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Udeshi ND, Xu C, Jiang Z, Gao SM, Yin Q, Luo W, Carr SA, Davis MM, Li J. Cell-surface Milieu Remodeling in Human Dendritic Cell Activation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:1023-1032. [PMID: 39132986 PMCID: PMC11408084 DOI: 10.4049/jimmunol.2400089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/22/2024] [Indexed: 08/13/2024]
Abstract
Dendritic cells (DCs) are specialized sentinel and APCs coordinating innate and adaptive immunity. Through proteins on their cell surface, DCs sense changes in the environment, internalize pathogens, present processed Ags, and communicate with other immune cells. By combining chemical labeling and quantitative mass spectrometry, we systematically profiled and compared the cell-surface proteomes of human primary conventional DCs (cDCs) in their resting and activated states. TLR activation by a lipopeptide globally reshaped the cell-surface proteome of cDCs, with >100 proteins upregulated or downregulated. By simultaneously elevating positive regulators and reducing inhibitory signals across multiple protein families, the remodeling creates a cell-surface milieu promoting immune responses. Still, cDCs maintain the stimulatory-to-inhibitory balance by leveraging a distinct set of inhibitory molecules. This analysis thus uncovers the molecular complexity and plasticity of the cDC cell surface and provides a roadmap for understanding cDC activation and signaling.
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Affiliation(s)
| | - Charles Xu
- The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Zuzhi Jiang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
- Yuanpei College, Peking University, Beijing, China
| | - Shihong Max Gao
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
| | - Qian Yin
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX
| | - Wei Luo
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Mark M Davis
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA
| | - Jiefu Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA
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2
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Berg Luecke L, Mesidor R, Littrell J, Carpenter M, Wojtkiewicz M, Gundry RL. Veneer Is a Webtool for Rapid, Standardized, and Transparent Interpretation, Annotation, and Reporting of Mammalian Cell Surface N-Glycocapture Data. J Proteome Res 2024; 23:3235-3248. [PMID: 38412263 PMCID: PMC11301670 DOI: 10.1021/acs.jproteome.3c00800] [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: 11/17/2023] [Revised: 01/23/2024] [Accepted: 02/12/2024] [Indexed: 02/29/2024]
Abstract
Currently, no consensus exists regarding criteria required to designate a protein within a proteomic data set as a cell surface protein. Most published proteomic studies rely on varied ontology annotations or computational predictions instead of experimental evidence when attributing protein localization. Consequently, standardized approaches for analyzing and reporting cell surface proteome data sets would increase confidence in localization claims and promote data use by other researchers. Recently, we developed Veneer, a web-based bioinformatic tool that analyzes results from cell surface N-glycocapture workflows─the most popular cell surface proteomics method used to date that generates experimental evidence of subcellular location. Veneer assigns protein localization based on defined experimental and bioinformatic evidence. In this study, we updated the criteria and process for assigning protein localization and added new functionality to Veneer. Results of Veneer analysis of 587 cell surface N-glycocapture data sets from 32 published studies demonstrate the importance of applying defined criteria when analyzing cell surface proteomics data sets and exemplify how Veneer can be used to assess experimental quality and facilitate data extraction for informing future biological studies and annotating public repositories.
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Affiliation(s)
- Linda Berg Luecke
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
- Department
of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Roneldine Mesidor
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Jack Littrell
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Morgan Carpenter
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Melinda Wojtkiewicz
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Rebekah L. Gundry
- CardiOmics
Program, Center for Heart and Vascular Research and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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3
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Manda V, Pavelka J, Lau E. Proteomics applications in next generation induced pluripotent stem cell models. Expert Rev Proteomics 2024; 21:217-228. [PMID: 38511670 PMCID: PMC11065590 DOI: 10.1080/14789450.2024.2334033] [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: 06/14/2023] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
INTRODUCTION Induced pluripotent stem (iPS) cell technology has transformed biomedical research. New opportunities now exist to create new organoids, microtissues, and body-on-a-chip systems for basic biology investigations and clinical translations. AREAS COVERED We discuss the utility of proteomics for attaining an unbiased view into protein expression changes during iPS cell differentiation, cell maturation, and tissue generation. The ability to discover cell-type specific protein markers during the differentiation and maturation of iPS-derived cells has led to new strategies to improve cell production yield and fidelity. In parallel, proteomic characterization of iPS-derived organoids is helping to realize the goal of bridging in vitro and in vivo systems. EXPERT OPINIONS We discuss some current challenges of proteomics in iPS cell research and future directions, including the integration of proteomic and transcriptomic data for systems-level analysis.
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Affiliation(s)
- Vyshnavi Manda
- Department of Medicine, Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jay Pavelka
- Department of Medicine, Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Edward Lau
- Department of Medicine, Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, Colorado, USA
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4
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Dieters-Castator DZ, Manzanillo P, Yang HY, Modak RV, Rardin MJ, Gibson BW. Magnetic Bead-Based Workflow for Sensitive and Streamlined Cell Surface Proteomics. J Proteome Res 2024; 23:618-632. [PMID: 38226771 DOI: 10.1021/acs.jproteome.3c00432] [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: 01/17/2024]
Abstract
Cell surface proteins represent an important class of molecules for therapeutic targeting and cellular phenotyping. However, their enrichment and detection via mass spectrometry-based proteomics remains challenging due to low abundance, post-translational modifications, hydrophobic regions, and processing requirements. To improve their identification, we optimized a Cell-Surface Capture (CSC) workflow that incorporates magnetic bead-based processing. Using this approach, we evaluated labeling conditions (biotin tags and catalysts), enrichment specificity (streptavidin beads), missed cleavages (lysis buffers), nonenzymatic deamidation (digestion and deglycosylation buffers), and data acquisition methods (DDA, DIA, and TMT). Our findings support the use of alkoxyamine-PEG4-biotin plus 5-methoxy-anthranilic acid, SDS/urea-based lysis buffers, single-pot solid-phased-enhanced sample-preparation (SP3), and streptavidin magnetic beads for maximal surfaceome coverage. Notably, with semiautomated processing, sample handling was simplified and between ∼600 and 900 cell surface N-glycoproteins were identified from only 25-200 μg of HeLa protein. CSC also revealed significant differences between in vitro monolayer cultures and in vivo tumor xenografts of murine CT26 colon adenocarcinoma samples that may aid in target identification for drug development. Overall, the improved efficiency of the magnetic-based CSC workflow identified both previously reported and novel N-glycosites with less material and high reproducibility that should help advance the field of surfaceomics by providing insight in cellular phenotypes not previously documented.
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Affiliation(s)
| | - Paolo Manzanillo
- Inflammation, Amgen Research, South San Francisco, California 94080, United States
| | - Han-Yin Yang
- Discovery Proteomics, Amgen Research, South San Francisco, California 94080, United States
| | - Rucha V Modak
- Inflammation, Amgen Research, South San Francisco, California 94080, United States
| | - Matthew J Rardin
- Discovery Proteomics, Amgen Research, South San Francisco, California 94080, United States
| | - Bradford W Gibson
- Discovery Proteomics, Amgen Research, South San Francisco, California 94080, United States
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5
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Sinenko SA, Tomilin AN. Metabolic control of induced pluripotency. Front Cell Dev Biol 2024; 11:1328522. [PMID: 38274274 PMCID: PMC10808704 DOI: 10.3389/fcell.2023.1328522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024] Open
Abstract
Pluripotent stem cells of the mammalian epiblast and their cultured counterparts-embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs)-have the capacity to differentiate in all cell types of adult organisms. An artificial process of reactivation of the pluripotency program in terminally differentiated cells was established in 2006, which allowed for the generation of induced pluripotent stem cells (iPSCs). This iPSC technology has become an invaluable tool in investigating the molecular mechanisms of human diseases and therapeutic drug development, and it also holds tremendous promise for iPSC applications in regenerative medicine. Since the process of induced reprogramming of differentiated cells to a pluripotent state was discovered, many questions about the molecular mechanisms involved in this process have been clarified. Studies conducted over the past 2 decades have established that metabolic pathways and retrograde mitochondrial signals are involved in the regulation of various aspects of stem cell biology, including differentiation, pluripotency acquisition, and maintenance. During the reprogramming process, cells undergo major transformations, progressing through three distinct stages that are regulated by different signaling pathways, transcription factor networks, and inputs from metabolic pathways. Among the main metabolic features of this process, representing a switch from the dominance of oxidative phosphorylation to aerobic glycolysis and anabolic processes, are many critical stage-specific metabolic signals that control the path of differentiated cells toward a pluripotent state. In this review, we discuss the achievements in the current understanding of the molecular mechanisms of processes controlled by metabolic pathways, and vice versa, during the reprogramming process.
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Affiliation(s)
- Sergey A. Sinenko
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
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6
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Yan T, Boatner LM, Cui L, Tontonoz PJ, Backus KM. Defining the Cell Surface Cysteinome Using Two-Step Enrichment Proteomics. JACS AU 2023; 3:3506-3523. [PMID: 38155636 PMCID: PMC10751780 DOI: 10.1021/jacsau.3c00707] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
The plasma membrane proteome is a rich resource of functionally important and therapeutically relevant protein targets. Distinguished by high hydrophobicity, heavy glycosylation, disulfide-rich sequences, and low overall abundance, the cell surface proteome remains undersampled in established proteomic pipelines, including our own cysteine chemoproteomics platforms. Here, we paired cell surface glycoprotein capture with cysteine chemoproteomics to establish a two-stage enrichment method that enables chemoproteomic profiling of cell Surface Cysteinome. Our "Cys-Surf" platform captures >2,800 total membrane protein cysteines in 1,046 proteins, including 1,907 residues not previously captured by bulk proteomic analysis. By pairing Cys-Surf with an isotopic chemoproteomic readout, we uncovered 821 total ligandable cysteines, including known and novel sites. Cys-Surf also robustly delineates redox-sensitive cysteines, including cysteines prone to activation-dependent changes to cysteine oxidation state and residues sensitive to addition of exogenous reductants. Exemplifying the capacity of Cys-Surf to delineate functionally important cysteines, we identified a redox sensitive cysteine in the low-density lipoprotein receptor (LDLR) that impacts both the protein localization and uptake of low-density lipoprotein (LDL) particles. Taken together, the Cys-Surf platform, distinguished by its two-stage enrichment paradigm, represents a tailored approach to delineate the functional and therapeutic potential of the plasma membrane cysteinome.
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Affiliation(s)
- Tianyang Yan
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Lisa M. Boatner
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Liujuan Cui
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, Los Angeles, California 90095, United States
| | - Peter J. Tontonoz
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, Los Angeles, California 90095, United States
| | - Keriann M. Backus
- Department
of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
- DOE
Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095, United States
- Jonsson
Comprehensive Cancer Center, UCLA, Los Angeles, California 90095, United States
- Eli
and Edythe
Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, California 90095, United States
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7
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Gupta A, Shaik SK, Balasubramanian L, Chakraborty U. MSCProfiler: a single cell image processing workflow to investigate mesenchymal stem cell heterogeneity. Biotechniques 2023; 75:195-209. [PMID: 37916466 DOI: 10.2144/btn-2023-0048] [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: 11/03/2023] Open
Abstract
Single cell cytometry has demonstrated plausible immuno-heterogeneity of mesenchymal stem cells (MSCs) owing to their multivariate stromal origin. To contribute successfully to next-generation stem cell therapeutics, a deeper understanding of their cellular morphology and immunophenotype is important. In this study, the authors describe MSCProfiler, an image analysis pipeline developed using CellProfiler software. This workflow can extract geometrical and texture features such as shape, size, eccentricity and entropy, along with intensity values of the surface markers from multiple single cell images obtained using imaging flow cytometry. This screening pipeline can be used to analyze geometrical and texture features of all types of MSCs across different passages hallmarked by enhanced feature extraction potential from brightfield and fluorescent images of the cells.
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Affiliation(s)
- Ayona Gupta
- Manipal Institute of Regenerative Medicine, Bengaluru, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | | | | | - Uttara Chakraborty
- Manipal Institute of Regenerative Medicine, Bengaluru, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
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8
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Yan T, Boatner LM, Cui L, Tontonoz P, Backus KM. Defining the Cell Surface Cysteinome using Two-step Enrichment Proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562832. [PMID: 37904933 PMCID: PMC10614875 DOI: 10.1101/2023.10.17.562832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
The plasma membrane proteome is a rich resource of functional and therapeutically relevant protein targets. Distinguished by high hydrophobicity, heavy glycosylation, disulfide-rich sequences, and low overall abundance, the cell surface proteome remains undersampled in established proteomic pipelines, including our own cysteine chemoproteomics platforms. Here we paired cell surface glycoprotein capture with cysteine chemoproteomics to establish a two-stage enrichment method that enables chemoproteomic profiling of cell Surface Cysteinome. Our "Cys-Surf" platform captures >2,800 total membrane protein cysteines in 1,046 proteins, including 1,907 residues not previously captured by bulk proteomic analysis. By pairing Cys-Surf with an isotopic chemoproteomic readout, we uncovered 821 total ligandable cysteines, including known and novel sites. Cys-Surf also robustly delineates redox-sensitive cysteines, including cysteines prone to activation-dependent changes to cysteine oxidation state and residues sensitive to addition of exogenous reductants. Exemplifying the capacity of Cys-Surf to delineate functionally important cysteines, we identified a redox sensitive cysteine in the low-density lipoprotein receptor (LDLR) that impacts both the protein localization and uptake of LDL particles. Taken together, the Cys-Surf platform, distinguished by its two-stage enrichment paradigm, represents a tailored approach to delineate the functional and therapeutic potential of the plasma membrane cysteinome.
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Affiliation(s)
- Tianyang Yan
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
| | - Lisa M. Boatner
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
| | - Liujuan Cui
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles; Los Angeles, CA 90095, USA
| | - Peter Tontonoz
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles; Los Angeles, CA 90095, USA
| | - Keriann M. Backus
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 (USA)
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (USA)
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095 (USA)
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095 (USA)
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095 (USA)
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de Jong E, Kocer A. Current Methods for Identifying Plasma Membrane Proteins as Cancer Biomarkers. MEMBRANES 2023; 13:409. [PMID: 37103836 PMCID: PMC10142483 DOI: 10.3390/membranes13040409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 06/19/2023]
Abstract
Plasma membrane proteins are a special class of biomolecules present on the cellular membrane. They provide the transport of ions, small molecules, and water in response to internal and external signals, define a cell's immunological identity, and facilitate intra- and intercellular communication. Since they are vital to almost all cellular functions, their mutants, or aberrant expression is linked to many diseases, including cancer, where they are a part of cancer cell-specific molecular signatures and phenotypes. In addition, their surface-exposed domains make them exciting biomarkers for targeting by imaging agents and drugs. This review looks at the challenges in identifying cancer-related cell membrane proteins and the current methodologies that solve most of the challenges. We classified the methodologies as biased, i.e., search cells for the presence of already known membrane proteins. Second, we discuss the unbiased methods that can identify proteins without prior knowledge of what they are. Finally, we discuss the potential impact of membrane proteins on the early detection and treatment of cancer.
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10
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Sun F, Suttapitugsakul S, Wu R. Systematic characterization of extracellular glycoproteins using mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:519-545. [PMID: 34047389 PMCID: PMC8627532 DOI: 10.1002/mas.21708] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 05/13/2023]
Abstract
Surface and secreted glycoproteins are essential to cells and regulate many extracellular events. Because of the diversity of glycans, the low abundance of many glycoproteins, and the complexity of biological samples, a system-wide investigation of extracellular glycoproteins is a daunting task. With the development of modern mass spectrometry (MS)-based proteomics, comprehensive analysis of different protein modifications including glycosylation has advanced dramatically. This review focuses on the investigation of extracellular glycoproteins using MS-based proteomics. We first discuss the methods for selectively enriching surface glycoproteins and investigating protein interactions on the cell surface, followed by the application of MS-based proteomics for surface glycoprotein dynamics analysis and biomarker discovery. We then summarize the methods to comprehensively study secreted glycoproteins by integrating various enrichment approaches with MS-based proteomics and their applications for global analysis of secreted glycoproteins in different biological samples. Collectively, MS significantly expands our knowledge of extracellular glycoproteins and enables us to identify extracellular glycoproteins as potential biomarkers for disease detection and drug targets for disease treatment.
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Affiliation(s)
| | | | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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11
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Liu Y, Bertels S, Reischl M, Peravali R, Bastmeyer M, Popova AA, Levkin PA. Droplet Microarray Based Screening Identifies Proteins for Maintaining Pluripotency of hiPSCs. Adv Healthc Mater 2022; 11:e2200718. [PMID: 35799451 DOI: 10.1002/adhm.202200718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/10/2022] [Indexed: 01/27/2023]
Abstract
Human induced pluripotent stem cells (hiPSCs) are crucial for disease modeling, drug discovery, and personalized medicine. Animal-derived materials hinderapplications of hiPSCs in medical fields. Thus, novel and well-defined substrate coatings capable of maintaining hiPSC pluripotency are important for advancing biomedical applications of hiPSCs. Here a miniaturized droplet microarray (DMA) platform to investigate 11 well-defined proteins, their 55 binary and 165 ternary combinations for their ability to maintainpluripotency of hiPSCs when applied as a surface coating, is used. Using this screening approach, ten protein group coatings are identified, which promote significantly higher NANOG expression of hiPSCs in comparison with Matrigel coating. With two of the identified coatings, long-term pluripotency maintenance of hiPSCs and subsequent differentiation into three germ layers are achieved. Compared with conventional high-throughput screening (HTS) in 96-well plates, the DMA platform uses only 83 µL of protein solution (0.83 µg total protein) and only ≈2.8 × 105 cells, decreasing the amount of proteins and cells ≈860 and 25-fold, respectively. The identified proteins will be essential for research and applications using hiPSCs, while the DMA platform demonstrates great potential for miniaturized HTS of scarce cells or expensive materials such as recombinant proteins.
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Affiliation(s)
- Yanxi Liu
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Sarah Bertels
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Markus Reischl
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Ravindra Peravali
- Institute of Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Martin Bastmeyer
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,Institute of Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Anna A Popova
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Pavel A Levkin
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,Institute of Organic Chemistry, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131, Karlsruhe, Germany
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12
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Somatic Reprogramming-Above and Beyond Pluripotency. Cells 2021; 10:cells10112888. [PMID: 34831113 PMCID: PMC8616127 DOI: 10.3390/cells10112888] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 12/11/2022] Open
Abstract
Pluripotent stem cells, having long been considered the fountain of youth, have caught the attention of many researchers from diverse backgrounds due to their capacity for unlimited self-renewal and potential to differentiate into all cell types. Over the past 15 years, the advanced development of induced pluripotent stem cells (iPSCs) has displayed an unparalleled potential for regenerative medicine, cell-based therapies, modeling human diseases in culture, and drug discovery. The transcription factor quartet (Oct4, Sox2, Klf4, and c-Myc) reprograms highly differentiated somatic cells back to a pluripotent state recapitulated embryonic stem cells (ESCs) in different aspects, including gene expression profile, epigenetic signature, and functional pluripotency. With the prior fruitful studies in SCNT and cell fusion experiments, iPSC finds its place and implicates that the differentiated somatic epigenome retains plasticity for re-gaining the pluripotency and further stretchability to reach a totipotency-like state. These achievements have revolutionized the concept and created a new avenue in biomedical sciences for clinical applications. With the advent of 15 years’ progress-making after iPSC discovery, this review is focused on how the current concept is established by revisiting those essential landmark studies and summarizing its current biomedical applications status to facilitate the new era entry of regenerative therapy.
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13
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Cell surface markers for immunophenotyping human pluripotent stem cell-derived cardiomyocytes. Pflugers Arch 2021; 473:1023-1039. [PMID: 33928456 DOI: 10.1007/s00424-021-02549-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/09/2021] [Accepted: 02/25/2021] [Indexed: 02/08/2023]
Abstract
Human pluripotent stem cells (hPSC) self-renew and represent a potentially unlimited source for the production of cardiomyocytes (CMs) suitable for studies of human cardiac development, drug discovery, cardiotoxicity testing, and disease modelling and for cell-based therapies. However, most cardiac differentiation protocols yield mixed cultures of atrial-, ventricular-, and pacemaker-like cells at various stages of development, as well as non-CMs. The proportions and maturation states of these cell types result from disparities among differentiation protocols and time of cultivation, as well as hPSC reprogramming inconsistencies and genetic background variations. The reproducible use of hPSC-CMs for research and therapy is therefore limited by issues of cell population heterogeneity and functional states of maturation. A validated method that overcomes issues of cell heterogeneity is immunophenotyping coupled with live cell sorting, an approach that relies on accessible surface markers restricted to the desired cell type(s). Here we review current progress in unravelling heterogeneity in hPSC-cardiac cultures and in the identification of surface markers suitable for defining cardiac identity, subtype specificity, and maturation states.
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14
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Parashar D, Geethadevi A, McAllister D, Ebben J, Peterson FC, Jensen DR, Bishop E, Pradeep S, Volkman BF, Dwinell MB, Chaluvally-Raghavan P, James MA. Targeted biologic inhibition of both tumor cell-intrinsic and intercellular CLPTM1L/CRR9-mediated chemotherapeutic drug resistance. NPJ Precis Oncol 2021; 5:16. [PMID: 33654182 PMCID: PMC7925570 DOI: 10.1038/s41698-021-00152-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/06/2021] [Indexed: 02/07/2023] Open
Abstract
Recurrence of therapy-resistant tumors is a principal problem in solid tumor oncology, particularly in ovarian cancer. Despite common complete responses to first line, platinum-based therapies, most women with ovarian cancer recur, and eventually, nearly all with recurrent disease develop platinum resistance. Likewise, both intrinsic and acquired resistance contribute to the dismal prognosis of pancreatic cancer. Our previous work and that of others has established CLPTM1L (cleft lip and palate transmembrane protein 1-like)/CRR9 (cisplatin resistance related protein 9) as a cytoprotective oncofetal protein that is present on the tumor cell surface. We show that CLPTM1L is broadly overexpressed and accumulated on the plasma membrane of ovarian tumor cells, while weakly or not expressed in normal tissues. High expression of CLPTM1L is associated with poor outcome in ovarian serous adenocarcinoma. Robust re-sensitization of resistant ovarian cancer cells to platinum-based therapy was achieved using human monoclonal biologics inhibiting CLPTM1L in both orthotopic isografts and patient-derived cisplatin resistant xenograft models. Furthermore, we demonstrate that in addition to cell-autonomous cytoprotection by CLPTM1L, extracellular CLPTM1L confers resistance to chemotherapeutic killing in an ectodomain-dependent fashion, and that this intercellular resistance mechanism is inhibited by anti-CLPTM1L biologics. Specifically, exosomal CLPTM1L from cisplatin-resistant ovarian carcinoma cell lines conferred resistance to cisplatin in drug-sensitive parental cell lines. CLPTM1L is present in extracellular vesicle fractions of tumor culture supernatants and in patients' serum with increasing abundance upon chemotherapy treatment. These findings have encouraging implications for the use of anti-CLPTM1L targeted biologics in the treatment of therapy-resistant tumors.
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Affiliation(s)
- Deepak Parashar
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Anjali Geethadevi
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Donna McAllister
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Johnathan Ebben
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | | | - Davin R Jensen
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Erin Bishop
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Sunila Pradeep
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian F Volkman
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Michael B Dwinell
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
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15
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Meyfour A, Pahlavan S, Mirzaei M, Krijgsveld J, Baharvand H, Salekdeh GH. The quest of cell surface markers for stem cell therapy. Cell Mol Life Sci 2021; 78:469-495. [PMID: 32710154 PMCID: PMC11073434 DOI: 10.1007/s00018-020-03602-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022]
Abstract
Stem cells and their derivatives are novel pharmaceutics that have the potential for use as tissue replacement therapies. However, the heterogeneous characteristics of stem cell cultures have hindered their biomedical applications. In theory and practice, when cell type-specific or stage-specific cell surface proteins are targeted by unique antibodies, they become highly efficient in detecting and isolating specific cell populations. There is a growing demand to identify reliable and actionable cell surface markers that facilitate purification of particular cell types at specific developmental stages for use in research and clinical applications. The identification of these markers as very important members of plasma membrane proteins, ion channels, transporters, and signaling molecules has directly benefited from proteomics and tools for proteomics-derived data analyses. Here, we review the methodologies that have played a role in the discovery of cell surface markers and introduce cutting edge single cell proteomics as an advanced tool. We also discuss currently available specific cell surface markers for stem cells and their lineages, with emphasis on the nervous system, heart, pancreas, and liver. The remaining gaps that pertain to the discovery of these markers and how single cell proteomics and identification of surface markers associated with the progenitor stages of certain terminally differentiated cells may pave the way for their use in regenerative medicine are also discussed.
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Affiliation(s)
- Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany
- Medical Faculty, Heidelberg University, Im Neuenheimer Feld 672, Heidelberg, Germany
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem St, P.O. Box: 16635-148, 1665659911, Tehran, Iran.
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16
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Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
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17
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Oldham RAA, Faber ML, Keppel TR, Buchberger AR, Waas M, Hari P, Gundry RL, Medin JA. Discovery and validation of surface N-glycoproteins in MM cell lines and patient samples uncovers immunotherapy targets. J Immunother Cancer 2020; 8:e000915. [PMID: 32771993 PMCID: PMC7418848 DOI: 10.1136/jitc-2020-000915] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Multiple myeloma (MM) is characterized by clonal expansion of malignant plasma cells in the bone marrow. While recent advances in treatment for MM have improved patient outcomes, the 5-year survival rate remains ~50%. A better understanding of the MM cell surface proteome could facilitate development of new directed therapies and assist in stratification and monitoring of patient outcomes. METHODS In this study, we first used a mass spectrometry (MS)-based discovery-driven cell surface capture (CSC) approach to map the cell surface N-glycoproteome of MM cell lines. Next, we developed targeted MS assays, and applied these to cell lines and primary patient samples to refine the list of candidate tumor markers. Candidates of interest detected by MS on MM patient samples were further validated using flow cytometry (FCM). RESULTS We identified 696 MM cell surface N-glycoproteins by CSC, and developed 73 targeted MS detection assays. MS-based validation using primary specimens detected 30 proteins with significantly higher abundance in patient MM cells than controls. Nine of these proteins were identified as potential immunotherapeutic targets, including five that were validated by FCM, confirming their expression on the cell surface of primary MM patient cells. CONCLUSIONS This MM surface N-glycoproteome will be a valuable resource in the development of biomarkers and therapeutics. Further, we anticipate that our targeted MS assays will have clinical benefit for the diagnosis, stratification, and treatment of MM patients.
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Affiliation(s)
- Robyn A A Oldham
- Medical Biophysics, University of Toronto Faculty of Medicine, Toronto, Ontario, Canada
- Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Mary L Faber
- Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Theodore R Keppel
- Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Amanda R Buchberger
- Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Matthew Waas
- Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Parameswaran Hari
- Division of Hematology Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Rebekah L Gundry
- Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jeffrey A Medin
- Medical Biophysics, University of Toronto Faculty of Medicine, Toronto, Ontario, Canada
- Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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18
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Waas M, Littrell J, Gundry RL. CIRFESS: An Interactive Resource for Querying the Set of Theoretically Detectable Peptides for Cell Surface and Extracellular Enrichment Proteomic Studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1389-1397. [PMID: 32212654 PMCID: PMC8116119 DOI: 10.1021/jasms.0c00021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Cell surface transmembrane, extracellular, and secreted proteins are high value targets for immunophenotyping, drug development, and studies related to intercellular communication in health and disease. As the number of specific and validated affinity reagents that target this subproteome are limited, mass spectrometry (MS)-based approaches will continue to play a critical role in enabling discovery and quantitation of these molecules. Given the technical considerations that make MS-based cell surface proteome studies uniquely challenging, it can be difficult to select an appropriate experimental approach. To this end, we have integrated multiple prediction strategies and annotations into a single online resource, Compiled Interactive Resource for Extracellular and Surface Studies (CIRFESS). CIRFESS enables rapid interrogation of the human proteome to reveal the cell surface proteome theoretically detectable by current approaches and highlights where current prediction strategies provide concordant and discordant information. We applied CIRFESS to identify the percentage of various subsets of the proteome which are expected to be captured by targeted enrichment strategies, including two established methods and one that is possible but not yet demonstrated. These results will inform the selection of available proteomic strategies and development of new strategies to enhance coverage of the cell surface and extracellular proteome. CIRFESS is available at www.cellsurfer.net/cirfess.
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Affiliation(s)
- Matthew Waas
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Jack Littrell
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine, and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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19
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Waas M, Snarrenberg ST, Littrell J, Jones Lipinski RA, Hansen PA, Corbett JA, Gundry RL. SurfaceGenie: a web-based application for prioritizing cell-type-specific marker candidates. Bioinformatics 2020; 36:3447-3456. [PMID: 32053146 PMCID: PMC7267825 DOI: 10.1093/bioinformatics/btaa092] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 12/16/2019] [Accepted: 02/05/2020] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Cell-type-specific surface proteins can be exploited as valuable markers for a range of applications including immunophenotyping live cells, targeted drug delivery and in vivo imaging. Despite their utility and relevance, the unique combination of molecules present at the cell surface are not yet described for most cell types. A significant challenge in analyzing 'omic' discovery datasets is the selection of candidate markers that are most applicable for downstream applications. RESULTS Here, we developed GenieScore, a prioritization metric that integrates a consensus-based prediction of cell surface localization with user-input data to rank-order candidate cell-type-specific surface markers. In this report, we demonstrate the utility of GenieScore for analyzing human and rodent data from proteomic and transcriptomic experiments in the areas of cancer, stem cell and islet biology. We also demonstrate that permutations of GenieScore, termed IsoGenieScore and OmniGenieScore, can efficiently prioritize co-expressed and intracellular cell-type-specific markers, respectively. AVAILABILITY AND IMPLEMENTATION Calculation of GenieScores and lookup of SPC scores is made freely accessible via the SurfaceGenie web application: www.cellsurfer.net/surfacegenie. CONTACT Rebekah.gundry@unmc.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shana T Snarrenberg
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jack Littrell
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Polly A Hansen
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - John A Corbett
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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20
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Affiliation(s)
| | | | - Ronghu Wu
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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21
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Li Y, Qin H, Ye M. An overview on enrichment methods for cell surface proteome profiling. J Sep Sci 2019; 43:292-312. [PMID: 31521063 DOI: 10.1002/jssc.201900700] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/17/2022]
Abstract
Cell surface proteins are essential for many important biological processes, including cell-cell interactions, signal transduction, and molecular transportation. With the characteristics of low abundance, high hydrophobicity, and high heterogeneity, it is difficult to get a comprehensive view of cell surface proteome by direct analysis. Thus, it is important to selectively enrich the cell surface proteins before liquid chromatography with mass spectrometry analysis. In recent years, a variety of enrichment methods have been developed. Based on the separation mechanism, these methods could be mainly classified into three types. The first type is based on their difference in the physicochemical property, such as size, density, charge, and hydrophobicity. The second one is based on the bimolecular affinity interaction with lectin or antibody. And the third type is based on the chemical covalent coupling to free side groups of surface-exposed proteins or carbohydrate chains, such as primary amines, carboxyl groups, glycan side chains. In addition, metabolic labeling and enzymatic reaction-based methods have also been employed to selectively isolate cell surface proteins. In this review, we will provide a comprehensive overview of the enrichment methods for cell surface proteome profiling.
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Affiliation(s)
- Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China
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22
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Chen Z, Huang J, Li L. Recent advances in mass spectrometry (MS)-based glycoproteomics in complex biological samples. Trends Analyt Chem 2019; 118:880-892. [PMID: 31579312 PMCID: PMC6774629 DOI: 10.1016/j.trac.2018.10.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein glycosylation plays a key role in various biological processes and disease-related pathological progression. Mass spectrometry (MS)-based glycoproteomics is a powerful approach that provides a system-wide profiling of the glycoproteome in a high-throughput manner. There have been numerous significant technological advances in this field, including improved glycopeptide enrichment, hybrid fragmentation techniques, emerging specialized software packages, and effective quantitation strategies, as well as more dedicated workflows. With increasingly sophisticated glycoproteomics tools on hand, researchers have extensively adapted this approach to explore different biological systems both in terms of in-depth glycoproteome profiling and comparative glycoproteome analysis. Quantitative glycoproteomics enables researchers to discover novel glycosylation-based biomarkers in various diseases with potential to offer better sensitivity and specificity for disease diagnosis. In this review, we present recent methodological developments in MS-based glycoproteomics and highlight its utility and applications in answering various questions in complex biological systems.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
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23
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Chen Z, Huang J, Li L. Recent advances in mass spectrometry (MS)-based glycoproteomics in complex biological samples. Trends Analyt Chem 2019. [PMID: 31579312 DOI: 10.1016/jtrac.2018.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Protein glycosylation plays a key role in various biological processes and disease-related pathological progression. Mass spectrometry (MS)-based glycoproteomics is a powerful approach that provides a system-wide profiling of the glycoproteome in a high-throughput manner. There have been numerous significant technological advances in this field, including improved glycopeptide enrichment, hybrid fragmentation techniques, emerging specialized software packages, and effective quantitation strategies, as well as more dedicated workflows. With increasingly sophisticated glycoproteomics tools on hand, researchers have extensively adapted this approach to explore different biological systems both in terms of in-depth glycoproteome profiling and comparative glycoproteome analysis. Quantitative glycoproteomics enables researchers to discover novel glycosylation-based biomarkers in various diseases with potential to offer better sensitivity and specificity for disease diagnosis. In this review, we present recent methodological developments in MS-based glycoproteomics and highlight its utility and applications in answering various questions in complex biological systems.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
- School of Life Sciences, Tianjin University, Tianjin, 300072, China
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24
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Sensitive profiling of cell surface proteome by using an optimized biotinylation method. J Proteomics 2019; 196:33-41. [PMID: 30707948 DOI: 10.1016/j.jprot.2019.01.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 01/23/2023]
Abstract
Cell surface proteins are responsible for many critical functions. Systematical profiling of these proteins would provide a unique molecular fingerprint to classify cells and provide important information to guide immunotherapy. Cell surface biotinylation method is one of the effective methods for cell surface proteome profiling. However, classical workflows suffer the disadvantage of poor sensitivity. In this work, we presented an optimized protocol which enabled identification of more cell surface proteins from a smaller number of cells. When this protocol was combined with a tip based fractionation scheme, 4510 proteins, including 2055 annotated cell surface-associated proteins, were identified with only 20 microgram protein digest, showing the superior sensitivity of the approach. To enable process 10 times fewer cells, a pipet tip based protocol was developed, which led to the identification of about 600 cell surface-associated proteins. Finally, the new protocol was applied to compare the cell surface proteomes of two breast cancer cell lines, BT474 and MCF7. It was found that many cell surface-associated proteins were differentially expressed. The new protocols were demonstrated to be easy to perform, time-saving, and yielding good selectivity and high sensitivity. We expect this protocol would have broad applications in the future. SIGNIFICANCE: Cell surface proteins confer specific cellular functions and are easily accessible. They are often used as drug targets and potential biomarkers for prognostic or diagnostic purposes. Thus, efficient methods for profiling cell surface proteins are highly demanded. Cell surface biotinylation method is one of the effective methods for cell surface proteome profiling. However, classical workflows suffer the disadvantage of poor sensitivity. In this work, we presented an optimized protocol which enabled identification of more cell surface proteins from a smaller number of starting cells. The new protocol is easier to perform, time-saving and has less protein loss. By using a special pipet tip, sensitive and in-depth cell surface proteome analysis could be achieved. In combination with label-free quantitative MS, the new protocol can be applied to the differential analysis of the cell surface proteomes between different cell lines to find genetically- or drug-induced changes. We expect this protocol would have broad application in cell surface protein studies, including the discovery of diagnostic marker proteins and potential therapeutic targets.
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25
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Clarke WR, Amundadottir L, James MA. CLPTM1L/CRR9 ectodomain interaction with GRP78 at the cell surface signals for survival and chemoresistance upon ER stress in pancreatic adenocarcinoma cells. Int J Cancer 2019; 144:1367-1378. [PMID: 30468251 DOI: 10.1002/ijc.32012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 09/24/2018] [Accepted: 11/09/2018] [Indexed: 12/15/2022]
Abstract
Altered regulation of endoplasmic reticulum (ER) homeostasis has been implicated in many cancers and has recently become a therapeutic and chemosensitization target of interest. We have identified Cleft Lip and Palate Transmembrane 1-Like (CLPTM1L)/Cisplatin Resistance Related Protein 9 (CRR9) as an ER stress related mediator of cytoprotection in pancreatic cancer. We recently demonstrated that CLPTM1L is highly expressed in pancreatic ductal adenocarcinoma and associated with poor outcome. Furthermore, we have discovered that CLPTM1L interacts with phosphoinositol-3-kinase-alpha at the tumor cell surface and causes up-regulation of Bcl-xL and pAkt mediated survival signaling. Here, we demonstrate surface relocalization and survival signaling by CLPTM1L triggered by endoplasmic reticular (ER) stress. We demonstrate the interaction of CLPTM1L with the central ER stress survival mediator, Glucose Regulated Protein 78 (GRP78)/Binding Immunoglobulin Protein (BiP) and PI3K-alpha /p110α. This interaction and surface relocalization of CLPTM1L and GRP78 is induced by ER stress, including that caused by treatment with gemcitabine. We demonstrate that the extracellular loop of CLPTM1L is required for gemcitabine resistance and interaction with GRP78. This interaction and the chemoresistance effect conferred by this pathway is targetable with our recently developed inhibitory CLPTM1L antibodies, which may represent novel modalities of chemosensitization and treatment of pancreatic adenocarcinoma. Anchorage independent growth, GRP78-mediated chemoresistance, and Akt phosphorylation were abrogated by inhibition of CLPTM1L. These findings demonstrate a novel and potentially targetable mechanism of cytoprotection and chemoresistance in pancreatic tumors.
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Affiliation(s)
- William R Clarke
- Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Laufey Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Gaithersburg, Maryland, USA
| | - Michael A James
- Department of Surgery, Division of Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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26
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Fujinaka CM, Waas M, Gundry RL. Mass Spectrometry-Based Identification of Extracellular Domains of Cell Surface N-Glycoproteins: Defining the Accessible Surfaceome for Immunophenotyping Stem Cells and Their Derivatives. Methods Mol Biol 2018; 1722:57-78. [PMID: 29264798 DOI: 10.1007/978-1-4939-7553-2_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Human stem cells and their progeny are valuable for a variety of research applications and have the potential to revolutionize approaches to regenerative medicine. However, we currently have limited tools to permit live isolation of homogeneous populations of cells apt for mechanistic studies or cellular therapies. While these challenges can be overcome through the use of immunophenotyping based on accessible cell surface markers, the success of this process depends on the availability of reliable antibodies and well-characterized markers, which are lacking for most stem cell lineages. This chapter outlines an iterative process for the development of new cell surface marker barcodes for identifying and selecting stem cell derived progeny of specific cell types, subtypes, and maturation stages, where antibody-independent identification of cell surface proteins is achieved using a modern chemoproteomic approach to specifically identify N-glycoproteins localized to the cell surface. By taking advantage of a large repository of available cell surfaceome data, proteins that are unlikely to confer cell type specificity can be rapidly eliminated from consideration. Subsequently, targeted quantitation by mass spectrometry can be used to refine candidates of interest, and a bioinformatic visualization tool is key to mapping experimental data to candidate protein sequences for the purpose of epitope selection during the antibody development phase. Overall, the process of developing cell surface barcodes for immunophenotyping is iterative and can include multiple rounds of discovery, refinement, and validation depending on the phenotypic resolution required.
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Affiliation(s)
- Chelsea M Fujinaka
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.
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27
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Shekari F, Baharvand H, Salekdeh GH. Organellar proteomics of embryonic stem cells. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 95:215-30. [PMID: 24985774 DOI: 10.1016/b978-0-12-800453-1.00007-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Embryonic stem cells (ESCs) are undifferentiated cells with two common remarkable features known as self-renewal and differentiation. Proteomics plays an increasingly important role in understanding molecular mechanisms underlying self-renewal and pluripotency of ESCs and their applications in cell therapy and developmental biology studies. As the function of a protein is strongly associated with its localization in cell, a complete and accurate picture of the proteome of ESCs cannot be achieved without knowing the subcellular locations of proteins. Subcellular fractionation allows enrichment of low abundant proteins and signaling complexes and reduces the complexity of the sample. It also provided insight into tracking proteins that shuttle between different compartments. Despite the substantial interest and efforts in ESC subcellular proteomics area, progress has been relatively limited. In this review, we present an overview on current status of ESCs organelle proteomics research and discuss challenges in subcellular proteomics.
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Affiliation(s)
- Faezeh Shekari
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran
| | - Hossein Baharvand
- Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran; Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.
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Haverland NA, Waas M, Ntai I, Keppel T, Gundry RL, Kelleher NL. Cell Surface Proteomics of N-Linked Glycoproteins for Typing of Human Lymphocytes. Proteomics 2018; 17. [PMID: 28834292 DOI: 10.1002/pmic.201700156] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/27/2017] [Indexed: 11/12/2022]
Abstract
Lymphocytes are immune cells that are critical for the maintenance of adaptive immunity. Differentiation of lymphoid progenitors yields B-, T-, and NK-cell subtypes that individually correlate with specific forms of leukemia or lymphoma. Therefore, it is imperative a precise method of cell categorization is utilized to detect differences in distinct disease states present in patients. One viable means of classification involves evaluation of the cell surface proteome of lymphoid malignancies. Specifically, this manuscript details the use of an antibody independent approach known as Cell Surface Capture Technology, to assess the N-glycoproteome of four human lymphocyte cell lines. Altogether, 404 cell surface N-glycoproteins were identified as markers for specific cell types involved in lymphocytic malignancies, including 82 N-glycoproteins that had not been previously been described for B or T cells within the Cell Surface Protein Atlas. Comparative analysis, hierarchical clustering techniques, and label-free quantitation were used to reveal proteins most informative for each cell type. Undoubtedly, the characterization of the cell surface proteome of lymphoid malignancies is a first step toward improving personalized diagnosis and treatment of leukemia and lymphoma.
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Affiliation(s)
- Nicole A Haverland
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ioanna Ntai
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Theodore Keppel
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
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Khristov V, Wan Q, Sharma R, Lotfi M, Maminishkis A, Bharti K. Polarized Human Retinal Pigment Epithelium Exhibits Distinct Surface Proteome on Apical and Basal Plasma Membranes. Methods Mol Biol 2018; 1722:223-247. [PMID: 29264809 DOI: 10.1007/978-1-4939-7553-2_15] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Surface proteins localized on the apical and basal plasma membranes are required for a cell to sense its environment and relay changes in ionic, cytokine, chemokine, and hormone levels to the inside of the cell. In a polarized cell, surface proteins are differentially localized on the apical or the basolateral sides of the cell. The retinal pigment epithelium (RPE) is an example of a polarized cell that performs a variety of functions that are dependent on its polarized state including trafficking of ions, fluid, and metabolites across the RPE monolayer. These functions are absolutely crucial for maintaining the health and integrity of adjacent photoreceptors, the photosensitive cells of the retina. Here we present a series of approaches to identify and validate the polarization state of cultured primary human RPE cells using immunostaining for RPE apical/basolateral markers, polarized cytokine secretion, electrophysiology, fluid transport, phagocytosis, and identification of plasma membrane proteins through cell surface capturing technology. These approaches are currently being used to validate the polarized state and the epithelial phenotype of human induced pluripotent stem (iPS) cell derived RPE cells. This work provides the basis for developing an autologous cell therapy for age-related macular degeneration using patient specific iPS cell derived RPE.
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Affiliation(s)
- Vladimir Khristov
- Section on Epithelial and Retinal Physiology and Disease, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Qin Wan
- Section on Epithelial and Retinal Physiology and Disease, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ruchi Sharma
- Unit on Ocular and Stem Cell Translational Research, National Eye Institute, National Institute of Health, Bethesda, MD, USA
| | - Mostafa Lotfi
- Section on Epithelial and Retinal Physiology and Disease, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arvydas Maminishkis
- Section on Epithelial and Retinal Physiology and Disease, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kapil Bharti
- Unit on Ocular and Stem Cell Translational Research, National Eye Institute, National Institute of Health, Bethesda, MD, USA.
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Shekari F, Nezari H, Larijani MR, Han CL, Baharvand H, Chen YJ, Salekdeh GH. Proteome analysis of human embryonic stem cells organelles. J Proteomics 2017; 162:108-118. [PMID: 28435121 DOI: 10.1016/j.jprot.2017.04.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 04/15/2017] [Accepted: 04/18/2017] [Indexed: 01/04/2023]
Abstract
As the functions of proteins are associated with their cellular localization, the comprehensive sub-cellular proteome knowledge of human embryonic stem cells (hESCs) is indispensable for ensuring a therapeutic effect. Here, we have utilized a sub-cellular proteomics approach to analyze the localization of proteins in the nucleus, mitochondria, crude membrane, cytoplasm, heavy and light microsomes. Out of 2002 reproducibly identified proteins, we detected 762 proteins in a single organelle whereas 160 proteins were found in all sub-cellular fractions. We verified the localization of identified proteins through databases and discussed the consistency of the obtained results. With regards to the ambiguity in the definition of a membrane protein, we tried to clearly define the plasma membrane, peripheral membrane and membrane proteins by annotation of these proteins in databases, along with predictions of transmembrane helices. Among ten enriched signaling pathways highlighted in our results, non-canonical Wnt signaling were analyzed in greater detail. The functions of three novel hESC membrane proteins (ERBB4, GGT1 and ZDHHC13) have been assessed in terms of pluripotency. Our report is the most comprehensive for organellar proteomics of hESCs. SIGNIFICANCE Mass spectrometric identification of proteins using a TripleTOF 5600 from nucleus, mitochondria, crude membrane, cytoplasm, heavy and light microsomal fractions highlighted the significance of the non-canonical Wnt signaling in human embryonic stem cells.
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Affiliation(s)
- Faezeh Shekari
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Hossein Nezari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehran Rezaei Larijani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Chia-Li Han
- Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan; Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hossein Baharvand
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran; Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan.
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.
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Mallanna SK, Waas M, Duncan SA, Gundry RL. N-glycoprotein surfaceome of human induced pluripotent stem cell derived hepatic endoderm. Proteomics 2017; 17. [PMID: 27966262 DOI: 10.1002/pmic.201600397] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 12/20/2022]
Abstract
Using cell surface capture technology, the cell surface N-glycoproteome of human-induced pluripotent stem cell derived hepatic endoderm cells was assessed. Altogether, 395 cell surface N-glycoproteins were identified, represented by 1273 N-glycopeptides. This study identified N-glycoproteins that are not predicted to be localized to the cell surface and provides experimental data that assist in resolving ambiguous or incorrectly annotated transmembrane topology annotations. In a proof-of-concept analysis, combining these data with other cell surface proteome datasets is useful for identifying potentially cell type and lineage restricted markers and drug targets to advance the use of stem cell technologies for mechanistic developmental studies, disease modeling, drug discovery, and regenerative medicine.
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Affiliation(s)
- Sunil K Mallanna
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA.,Present address: National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Stephen A Duncan
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
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Chauhan S, Danielson S, Clements V, Edwards N, Ostrand-Rosenberg S, Fenselau C. Surface Glycoproteins of Exosomes Shed by Myeloid-Derived Suppressor Cells Contribute to Function. J Proteome Res 2017; 16:238-246. [PMID: 27728760 PMCID: PMC6127855 DOI: 10.1021/acs.jproteome.6b00811] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In this report, we use a proteomic strategy to identify glycoproteins on the surface of exosomes derived from myeloid-derived suppressor cells (MDSCs), and then test if selected glycoproteins contribute to exosome-mediated chemotaxis and migration of MDSCs. We report successful modification of a surface chemistry method for use with exosomes and identify 21 surface N-glycoproteins on exosomes released by mouse mammary carcinoma-induced MDSCs. These glycoprotein identities and functionalities are compared with 93 N-linked glycoproteins identified on the surface of the parental cells. As with the lysate proteomes examined previously, the exosome surface N-glycoproteins are primarily a subset of the glycoproteins on the surface of the suppressor cells that released them, with related functions and related potential as therapeutic targets. The "don't eat me" molecule CD47 and its binding partners thrombospondin-1 (TSP1) and signal regulatory protein α (SIRPα) were among the surface N-glycoproteins detected. Functional bioassays using antibodies to these three molecules demonstrated that CD47, TSP1, and to a lesser extent SIRPα facilitate exosome-mediated MDSC chemotaxis and migration.
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Affiliation(s)
- Sitara Chauhan
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Steven Danielson
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Virginia Clements
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Nathan Edwards
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, D.C. 20057, United States
| | - Suzanne Ostrand-Rosenberg
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Catherine Fenselau
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
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Abstract
Chemical tools have accelerated progress in glycoscience, reducing experimental barriers to studying protein glycosylation, the most widespread and complex form of posttranslational modification. For example, chemical glycoproteomics technologies have enabled the identification of specific glycosylation sites and glycan structures that modulate protein function in a number of biological processes. This field is now entering a stage of logarithmic growth, during which chemical innovations combined with mass spectrometry advances could make it possible to fully characterize the human glycoproteome. In this review, we describe the important role that chemical glycoproteomics methods are playing in such efforts. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Our goal with this survey is to provide a foundation on which continued technological advancements can be made to promote further explorations of protein glycosylation.
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Affiliation(s)
- Krishnan K. Palaniappan
- Verily Life Sciences, 269 East Grand Ave., South San Francisco, California 94080, United States
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States
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Vit O, Man P, Kadek A, Hausner J, Sklenar J, Harant K, Novak P, Scigelova M, Woffendin G, Petrak J. Large-scale identification of membrane proteins based on analysis of trypsin-protected transmembrane segments. J Proteomics 2016; 149:15-22. [DOI: 10.1016/j.jprot.2016.03.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/03/2016] [Accepted: 03/04/2016] [Indexed: 01/06/2023]
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Mallanna SK, Cayo MA, Twaroski K, Gundry RL, Duncan SA. Mapping the Cell-Surface N-Glycoproteome of Human Hepatocytes Reveals Markers for Selecting a Homogeneous Population of iPSC-Derived Hepatocytes. Stem Cell Reports 2016; 7:543-556. [PMID: 27569060 PMCID: PMC5032032 DOI: 10.1016/j.stemcr.2016.07.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/18/2016] [Accepted: 07/20/2016] [Indexed: 02/07/2023] Open
Abstract
When comparing hepatic phenotypes between iPSC-derived hepatocyte-like cells from different liver disease patients, cell heterogeneity can confound interpretation. We proposed that homogeneous cell populations could be generated by fluorescence-activated cell sorting (FACS). Using cell-surface capture proteomics, we identified a total of 300 glycoproteins on hepatocytes. Analyses of the expression profiles during the differentiation of iPSCs revealed that SLC10A1, CLRN3, and AADAC were highly enriched during the final stages of hepatocyte differentiation. FACS purification of hepatocyte-like cells expressing SLC10A1, CLRN3, or AADAC demonstrated enrichment of cells with hepatocyte characteristics. Moreover, transcriptome analyses revealed that cells expressing the liver gene regulatory network were enriched while cells expressing a pluripotent stem cell network were depleted. In conclusion, we report an extensive catalog of cell-surface N-linked glycoproteins expressed in primary hepatocytes and identify cell-surface proteins that facilitate the purification of homogeneous populations of iPSC-derived hepatocyte-like cells. Identified N-linked glycoproteins occupying surface of primary human hepatocytes SLC10A1, CLRN3, and AADAC are expressed on ∼25% of iPSC-derived hepatocytes FACS with these markers enriches hepatic character in iPSC-derived hepatocytes SLC10A1 sorted cells provide homogeneous populations of hepatocyte-like cells
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Affiliation(s)
- Sunil K Mallanna
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Max A Cayo
- Department of Cell Biology, Neurobiology and Anatomy, Program in Regenerative Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kirk Twaroski
- Department of Cell Biology, Neurobiology and Anatomy, Program in Regenerative Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55454, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stephen A Duncan
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA.
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Vit O, Petrak J. Integral membrane proteins in proteomics. How to break open the black box? J Proteomics 2016; 153:8-20. [PMID: 27530594 DOI: 10.1016/j.jprot.2016.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/30/2016] [Accepted: 08/09/2016] [Indexed: 12/22/2022]
Abstract
Integral membrane proteins (IMPs) are coded by 20-30% of human genes and execute important functions - transmembrane transport, signal transduction, cell-cell communication, cell adhesion to the extracellular matrix, and many other processes. Due to their hydrophobicity, low expression and lack of trypsin cleavage sites in their transmembrane segments, IMPs have been generally under-represented in routine proteomic analyses. However, the field of membrane proteomics has changed markedly in the past decade, namely due to the introduction of filter assisted sample preparation (FASP), the establishment of cell surface capture (CSC) protocols, and the development of methods that enable analysis of the hydrophobic transmembrane segments. This review will summarize the recent developments in the field and outline the most successful strategies for the analysis of integral membrane proteins. SIGNIFICANCE Integral membrane proteins (IMPs) are attractive therapeutic targets mostly due to their many important functions. However, our knowledge of the membrane proteome is severely limited to effectively exploit their potential. This is mostly due to the lack of appropriate techniques or methods compatible with the typical features of IMPs, namely hydrophobicity, low expression and lack of trypsin cleavage sites. This review summarizes the most recent development in membrane proteomics and outlines the most successful strategies for their large-scale analysis.
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Affiliation(s)
- O Vit
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic.
| | - J Petrak
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic
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Boheler KR, Gundry RL. Concise Review: Cell Surface N-Linked Glycoproteins as Potential Stem Cell Markers and Drug Targets. Stem Cells Transl Med 2016; 6:131-138. [PMID: 28170199 PMCID: PMC5442750 DOI: 10.5966/sctm.2016-0109] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/13/2016] [Indexed: 12/28/2022] Open
Abstract
Stem cells and their derivatives hold great promise to advance regenerative medicine. Critical to the progression of this field is the identification and utilization of antibody‐accessible cell‐surface proteins for immunophenotyping and cell sorting—techniques essential for assessment and isolation of defined cell populations with known functional and therapeutic properties. Beyond their utility for cell identification and selection, cell‐surface proteins are also major targets for pharmacological intervention. Although comprehensive cell‐surface protein maps are highly valuable, they have been difficult to define until recently. In this review, we discuss the application of a contemporary targeted chemoproteomic‐based technique for defining the cell‐surface proteomes of stem and progenitor cells. In applying this approach to pluripotent stem cells (PSCs), these studies have improved the biological understanding of these cells, led to the enhanced use and development of antibodies suitable for immunophenotyping and sorting, and contributed to the repurposing of existing drugs without the need for high‐throughput screening. The utility of this latter approach was first demonstrated with human PSCs (hPSCs) through the identification of small molecules that are selectively toxic to hPSCs and have the potential for eliminating confounding and tumorigenic cells in hPSC‐derived progeny destined for research and transplantation. Overall, the cutting‐edge technologies reviewed here will accelerate the development of novel cell‐surface protein targets for immunophenotyping, new reagents to improve the isolation of therapeutically qualified cells, and pharmacological studies to advance the treatment of intractable diseases amenable to cell‐replacement therapies. Stem Cells Translational Medicine2017;6:131–138
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Affiliation(s)
- Kenneth R. Boheler
- Stem Cell and Regenerative Medicine Consortium, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Special Administrative Region, People's Republic of China
| | - Rebekah L. Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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Ducret A, Kux van Geijtenbeek S, Röder D, Simon S, Chin D, Berrera M, Gruenbaum L, Ji C, Cutler P. Identification of six cell surface proteins for specific liver targeting. Proteomics Clin Appl 2016; 9:651-61. [PMID: 26097162 DOI: 10.1002/prca.201400194] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/27/2015] [Accepted: 06/08/2015] [Indexed: 01/09/2023]
Abstract
PURPOSE Cell surface proteins are the primary means for a cell to sense and interact with its environment and their dysregulation has been linked to numerous diseases. In particular, the identification of proteins specific to a single tissue type or to a given disease phenotype may enable the characterization of novel therapeutic targets. We tested here the feasibility of a cell surface proteomics approach to identify pertinent markers directly in a clinically relevant tissue. EXPERIMENTAL DESIGN We analyzed the cell surface proteome of freshly isolated primary heptatocytes using a glycocapture-specific approach combined with a robust bioinformatics filtering. RESULTS Using primary lung epithelial cell cultures as negative controls, we identified 32 hepatocyte-specific cell surface proteins candidates. We used mRNA expression to select six markers that may provide adequate specificity for targeting therapeutics to the liver. CONCLUSIONS AND CLINICAL RELEVANCE We demonstrate the feasibility and the importance of conducting such studies directly in a clinically relevant tissue. In particular, the cell surface proteome of freshly isolated hepatocytes differed substantially from cultured cell lines.
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Affiliation(s)
- Axel Ducret
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Sabine Kux van Geijtenbeek
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Daniel Röder
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Sandrine Simon
- Drug Disposition and Safety, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Daniel Chin
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Marco Berrera
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Lore Gruenbaum
- Translational Medicine - Infectious Diseases, Pharma Research and Early Development (pRED), Roche Innovation Center New York, New York, NY, USA
| | - Changhua Ji
- External Alliances and Portfolio Management, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Shanghai, Pudong, Shanghai, P. R. China
| | - Paul Cutler
- Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
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Graessel A, Hauck SM, von Toerne C, Kloppmann E, Goldberg T, Koppensteiner H, Schindler M, Knapp B, Krause L, Dietz K, Schmidt-Weber CB, Suttner K. A Combined Omics Approach to Generate the Surface Atlas of Human Naive CD4+ T Cells during Early T-Cell Receptor Activation. Mol Cell Proteomics 2015; 14:2085-102. [PMID: 25991687 DOI: 10.1074/mcp.m114.045690] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Indexed: 12/24/2022] Open
Abstract
Naive CD4(+) T cells are the common precursors of multiple effector and memory T-cell subsets and possess a high plasticity in terms of differentiation potential. This stem-cell-like character is important for cell therapies aiming at regeneration of specific immunity. Cell surface proteins are crucial for recognition and response to signals mediated by other cells or environmental changes. Knowledge of cell surface proteins of human naive CD4(+) T cells and their changes during the early phase of T-cell activation is urgently needed for a guided differentiation of naive T cells and may support the selection of pluripotent cells for cell therapy. Periodate oxidation and aniline-catalyzed oxime ligation technology was applied with subsequent quantitative liquid chromatography-tandem MS to generate a data set describing the surface proteome of primary human naive CD4(+) T cells and to monitor dynamic changes during the early phase of activation. This led to the identification of 173 N-glycosylated surface proteins. To independently confirm the proteomic data set and to analyze the cell surface by an alternative technique a systematic phenotypic expression analysis of surface antigens via flow cytometry was performed. This screening expanded the previous data set, resulting in 229 surface proteins, which were expressed on naive unstimulated and activated CD4(+) T cells. Furthermore, we generated a surface expression atlas based on transcriptome data, experimental annotation, and predicted subcellular localization, and correlated the proteomics result with this transcriptional data set. This extensive surface atlas provides an overall naive CD4(+) T cell surface resource and will enable future studies aiming at a deeper understanding of mechanisms of T-cell biology allowing the identification of novel immune targets usable for the development of therapeutic treatments.
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Affiliation(s)
- Anke Graessel
- From the ‡Center of Allergy and Environment (ZAUM), Technische Universität und Helmholtz Zentrum München, Munich, Germany
| | - Stefanie M Hauck
- §Research Unit Protein Science, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Edda Kloppmann
- ¶Department of Informatics, Bioinformatics & Computational Biology i12, Technische Universität München, Garching/Munich, Germany; ‖New York Consortium on Membrane Protein Structure (NYCOMPS), New York Structural Biology Center, New York, New York 10027
| | - Tatyana Goldberg
- ¶Department of Informatics, Bioinformatics & Computational Biology i12, Technische Universität München, Garching/Munich, Germany; **TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Technische Universität München, Munich, Germany
| | | | - Michael Schindler
- ‡‡Institute of Virology, Helmholtz Zentrum München, Neuherberg, Germany; §§Institute of Medical Virology and Epidemiology of Viral Diseases, University Clinic Tübingen, Tübingen, Germany
| | - Bettina Knapp
- ¶¶Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Linda Krause
- ¶¶Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Katharina Dietz
- From the ‡Center of Allergy and Environment (ZAUM), Technische Universität und Helmholtz Zentrum München, Munich, Germany; ‖‖DZL- Member of the German Lung Research Center
| | - Carsten B Schmidt-Weber
- From the ‡Center of Allergy and Environment (ZAUM), Technische Universität und Helmholtz Zentrum München, Munich, Germany; ‖‖DZL- Member of the German Lung Research Center
| | - Kathrin Suttner
- From the ‡Center of Allergy and Environment (ZAUM), Technische Universität und Helmholtz Zentrum München, Munich, Germany; ‖‖DZL- Member of the German Lung Research Center
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Kropp EM, Bhattacharya S, Waas M, Chuppa SL, Hadjantonakis AK, Boheler KR, Gundry RL. N-glycoprotein surfaceomes of four developmentally distinct mouse cell types. Proteomics Clin Appl 2015; 8:603-9. [PMID: 24920426 DOI: 10.1002/prca.201400021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/06/2014] [Accepted: 06/06/2014] [Indexed: 11/12/2022]
Abstract
PURPOSE Detailed knowledge of cell surface proteins present during early embryonic development remains limited for most cell lineages. Due to the relevance of cell surface proteins in their functional roles controlling cell signaling and their utility as accessible, nongenetic markers for cell identification and sorting, the goal of this study was to provide new information regarding the cell surface proteins present during early mouse embryonic development. EXPERIMENTAL DESIGN Using the cell surface capture technology, the cell surface N-glycoproteomes of three cell lines and one in vitro differentiated cell type representing distinct cell fates and stages in mouse embryogenesis were assessed. RESULTS Altogether, more than 600 cell surface N-glycoproteins were identified represented by >5500 N-glycopeptides. CONCLUSIONS AND CLINICAL RELEVANCE The development of new, informative cell surface markers for the reliable identification and isolation of functionally defined subsets of cells from early developmental stages will advance the use of stem cell technologies for mechanistic developmental studies, including disease modeling and drug discovery.
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Affiliation(s)
- Erin M Kropp
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
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Poon E, Keung W, Liang Y, Ramalingam R, Yan B, Zhang S, Chopra A, Moore J, Herren A, Lieu DK, Wong HS, Weng Z, Wong OT, Lam YW, Tomaselli GF, Chen C, Boheler KR, Li RA. Proteomic Analysis of Human Pluripotent Stem Cell-Derived, Fetal, and Adult Ventricular Cardiomyocytes Reveals Pathways Crucial for Cardiac Metabolism and Maturation. ACTA ACUST UNITED AC 2015; 8:427-36. [PMID: 25759434 DOI: 10.1161/circgenetics.114.000918] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 02/18/2015] [Indexed: 12/21/2022]
Abstract
BACKGROUND Differentiation of pluripotent human embryonic stem cells (hESCs) to the cardiac lineage represents a potentially unlimited source of ventricular cardiomyocytes (VCMs), but hESC-VCMs are developmentally immature. Previous attempts to profile hESC-VCMs primarily relied on transcriptomic approaches, but the global proteome has not been examined. Furthermore, most hESC-CM studies focus on pathways important for cardiac differentiation, rather than regulatory mechanisms for CM maturation. We hypothesized that gene products and pathways crucial for maturation can be identified by comparing the proteomes of hESCs, hESC-derived VCMs, human fetal and human adult ventricular and atrial CMs. METHODS AND RESULTS Using two-dimensional-differential-in-gel electrophoresis, 121 differentially expressed (>1.5-fold; P<0.05) proteins were detected. The data set implicated a role of the peroxisome proliferator-activated receptor α signaling in cardiac maturation. Consistently, WY-14643, a peroxisome proliferator-activated receptor α agonist, increased fatty oxidative enzyme level, hyperpolarized mitochondrial membrane potential and induced a more organized morphology. Along this line, treatment with the thyroid hormone triiodothyronine increased the dynamic tension developed in engineered human ventricular cardiac microtissue by 3-fold, signifying their maturation. CONCLUSIONS We conclude that the peroxisome proliferator-activated receptor α and thyroid hormone pathways modulate the metabolism and maturation of hESC-VCMs and their engineered tissue constructs. These results may lead to mechanism-based methods for deriving mature chamber-specific CMs.
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Affiliation(s)
- Ellen Poon
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Wendy Keung
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Yimin Liang
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Rajkumar Ramalingam
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Bin Yan
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Shaohong Zhang
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Anant Chopra
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Jennifer Moore
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Anthony Herren
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Deborah K Lieu
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Hau San Wong
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Zhihui Weng
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - On Tik Wong
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Yun Wah Lam
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Gordon F Tomaselli
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Christopher Chen
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Kenneth R Boheler
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.)
| | - Ronald A Li
- From the Stem Cell and Regenerative Medicine Consortium (E.P., W.K., B.Y., Z.W., O.T. W., K.R.B., R.A.L.) and Department of Physiology, LKS Faculty of Medicine (E.P., W.K., B.Y., Z.W., O.T.W., K.R.B., R.A.L.), University of Hong Kong, Hong Kong, P.R. China; Departments of Biology and Chemistry (Y.M.L., R.R., Y.W.L.) and Computer Science (H.S.W.), City University of Hong Kong, Hong Kong, P.R. China; Department of Computer Science, Guangzhou University, Guangzhou, P.R. China (S.Z.); Department of Bioengineering, Boston University, MA (A.C., C.C.); Harvard Wyss Institute for Biologically Inspired Engineering, Boston, MA (A.C., C.C.); Department of Cell Biology and Human Anatomy, University of California, Davis (J.M., A.H., D.K.L.); Cardiovascular Research Center, Mount Sinai School of Medicine, New York (D.K.L., R.A.L.); and Division of Cardiology, Johns Hopkins University, Baltimore, MD (G.F.T., K.R.B.).
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Parker SJ, Raedschelders K, Van Eyk JE. Emerging proteomic technologies for elucidating context-dependent cellular signaling events: A big challenge of tiny proportions. Proteomics 2015; 15:1486-502. [PMID: 25545106 DOI: 10.1002/pmic.201400448] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 10/31/2014] [Accepted: 12/23/2014] [Indexed: 12/11/2022]
Abstract
Aberrant cell signaling events either drive or compensate for nearly all pathologies. A thorough description and quantification of maladaptive signaling flux in disease is a critical step in drug development, and complex proteomic approaches can provide valuable mechanistic insights. Traditional proteomics-based signaling analyses rely heavily on in vitro cellular monoculture. The characterization of these simplified systems generates a rich understanding of the basic components and complex interactions of many signaling networks, but they cannot capture the full complexity of the microenvironments in which pathologies are ultimately made manifest. Unfortunately, techniques that can directly interrogate signaling in situ often yield mass-limited starting materials that are incompatible with traditional proteomics workflows. This review provides an overview of established and emerging techniques that are applicable to context-dependent proteomics. Analytical approaches are illustrated through recent proteomics-based studies in which selective sample acquisition strategies preserve context-dependent information, and where the challenge of minimal starting material is met by optimized sensitivity and coverage. This review is organized into three major technological themes: (i) LC methods in line with MS; (ii) antibody-based approaches; (iii) MS imaging with a discussion of data integration and systems modeling. Finally, we conclude with future perspectives and implications of context-dependent proteomics.
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Affiliation(s)
- Sarah J Parker
- Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Advanced Clinical Biosystems Research Institute, Los Angeles, CA, USA; Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Zizkova M, Sucha R, Tyleckova J, Jarkovska K, Mairychova K, Kotrcova E, Marsala M, Gadher SJ, Kovarova H. Proteome-wide analysis of neural stem cell differentiation to facilitate transition to cell replacement therapies. Expert Rev Proteomics 2014; 12:83-95. [PMID: 25363140 DOI: 10.1586/14789450.2015.977381] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Neurodegenerative diseases are devastating disorders and the demands on their treatment are set to rise in connection with higher disease incidence. Knowledge of the spatiotemporal profile of cellular protein expression during neural differentiation and definition of a set of markers highly specific for targeted neural populations is a key challenge. Intracellular proteins may be utilized as a readout for follow-up transplantation and cell surface proteins may facilitate isolation of the cell subpopulations, while secreted proteins could help unravel intercellular communication and immunomodulation. This review summarizes the potential of proteomics in revealing molecular mechanisms underlying neural differentiation of stem cells and presents novel candidate proteins of neural subpopulations, where understanding of their functionality may accelerate transition to cell replacement therapies.
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Affiliation(s)
- Martina Zizkova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, AS CR, v.v.i., Libechov, Czech Republic
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Sun B. Proteomics and glycoproteomics of pluripotent stem-cell surface proteins. Proteomics 2014; 15:1152-63. [DOI: 10.1002/pmic.201400300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/07/2014] [Accepted: 09/08/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Bingyun Sun
- Department of Chemistry and Department of Molecular Biology and Biochemistry, Simon Fraser University; Burnaby British Columbia Canada
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Bhattacharya S, Burridge PW, Kropp EM, Chuppa SL, Kwok WM, Wu JC, Boheler KR, Gundry RL. High efficiency differentiation of human pluripotent stem cells to cardiomyocytes and characterization by flow cytometry. J Vis Exp 2014:52010. [PMID: 25286293 DOI: 10.3791/52010] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
There is an urgent need to develop approaches for repairing the damaged heart, discovering new therapeutic drugs that do not have toxic effects on the heart, and improving strategies to accurately model heart disease. The potential of exploiting human induced pluripotent stem cell (hiPSC) technology to generate cardiac muscle "in a dish" for these applications continues to generate high enthusiasm. In recent years, the ability to efficiently generate cardiomyogenic cells from human pluripotent stem cells (hPSCs) has greatly improved, offering us new opportunities to model very early stages of human cardiac development not otherwise accessible. In contrast to many previous methods, the cardiomyocyte differentiation protocol described here does not require cell aggregation or the addition of Activin A or BMP4 and robustly generates cultures of cells that are highly positive for cardiac troponin I and T (TNNI3, TNNT2), iroquois-class homeodomain protein IRX-4 (IRX4), myosin regulatory light chain 2, ventricular/cardiac muscle isoform (MLC2v) and myosin regulatory light chain 2, atrial isoform (MLC2a) by day 10 across all human embryonic stem cell (hESC) and hiPSC lines tested to date. Cells can be passaged and maintained for more than 90 days in culture. The strategy is technically simple to implement and cost-effective. Characterization of cardiomyocytes derived from pluripotent cells often includes the analysis of reference markers, both at the mRNA and protein level. For protein analysis, flow cytometry is a powerful analytical tool for assessing quality of cells in culture and determining subpopulation homogeneity. However, technical variation in sample preparation can significantly affect quality of flow cytometry data. Thus, standardization of staining protocols should facilitate comparisons among various differentiation strategies. Accordingly, optimized staining protocols for the analysis of IRX4, MLC2v, MLC2a, TNNI3, and TNNT2 by flow cytometry are described.
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Affiliation(s)
| | - Paul W Burridge
- Stanford Cardiovascular Institute, Stanford University School of Medicine
| | - Erin M Kropp
- Department of Biochemistry, Medical College of Wisconsin
| | | | - Wai-Meng Kwok
- Department of Anesthesiology, Medical College of Wisconsin
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine
| | - Kenneth R Boheler
- Stem Cell and Regenerative Medicine Consortium, LKS Faculty of Medicine, Hong Kong University; Division of Cardiology, Johns Hopkins University School of Medicine
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin; Cardiovascular Research Center, Biotechnology and Bioengineering Center, Medical College of Wisconsin;
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46
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Warlich E, Schambach A, Lock D, Wedekind D, Glage S, Eckardt D, Bosio A, Knöbel S. FAS-based cell depletion facilitates the selective isolation of mouse induced pluripotent stem cells. PLoS One 2014; 9:e102171. [PMID: 25029550 PMCID: PMC4100888 DOI: 10.1371/journal.pone.0102171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 06/16/2014] [Indexed: 11/26/2022] Open
Abstract
Cellular reprogramming of somatic cells into induced pluripotent stem cells (iPSC) opens up new avenues for basic research and regenerative medicine. However, the low efficiency of the procedure remains a major limitation. To identify iPSC, many studies to date relied on the activation of pluripotency-associated transcription factors. Such strategies are either retrospective or depend on genetically modified reporter cells. We aimed at identifying naturally occurring surface proteins in a systematic approach, focusing on antibody-targeted markers to enable live-cell identification and selective isolation. We tested 170 antibodies for differential expression between mouse embryonic fibroblasts (MEF) and mouse pluripotent stem cells (PSC). Differentially expressed markers were evaluated for their ability to identify and isolate iPSC in reprogramming cultures. Epithelial cell adhesion molecule (EPCAM) and stage-specific embryonic antigen 1 (SSEA1) were upregulated early during reprogramming and enabled enrichment of OCT4 expressing cells by magnetic cell sorting. Downregulation of somatic marker FAS was equally suitable to enrich OCT4 expressing cells, which has not been described so far. Furthermore, FAS downregulation correlated with viral transgene silencing. Finally, using the marker SSEA-1 we exemplified that magnetic separation enables the establishment of bona fide iPSC and propose strategies to enrich iPSC from a variety of human source tissues.
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Affiliation(s)
- Eva Warlich
- Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- REBIRTH Cluster of Excellence, Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- REBIRTH Cluster of Excellence, Hannover, Germany
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Dominik Lock
- Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Dirk Wedekind
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
| | - Silke Glage
- REBIRTH Cluster of Excellence, Hannover, Germany
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany
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47
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Boheler KR, Bhattacharya S, Kropp EM, Chuppa S, Riordon DR, Bausch-Fluck D, Burridge PW, Wu JC, Wersto RP, Chan GCF, Rao S, Wollscheid B, Gundry RL. A human pluripotent stem cell surface N-glycoproteome resource reveals markers, extracellular epitopes, and drug targets. Stem Cell Reports 2014; 3:185-203. [PMID: 25068131 PMCID: PMC4110789 DOI: 10.1016/j.stemcr.2014.05.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 04/30/2014] [Accepted: 05/05/2014] [Indexed: 01/07/2023] Open
Abstract
Detailed knowledge of cell-surface proteins for isolating well-defined populations of human pluripotent stem cells (hPSCs) would significantly enhance their characterization and translational potential. Through a chemoproteomic approach, we developed a cell-surface proteome inventory containing 496 N-linked glycoproteins on human embryonic (hESCs) and induced PSCs (hiPSCs). Against a backdrop of human fibroblasts and 50 other cell types, >100 surface proteins of interest for hPSCs were revealed. The >30 positive and negative markers verified here by orthogonal approaches provide experimental justification for the rational selection of pluripotency and lineage markers, epitopes for cell isolation, and reagents for the characterization of putative hiPSC lines. Comparative differences between the chemoproteomic-defined surfaceome and the transcriptome-predicted surfaceome directly led to the discovery that STF-31, a reported GLUT-1 inhibitor, is toxic to hPSCs and efficient for selective elimination of hPSCs from mixed cultures. 496 cell surface N-glycoproteins on hPSCs N-glycosylation site identification dictates accessible epitopes >30 positive and negative selection markers for hPSCs are validated STF-31 is selectively toxic to hPSCs
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Affiliation(s)
- Kenneth R Boheler
- Stem Cell and Regenerative Medicine Consortium, LKS Faculty of Medicine, Hong Kong University, Hong Kong, SAR ; National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA ; Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Subarna Bhattacharya
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Erin M Kropp
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sandra Chuppa
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Daniel R Riordon
- National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Damaris Bausch-Fluck
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland
| | - Paul W Burridge
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert P Wersto
- National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Godfrey Chi Fung Chan
- Stem Cell and Regenerative Medicine Consortium, LKS Faculty of Medicine, Hong Kong University, Hong Kong, SAR ; Department of Pediatrics & Adolescent Medicine, Hong Kong University, Hong Kong, SAR
| | - Sridhar Rao
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA ; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA ; Blood Research Institute, Blood Center of Wisconsin, Milwaukee, WI 53226, USA
| | - Bernd Wollscheid
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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48
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McGivern JV, Ebert AD. Exploiting pluripotent stem cell technology for drug discovery, screening, safety, and toxicology assessments. Adv Drug Deliv Rev 2014; 69-70:170-8. [PMID: 24309014 DOI: 10.1016/j.addr.2013.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/11/2013] [Accepted: 11/24/2013] [Indexed: 02/06/2023]
Abstract
In order for the pharmaceutical industry to maintain a constant flow of novel drugs and therapeutics into the clinic, compounds must be thoroughly validated for safety and efficacy in multiple biological and biochemical systems. Pluripotent stem cells, because of their ability to develop into any cell type in the body and recapitulate human disease, may be an important cellular system to add to the drug development repertoire. This review will discuss some of the benefits of using pluripotent stem cells for drug discovery and safety studies as well as some of the recent applications of stem cells in drug screening studies. We will also address some of the hurdles that need to be overcome in order to make stem cell-based approaches an efficient and effective tool in the quest to produce clinically successful drug compounds.
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49
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Borooah S, Phillips M, Bilican B, Wright A, Wilmut I, Chandran S, Gamm D, Dhillon B. Using human induced pluripotent stem cells to treat retinal disease. Prog Retin Eye Res 2013; 37:163-81. [PMID: 24104210 PMCID: PMC3841575 DOI: 10.1016/j.preteyeres.2013.09.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 09/06/2013] [Accepted: 09/16/2013] [Indexed: 02/08/2023]
Abstract
The eye is an ideal target for exploiting the potential of human induced pluripotent stem cell (hiPSC) technology in order to understand disease pathways and explore novel therapeutic strategies for inherited retinal disease. The aim of this article is to map the pathway from state-of-the art laboratory-based discoveries to realising the translational potential of this emerging technique. We describe the relevance and routes to establishing hiPSCs in selected models of human retinal disease. Additionally, we define pathways for applying hiPSC technology in treating currently incurable, progressive and blinding retinal disease.
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Affiliation(s)
- S. Borooah
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, UK
- Ophthalmology, School of Clinical Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - M.J. Phillips
- Waisman Center, University of Wisconsin School of Medicine and Public Health, 1500 Highland Ave, Madison, WI 53705, USA
| | - B. Bilican
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - A.F. Wright
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - I. Wilmut
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - S. Chandran
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - D. Gamm
- Waisman Center, University of Wisconsin School of Medicine and Public Health, 1500 Highland Ave, Madison, WI 53705, USA
- Department of Ophthalmology and Visual Sciences, McPherson Eye Research Institute, University of Wisconsin School of Medicine and Public Health, 1500 Highland Ave, Madison, WI 53705, USA
| | - B. Dhillon
- Ophthalmology, School of Clinical Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK
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50
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Ueda K. Glycoproteomic strategies: From discovery to clinical application of cancer carbohydrate biomarkers. Proteomics Clin Appl 2013; 7:607-17. [PMID: 23640819 DOI: 10.1002/prca.201200123] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 12/27/2012] [Indexed: 12/15/2022]
Abstract
Carbohydrate antigens are the most frequently and traditionally used biomarkers for cancer, such as CA19-9, CA125, DUPAN-II, AFP-L3, and many others. The diagnostic potential of them was simply based on the cancer-specific alterations of glycan structures on particular glycoproteins in serum/plasma. In spite of the facts that glycosylation disorders are feasible for cancer biomarkers and glycomic analysis technologies to explore them have been rapidly developed, it remains difficult to sensitively screen glycan structure changes on cancer-associated glycoproteins from clinical specimens. Moreover, a lot of additional issues should be appropriately addressed for the clinical application of newly identified glycosylation biomarkers, including analytical throughput, quantitative confirmation of structural changes, and biological explanation for the alterations. In the last decade, significant improvement of mass spectrometric techniques is being made in the aspects of both hardware spec and preanalytical purification procedures for glycoprotein analysis. Here we review potential approaches to perform comprehensive analysis of glycoproteomic biomarker screening from serum/plasma and to realize high-throughput validation of site-specific oligosaccharide variations. The power and problems of mass spectrometric applications on the clinical use of carbohydrate biomarkers are also discussed in this review.
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Affiliation(s)
- Koji Ueda
- Laboratory for Biomarker Development, Center for Genomic Medicine, RIKEN, Minato-ku, Tokyo, Japan.
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