang G, Cheng K, Zou H. High-Sensitivity N-Glycoproteomic Analysis of Mouse Brain Tissue by Protein Extraction with a Mild Detergent of N-Dodecyl β-D-Maltoside. Anal Chem 2015; 87:2054-7. [DOI: 10.1021/ac504700t] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jing Liu
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangjun Wang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Jiawei Mao
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhang Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheyi Liu
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang Huang
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Cheng
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanfa Zou
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
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25
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Direct digestion of proteins in living cells into peptides for proteomic analysis. Anal Bioanal Chem 2014; 407:1027-32. [DOI: 10.1007/s00216-014-8173-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/03/2014] [Accepted: 09/08/2014] [Indexed: 12/28/2022]
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26
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Multi-enzyme digestion FASP and the 'Total Protein Approach'-based absolute quantification of the Escherichia coli proteome. J Proteomics 2014; 109:322-31. [PMID: 25063446 DOI: 10.1016/j.jprot.2014.07.012] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/23/2014] [Accepted: 07/14/2014] [Indexed: 11/24/2022]
Abstract
UNLABELLED We describe a proteomic approach combining the multi-enzyme digestion FASP-sample processing strategy and the 'Total Protein Approach' applied to absolute quantification of proteins in Escherichia coli. Consecutive digestion of whole cell lysates with LysC and trypsin allowed the generation of two populations of peptides at a yield of 76%. Subsequent two 4-hour LC-MS/MS analyses allowed the identification of 19,000 unique peptides per sample. Notably, only 1.2 and 2.4% of the identified peptides were found to be incompletely cleaved by the LysC and trypsin, respectively. The analysis resulted in the identification of 2200 proteins per sample. We show high reproducibility of the approach, allowing the accurate estimation of cellular protein concentrations. Quantitative analysis of the DNA content per sample enabled the calculation of the protein content per bacterial cell and, as a result, estimation of protein copy numbers. The accuracy of these estimations was confirmed by analyzing protein complexes with known subunit stoichiometry and cellular abundances. In stationary culture, a single bacterium contains about 6500 copies of ribosomes, 300 molecules of RNA polymerase and 10 DNA polymerase assembles. The here presented experimental and computational workflow offers an easy way to analyze proteomes quantitatively. BIOLOGICAL SIGNIFICANCE We demonstrate a proteomic workflow for in-depth analysis of small proteomes with minimal fractionation extent and mass spectrometry measuring time. For the first time we provide the quantitative picture of the Escherichia coli proteome at protein copy number.
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27
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Maurer M, Müller AC, Parapatics K, Pickl WF, Wagner C, Rudashevskaya EL, Breitwieser FP, Colinge J, Garg K, Griss J, Bennett KL, Wagner SN. Comprehensive comparative and semiquantitative proteome of a very low number of native and matched epstein-barr-virus-transformed B lymphocytes infiltrating human melanoma. J Proteome Res 2014; 13:2830-45. [PMID: 24803318 DOI: 10.1021/pr401270y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Melanoma, the deadliest form of skin cancer, is highly immunogenic and frequently infiltrated with immune cells including B cells. The role of tumor-infiltrating B cells (TIBCs) in melanoma is as yet unresolved, possibly due to technical challenges in obtaining TIBCs in sufficient quantity for extensive studies and due to the limited life span of B cells in vitro. A comprehensive workflow has thus been developed for successful isolation and proteomic analysis of a low number of TIBCs from fresh, human melanoma tissue. In addition, we generated in vitro-proliferating TIBC cultures using simultaneous stimulation with Epstein-Barr virus (EBV) and the TLR9 ligand CpG-oligodesoxynucleotide (CpG ODN). The FASP method and iTRAQ labeling were utilized to obtain a comparative, semiquantitative proteome to assess EBV-induced changes in TIBCs. By using as few as 100 000 B cells (∼5 μg protein)/sample for our proteomic study, a total number of 6507 proteins were identified. EBV-induced changes in TIBCs are similar to those already reported for peripheral B cells and largely involve changes in cell cycle proliferation, apoptosis, and interferon response, while most of the proteins were not significantly altered. This study provides an essential, further step toward detailed characterization of TIBCs including functional in vitro analysis.
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Affiliation(s)
- Margarita Maurer
- Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna , Waehringer Guertel 18-20, A-1090 Vienna, Austria
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28
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Boucheron N, Tschismarov R, Goeschl L, Moser MA, Lagger S, Sakaguchi S, Winter M, Lenz F, Vitko D, Breitwieser FP, Müller L, Hassan H, Bennett KL, Colinge J, Schreiner W, Egawa T, Taniuchi I, Matthias P, Seiser C, Ellmeier W. CD4(+) T cell lineage integrity is controlled by the histone deacetylases HDAC1 and HDAC2. Nat Immunol 2014; 15:439-448. [PMID: 24681565 PMCID: PMC4346201 DOI: 10.1038/ni.2864] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 03/05/2014] [Indexed: 12/15/2022]
Abstract
Molecular mechanisms that maintain lineage integrity of helper T cells are largely unknown. Here we show histone deacetylases 1 and 2 (HDAC1 and HDAC2) as crucial regulators of this process. Loss of HDAC1 and HDAC2 during late T cell development led to the appearance of major histocompatibility complex (MHC) class II-selected CD4(+) helper T cells that expressed CD8-lineage genes such as Cd8a and Cd8b1. HDAC1 and HDAC2-deficient T helper type 0 (TH0) and TH1 cells further upregulated CD8-lineage genes and acquired a CD8(+) effector T cell program in a manner dependent on Runx-CBFβ complexes, whereas TH2 cells repressed features of the CD8(+) lineage independently of HDAC1 and HDAC2. These results demonstrate that HDAC1 and HDAC2 maintain integrity of the CD4 lineage by repressing Runx-CBFβ complexes that otherwise induce a CD8(+) effector T cell-like program in CD4(+) T cells.
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Affiliation(s)
- Nicole Boucheron
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Roland Tschismarov
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Lisa Goeschl
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, A-1090 Vienna, Austria
- Division of Rheumatology, Medicine III, Medical University of Vienna, 1090 Vienna, Austria
| | - Mirjam A. Moser
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Vienna Biocenter, Medical University of Vienna, 1030 Vienna, Austria
| | - Sabine Lagger
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Vienna Biocenter, Medical University of Vienna, 1030 Vienna, Austria
| | - Shinya Sakaguchi
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Mircea Winter
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Vienna Biocenter, Medical University of Vienna, 1030 Vienna, Austria
| | - Florian Lenz
- Division of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, 1090 Vienna, Austria
| | - Dijana Vitko
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Florian P. Breitwieser
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Lena Müller
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Hammad Hassan
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Jacques Colinge
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Wolfgang Schreiner
- Division of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, 1090 Vienna, Austria
| | - Takeshi Egawa
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS-RCAI), Yokohama, Kanagawa 230-0045, Japan
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, 4058 Basel, Switzerland and University of Basel, Faculty of Sciences, 4051 Basel, Switzerland
| | - Christian Seiser
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Vienna Biocenter, Medical University of Vienna, 1030 Vienna, Austria
| | - Wilfried Ellmeier
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, A-1090 Vienna, Austria
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29
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Wang N, Tang Y, Chen L, Li L. Microbore liquid chromatography ultraviolet detection for quantification of total peptide amount and its application for assessing sample quality in shotgun proteome analysis of hundreds of cells. J Chromatogr A 2014; 1338:51-7. [PMID: 24630977 DOI: 10.1016/j.chroma.2014.02.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 02/15/2014] [Accepted: 02/17/2014] [Indexed: 11/30/2022]
Abstract
Mass spectrometric profiling of the proteome of a small number of cells requires not only a sensitive instrument for protein/peptide separation and detection, but also a robust sample preparation protocol to process a very small amount of proteins (<1μg) present in few cells. We have developed and evaluated the performance of a microbore liquid chromatography (LC) UV detection system for quantifying the total amount of peptides in a shotgun proteome analysis workflow that is tailored for the analysis of hundreds of cancer cells. Upon the sample injection into a 1-mm-diameter reversed phase column, a step-gradient was used to first remove salts and other impurities and then elute the peptides quickly without much separation. The UV absorbance of eluted peptides at 214nm was used for peptide quantification with the aid of a calibration curve of a tryptic digest of a mixture of four standard proteins. Two linear calibration regions could be obtained in the peptide amount ranging from 0.03μg to 0.3μg and from 0.6μg to 5μg. The limit of quantification (LOQ) was determined to be 30ng (or 39ng in the linear calibration range). However, the presence of background proteins, mainly keratins, introduced during the sample preparation process was found to be the limiting factor in quantifying a lower amount of peptides from a cell lysate digest. With background absorbance from the digest of contaminant proteins in a solution, the LOQ was found to be 200ng. This nondestructive microbore LC-UV method should be useful in assessing sample quality during the development and applications of an efficient sample preparation method for proteome analysis of a small number of cells. As an example, this method was used for quantifying the peptides generated from breast cancer MCF-7 cell extracts with a limited number of cells: 250, 500 and 1000 cells. Using capillary LC quadrupole time-of-flight mass spectrometry, 81-126, 122-154 and 256-282 proteins could be identified from 250, 500, and 1000 cells, respectively, in duplicate experiments. This method was also applied for the analysis of biological triplicate samples of MCF-7 cells. The average numbers of peptides and proteins detected from the experimental triplicate analyses of biological triplicate samples were 400±71 (9 datasets) and 124±14, respectively, from 250 cells, and 531±44 and 162±16, respectively, from 500 cells.
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Affiliation(s)
- Nan Wang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Yanan Tang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Lu Chen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.
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