1
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Geri JB, Pao W. Elucidating the Cell Surfaceome to Accelerate Cancer Drug Development. Cancer Discov 2024; 14:639-642. [PMID: 38571413 DOI: 10.1158/2159-8290.cd-24-0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
SUMMARY Cell surface proteins represent ideal therapeutic targets because of their accessibility to antibodies, T cell-directed therapies, and radiotherapies, but there are only 25 therapeutically relevant cell surface targets for which cancer therapies are approved in the United States or European Union. This commentary calls for intensified research into mapping the universe of cell surface proteins - the cell surfaceome - in order to accelerate cancer drug development.
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Affiliation(s)
- Jacob B Geri
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, New York
| | - William Pao
- Reveal Therapeutics, Inc., New York, New York
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2
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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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3
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Tripathi R, Guglani A, Ghorpade R, Wang B. Biotin conjugates in targeted drug delivery: is it mediated by a biotin transporter, a yet to be identified receptor, or (an)other unknown mechanism(s)? J Enzyme Inhib Med Chem 2023; 38:2276663. [PMID: 37955285 PMCID: PMC10653662 DOI: 10.1080/14756366.2023.2276663] [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: 08/08/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023] Open
Abstract
Conjugation of drugs with biotin is a widely studied strategy for targeted drug delivery. The structure-activity relationship (SAR) studies through H3-biotin competition experiments conclude with the presence of a free carboxylic acid being essential for its uptake via the sodium-dependent multivitamin transporter (SMVT, the major biotin transporter). However, biotin conjugation with a payload requires modification of the carboxylic acid to an amide or ester group. Then, there is the question as to how/whether the uptake of biotin conjugates goes through the SMVT. If not, then what is the mechanism? Herein, we present known uptake mechanisms of biotin and its applications reported in the literature. We also critically analyse possible uptake mechanism(s) of biotin conjugates to address the disconnect between the results from SMVT-based SAR and "biotin-facilitated" targeted drug delivery. We believe understanding the uptake mechanism of biotin conjugates is critical for their future applications and further development.
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Affiliation(s)
- Ravi Tripathi
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Anchala Guglani
- Department of Biology, Georgia State University, Atlanta, GA, USA
| | - Rujuta Ghorpade
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
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4
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de Haan N, Song M, Grant OC, Ye Z, Khoder Agha F, Koed Møller Aasted M, Woods RJ, Vakhrushev SY, Wandall HH. Sensitive and Specific Global Cell Surface N-Glycoproteomics Shows Profound Differences Between Glycosylation Sites and Subcellular Components. Anal Chem 2023; 95:17328-17336. [PMID: 37956981 PMCID: PMC10688226 DOI: 10.1021/acs.analchem.3c03626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/02/2023] [Indexed: 11/21/2023]
Abstract
Cell surface glycans are essential for establishing cell communication, adhesion, and migration. However, it remains challenging to obtain cell surface-specific information about glycoconjugate structures. Acquiring this information is essential for unraveling the functional role of glycans and for exploiting them as clinical targets. To specifically analyze the N-glycoprotein forms expressed at the cell surface, we developed a C18 liquid chromatography (LC)-mass spectrometry (MS)-based glycoproteomics method in combination with highly specific cell surface protein labeling and enrichment using a biotin label. The surface-specificity of the method was validated by MS-based proteomics of subcellular component marker proteins. Using the human keratinocytes N/TERT-1 as a model system, we identified and quantified the glycosylation of hundreds of cell surface N-glycosylation sites. This approach allowed us to study the glycoforms present at the functional relevant cell surface, omitting immaturely glycosylated proteins present in the secretory pathway. Interestingly, the different stages of N-glycan processing at individual sites displayed at the cell surface were found to correlate with their accessibility for ER-residing processing enzymes, as investigated through molecular dynamics simulations. Using the new approach, we compared N-glycosylation sites of proteins expressed on the cell surface to their counterparts in a total cell lysate, showing profound differences in glycosylation between the subcellular components and indicating the relevance of the method for future studies in understanding contextual glycan functions.
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Affiliation(s)
- Noortje de Haan
- Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333, ZA, The Netherlands
| | - Ming Song
- Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Oliver C. Grant
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Zilu Ye
- Novo
Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Fawzi Khoder Agha
- Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | | | - Robert J. Woods
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Sergey Y. Vakhrushev
- Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Hans H. Wandall
- Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
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5
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Das A, Behera RN, Kapoor A, Ambatipudi K. The Potential of Meta-Proteomics and Artificial Intelligence to Establish the Next Generation of Probiotics for Personalized Healthcare. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:17528-17542. [PMID: 37955263 DOI: 10.1021/acs.jafc.3c03834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
The symbiosis of probiotic bacteria with humans has rendered various health benefits while providing nutrition and a suitable environment for their survival. However, the probiotics must survive unfavorable gut conditions to exert beneficial effects. The intrinsic resistance of probiotics to survive harsh conditions results from a myriad of proteins. Interaction of microbial proteins with the host is indispensable for modulating the gut microbiome, such as interaction with cell receptors and protective action against pathogens. The complex interplay of proteins should be unraveled by utilizing metaproteomic strategies. The contribution of probiotics to health is now widely accepted. However, due to the inconsistency of generalized probiotics, contemporary research toward precision probiotics has gained momentum for customized treatment. This review explores the application of metaproteomics and AI/ML algorithms in resolving multiomics data analysis and in silico prediction of microbial features for screening specific beneficial probiotic organisms. Implementing these integrative strategies could augment the potential of precision probiotics for personalized healthcare.
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Affiliation(s)
- Arpita Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Rama N Behera
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Ayushi Kapoor
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Kiran Ambatipudi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India
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6
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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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7
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Langó T, Kuffa K, Tóth G, Turiák L, Drahos L, Tusnády GE. Comprehensive Discovery of the Accessible Primary Amino Group-Containing Segments from Cell Surface Proteins by Fine-Tuning a High-Throughput Biotinylation Method. Int J Mol Sci 2022; 24:ijms24010273. [PMID: 36613715 PMCID: PMC9820203 DOI: 10.3390/ijms24010273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Cell surface proteins, including transmembrane and other surface-anchored proteins, play a key role in several critical cellular processes and have a strong diagnostic value. The development of quick and robust experimental methods remains vital for the accurate and comprehensive characterization of the cell surface subproteome of individual cells. Here we present a high-throughput technique which relies on the biotinylation of the accessible primary amino groups in the extracellular segments of the proteins, using HL60 as a model cell line. Several steps of the method have been thoroughly optimized to capture labeled surface proteins selectively and in larger quantities. These include the following: improving the efficiency of the cell surface biotinylation; reducing the endogen protease activity; applying an optimal amount of affinity column and elution steps for labeled peptide enrichment; and examining the effect of various solid-phase extraction methods, different HPLC gradients, and various tandem mass spectrometry settings. Using the optimized workflow, we identified at least 1700 surface-associated individual labeled peptides (~6000-7000 redundant peptides) from the model cell surface in a single nanoHPLC-MS/MS run. The presented method can provide a comprehensive and specific list of the cell surface available protein segments that could be potential targets in various bioinformatics and molecular biology research.
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Affiliation(s)
- Tamás Langó
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
- Correspondence:
| | - Katalin Kuffa
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány P. stny. 1/C, H-1117 Budapest, Hungary
| | - Gábor Tóth
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
| | - Gábor E. Tusnády
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok krt 2, H-1117 Budapest, Hungary
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8
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Surface protein profiling of prostate-derived extracellular vesicles by mass spectrometry and proximity assays. Commun Biol 2022; 5:1402. [PMID: 36550367 PMCID: PMC9780212 DOI: 10.1038/s42003-022-04349-x] [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: 05/25/2021] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
Extracellular vesicles (EVs) are mediators of intercellular communication and a promising class of biomarkers. Surface proteins of EVs play decisive roles in establishing a connection with recipient cells, and they are putative targets for diagnostic assays. Analysis of the surface proteins can thus both illuminate the biological functions of EVs and help identify potential biomarkers. We developed a strategy combining high-resolution mass spectrometry (HRMS) and proximity ligation assays (PLA) to first identify and then validate surface proteins discovered on EVs. We applied our workflow to investigate surface proteins of small EVs found in seminal fluid (SF-sEV). We identified 1,014 surface proteins and verified the presence of a subset of these on the surface of SF-sEVs. Our work demonstrates a general strategy for deep analysis of EVs' surface proteins across patients and pathological conditions, proceeding from unbiased screening by HRMS to ultra-sensitive targeted analyses via PLA.
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9
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Pauwels J, Fijałkowska D, Eyckerman S, Gevaert K. Mass spectrometry and the cellular surfaceome. MASS SPECTROMETRY REVIEWS 2022; 41:804-841. [PMID: 33655572 DOI: 10.1002/mas.21690] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
The collection of exposed plasma membrane proteins, collectively termed the surfaceome, is involved in multiple vital cellular processes, such as the communication of cells with their surroundings and the regulation of transport across the lipid bilayer. The surfaceome also plays key roles in the immune system by recognizing and presenting antigens, with its possible malfunctioning linked to disease. Surface proteins have long been explored as potential cell markers, disease biomarkers, and therapeutic drug targets. Despite its importance, a detailed study of the surfaceome continues to pose major challenges for mass spectrometry-driven proteomics due to the inherent biophysical characteristics of surface proteins. Their inefficient extraction from hydrophobic membranes to an aqueous medium and their lower abundance compared to intracellular proteins hamper the analysis of surface proteins, which are therefore usually underrepresented in proteomic datasets. To tackle such problems, several innovative analytical methodologies have been developed. This review aims at providing an extensive overview of the different methods for surfaceome analysis, with respective considerations for downstream mass spectrometry-based proteomics.
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Affiliation(s)
- Jarne Pauwels
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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10
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Karcini A, Lazar IM. The SKBR3 cell-membrane proteome reveals telltales of aberrant cancer cell proliferation and targets for precision medicine applications. Sci Rep 2022; 12:10847. [PMID: 35760832 PMCID: PMC9237123 DOI: 10.1038/s41598-022-14418-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/07/2022] [Indexed: 12/14/2022] Open
Abstract
The plasma membrane proteome resides at the interface between the extra- and intra-cellular environment and through its various roles in signal transduction, immune recognition, nutrient transport, and cell-cell/cell-matrix interactions plays an absolutely critical role in determining the fate of a cell. Our work was aimed at exploring the cell-membrane proteome of a HER2+ breast-cancer cell line (SKBR3) to identify triggers responsible for uncontrolled cell proliferation and intrinsic resources that enable detection and therapeutic interventions. To mimic environmental conditions that enable cancer cells to evolve adaptation/survival traits, cell culture was performed under serum-rich and serum-deprived conditions. Proteomic analysis enabled the identification of ~ 2000 cell-membrane proteins. Classification into proteins with receptor/enzymatic activity, CD antigens, transporters, and cell adhesion/junction proteins uncovered overlapping roles in processes that drive cell growth, apoptosis, differentiation, immune response, adhesion and migration, as well as alternate pathways for proliferation. The large number of tumor markers (> 50) and putative drug targets (> 100) exposed a vast potential for yet unexplored detection and targeting opportunities, whereas the presence of 15 antigen immunological markers enabled an assessment of epithelial, mesenchymal or stemness characteristics. Serum-starved cells displayed altered processes related to mitochondrial OXPHOS/ATP synthesis, protein folding and localization, while serum-treated cells exhibited attributes that support tissue invasion and metastasis. Altogether, our findings advance the understanding of the biological triggers that sustain aberrant cancer cell proliferation, survival and development of resistance to therapeutic drugs, and reveal vast innate opportunities for guiding immunological profiling and precision medicine applications aimed at target selection or drug discovery.
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Affiliation(s)
- Arba Karcini
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Iulia M Lazar
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, 24061, USA.
- Virginia Tech Carilion School of Medicine, Roanoke, VA, 24016, USA.
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11
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Liu G, Choi MH, Ma H, Guo X, Lo PC, Kim J, Zhang L. Bioorthogonal Conjugation-Assisted Purification Method for Profiling Cell Surface Proteome. Anal Chem 2022; 94:1901-1909. [PMID: 35019258 DOI: 10.1021/acs.analchem.1c05187] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Surface biotinylation has been widely adapted in profiling the cellular proteome associated with the plasma membrane. However, the workflow is subject to interference from the cytoplasmic biotin-associated proteins that compete for streptavidin-binding during purification. Here we established a bioorthogonal conjugation-assisted purification (BCAP) workflow that utilizes the Staudinger chemoselective ligation to label and isolate surface-associated proteins while minimizing the binding of endogenous biotin-associated proteins. Label-free quantitative proteomics demonstrated that BCAP is efficient in isolating cell surface proteins with excellent reproducibility. Subsequently, we applied BCAP to compare the surface proteome of proliferating and senescent mouse embryonic fibroblasts (MEFs). Among the results, EHD2 was identified and validated as a novel protein that is enhanced at the cell surface of senescent MEFs. We expect that BCAP will have broad applications in profiling cell surface proteomes in the future.
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Affiliation(s)
- Guopan Liu
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon 999077, Hong Kong China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Ming Ho Choi
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon 999077, Hong Kong China
| | - Haiying Ma
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon 999077, Hong Kong China
| | - Xuejiao Guo
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon 999077, Hong Kong China
| | - Pui-Chi Lo
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon 999077, Hong Kong China
| | - Jinyong Kim
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon 999077, Hong Kong China
| | - Liang Zhang
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon 999077, Hong Kong China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
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12
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Reyes-Alvarez E, Walker TJ, Mulligan LM. Evaluating Cell Membrane Localization and Intracellular Transport of Proteins by Biotinylation. Methods Mol Biol 2022; 2508:197-209. [PMID: 35737242 DOI: 10.1007/978-1-0716-2376-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Protein translocation to the cell membrane and transport through intracellular compartments are dynamic processes frequently altered in cancer cells. Abnormal protein localization can affect key cell functions, including transduction of extracellular signals and organization of the cytoskeleton, significantly affecting oncogenicity and therapeutic responses. In this chapter, we describe a surface protein biotinylation method that allows the study of membrane localization and endosomal transport of membrane-associated proteins. Surface biotinylation can be used to evaluate baseline protein levels at the membrane, and other processes such as internalization, recycling, and degradation of proteins in response to different treatments or as a consequence of oncogenic mutations. Further, the combination of this technique with other strategies, such as treatments with transport inhibitors, allows investigation of specific steps of protein trafficking through the cell.
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Affiliation(s)
- Eduardo Reyes-Alvarez
- Division of Cancer Biology and Genetics, Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Timothy J Walker
- Division of Cancer Biology and Genetics, Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Lois M Mulligan
- Division of Cancer Biology and Genetics, Cancer Research Institute, Queen's University, Kingston, ON, Canada.
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13
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Lu C, Glisovic-Aplenc T, Bernt KM, Nestler K, Cesare J, Cao L, Lee H, Fazelinia H, Chinwalla A, Xu Y, Shestova O, Xing Y, Gill S, Li M, Garcia B, Aplenc R. Longitudinal Large-Scale Semiquantitative Proteomic Data Stability Across Multiple Instrument Platforms. J Proteome Res 2021; 20:5203-5211. [PMID: 34669412 DOI: 10.1021/acs.jproteome.1c00624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the rapid developments in mass spectrometry (MS)-based proteomics methods, label-free semiquantitative proteomics has become an increasingly popular tool for profiling global protein abundances in an unbiased manner. However, the reproducibility of these data across time and LC-MS platforms is not well characterized. Here, we evaluate the performance of three LC-MS platforms (Orbitrap Elite, Q Exactive HF, and Orbitrap Fusion) in label-free semiquantitative analysis of cell surface proteins over a six-year period. Sucrose gradient ultracentrifugation was used for surfaceome enrichment, following gel separation for in-depth protein identification. With our established workflow, we consistently detected and reproducibly quantified >2300 putative cell surface proteins in a human acute myeloid leukemia (AML) cell line on all three platforms. To our knowledge this is the first study reporting highly reproducible semiquantitative proteomic data collection of biological replicates across multiple years and LC-MS platforms. These data provide experimental justification for semiquantitative proteomic study designs that are executed over multiyear time intervals and on different platforms. Multiyear and multiplatform experimental designs will likely enable larger scale proteomic studies and facilitate longitudinal proteomic studies by investigators lacking access to high throughput MS facilities. Data are available via ProteomeXchange with identifier PXD022721.
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Affiliation(s)
- Congcong Lu
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Tina Glisovic-Aplenc
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Kathrin M Bernt
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Kevin Nestler
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Joseph Cesare
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Lusha Cao
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Hyoungjoo Lee
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Hossein Fazelinia
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Asif Chinwalla
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States
| | - Yang Xu
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Olga Shestova
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Yi Xing
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Saar Gill
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin Garcia
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Richard Aplenc
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
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14
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Recovery of Sea Star Egg Cell Surface Proteins Released at Fertilization. Methods Mol Biol 2021. [PMID: 33074539 DOI: 10.1007/978-1-0716-0974-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
To provide a better understanding of the composition of the egg cell membrane, we describe a method in which proteins and peptides that are either naturally released by the egg or cleaved by sperm proteases can be collected, analyzed, and identified. Such molecules are captured and isolated from the surrounding seawater via biotinylation, before being concentrated by an affinity interaction and subsequently analyzed by western blotting and mass spectrometry.
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15
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Li Y, Wang Y, Yao Y, Lyu J, Qiao Q, Mao J, Xu Z, Ye M. Rapid Enzyme-Mediated Biotinylation for Cell Surface Proteome Profiling. Anal Chem 2021; 93:4542-4551. [PMID: 33660993 DOI: 10.1021/acs.analchem.0c04970] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cell surface is the primary site for sensing extracellular stimuli. The knowledge of the transient changes on the surfaceome upon a perturbation is very important as the initial changed proteins could be driving molecules for some phenotype. In this study, we report a fast cell surface labeling strategy based on peroxidase-mediated oxidative tyrosine coupling strategy, enabling efficient and selective cell surface labeling within seconds. With a labeling time of 1 min, 2684 proteins, including 1370 (51%) cell surface-annotated proteins (cell surface/plasma membrane/extracellular), 732 transmembrane proteins, and 81 cluster of differentiation antigens, were identified from HeLa cells. By comparison with the negative control experiment using quantitative proteomics, 500 (68%) out of the 731 significantly enriched proteins (p-value < 0.05, ≥2-fold) in positive experimental samples were cell surface-annotated proteins. Finally, this technology was applied to track the dynamic changes of the surfaceome upon insulin stimulation at two time points (5 min and 2 h) in HepG2 cells. Thirty-two proteins, including INSR, CTNNB1, TFRC, IGF2R, and SORT1, were found to be significantly regulated (p-value < 0.01, ≥1.5-fold) after insulin exposure by different mechanisms. We envision that this technique could be a powerful tool to analyze the transient changes of the surfaceome with a good time resolution and to delineate the temporal and spatial regulation of cellular signaling.
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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, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yating Yao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Jiawen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Jiawei Mao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
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16
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Lung cancer: progression of heat shock protein 70 in association with flap endonuclease 1 protein. 3 Biotech 2021; 11:141. [PMID: 33708464 DOI: 10.1007/s13205-020-02598-3] [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: 09/29/2020] [Accepted: 12/17/2020] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is one of the leading causes of cancer deaths worldwide and existing approaches are not enough to manage, and hence, it is important to concentrate on new drug strategies. This study was aimed to identify the interacting partner of Flap endonuclease 1 (FEN1) and its role in cancer treatment. We identified a new FEN1 interacting partner confirmed it as Heat Shock Protein 70 (HSP 70), and its effect on FEN1 expression, in vitro. Additionally, we found that the 5-Fluorouracil's (5-FU) function was significantly improved when used in combination with HSP 70 inhibitor (KNK 437). The findings are interesting, elucidating the synergistic mechanism between two compounds which helps to develop a novel management strategy for over-expressed FEN1 in the lung. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02598-3.
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17
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Ito S, Oishi M, Ogata S, Uemura T, Couraud PO, Masuda T, Ohtsuki S. Identification of Cell-Surface Proteins Endocytosed by Human Brain Microvascular Endothelial Cells In Vitro. Pharmaceutics 2020; 12:pharmaceutics12060579. [PMID: 32585920 PMCID: PMC7356521 DOI: 10.3390/pharmaceutics12060579] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 12/19/2022] Open
Abstract
Cell-surface proteins that can endocytose into brain microvascular endothelial cells serve as promising candidates for receptor-mediated transcytosis across the blood–brain barrier (BBB). Here, we comprehensively screened endocytic cell-surface proteins in hCMEC/D3 cells, a model of human brain microvascular endothelial cells, using surface biotinylation methodology and sequential window acquisition of all theoretical fragment-ion spectra-mass spectrometry (SWATH-MS)-based quantitative proteomics. Using this method, we identified 125 endocytic cell-surface proteins from hCMEC/D3 cells. Of these, 34 cell-surface proteins were selectively internalized into human brain microvascular endothelial cells, but not into human umbilical vein endothelial cells (HUVECs), a model of human peripheral microvascular endothelial cells. Two cell-surface proteins, intercellular adhesion molecule-1 (ICAM1) and podocalyxin (PODXL), were identified as BBB-localized endocytic cell-surface proteins in humans, using open mRNA and protein databases. Immunohistochemical evaluation confirmed PODXL expression in the plasma membrane of hCMEC/D3 cells and revealed that anti-PODXL antibody-labeled cell-surface PODXL internalized into hCMEC/D3 cells. Immunohistochemistry further revealed that PODXL is localized at the luminal side of human brain microvessels, supporting its potential suitability for translational applications. In conclusion, our findings highlight novel endocytic cell-surface proteins capable of internalizing into human brain microvascular endothelial cells. ICAM1 or PODXL targeted antibody or ligand-labeled biopharmaceuticals and nanocarriers may provide effective targeted delivery to the brain across the BBB for the treatment of central nervous system (CNS) diseases.
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Affiliation(s)
- Shingo Ito
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan; (S.I.); (T.M.)
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan;
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan; (S.O.); (T.U.)
| | - Mariko Oishi
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan;
| | - Seiryo Ogata
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan; (S.O.); (T.U.)
| | - Tatsuki Uemura
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan; (S.O.); (T.U.)
| | - Pierre-Olivier Couraud
- Institut Cochin, Universite de Paris, Inserm U1016, CNRS UMR8104, 22 rue Méchain, 75014 Paris, France;
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan; (S.I.); (T.M.)
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan;
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan; (S.O.); (T.U.)
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan; (S.I.); (T.M.)
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan;
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan; (S.O.); (T.U.)
- Correspondence: ; Tel.: +81-96-371-4323
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18
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Akdag M, Yunt ZS, Kamacioglu A, Qureshi MH, Akarlar BA, Ozlu N. Proximal Biotinylation-Based Combinatory Approach for Isolating Integral Plasma Membrane Proteins. J Proteome Res 2020; 19:3583-3592. [DOI: 10.1021/acs.jproteome.0c00113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Mehmet Akdag
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Zeynep Sabahat Yunt
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Altug Kamacioglu
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | | | - Busra A. Akarlar
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Nurhan Ozlu
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
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19
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Improved sensitivity in cell surface protein detection by combining chemical labeling with mechanical lysis in a colorectal cancer cell model. Biotechnol Lett 2020; 42:683-695. [DOI: 10.1007/s10529-020-02824-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/26/2020] [Indexed: 10/25/2022]
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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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Molecular phenotyping of the surfaceome of migratory chondroprogenitors and mesenchymal stem cells using biotinylation, glycocapture and quantitative LC-MS/MS proteomic analysis. Sci Rep 2019; 9:9018. [PMID: 31227739 PMCID: PMC6588563 DOI: 10.1038/s41598-019-44957-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 04/24/2019] [Indexed: 12/16/2022] Open
Abstract
The complement of cell surface proteins, collectively referred to as the surfaceome, is a useful indicator of normal differentiation processes, and the development of pathologies such as osteoarthritis (OA). We employed biochemical and proteomic tools to explore the surfaceome and to define biomarkers in chondrogenic progenitor cells (CPC) derived from human OA knee articular cartilage. These cells have great therapeutic potential, but their unexplored biology limits their clinical application. We performed biotinylation combined with glycocapture and high throughput shotgun proteomics to define the surface proteome of human bone marrow mesenchymal stem cells (MSCs) and human CPCs. We prepared cell surface protein-enriched fractions from MSCs and CPCs, and then a proteomic approach was used to compare and evaluate protein changes between undifferentiated MSCs and CPCs. 1256 proteins were identified in the study, of which 791 (63%) were plasma membrane, cell surface or extracellular matrix proteins. Proteins constituting the surfaceome were annotated and categorized. Our results provide, for the first time, a repository of quantitative proteomic data on the surfaceome of two closely related cell types relevant to cartilage biology and OA. These results may provide novel insights into the transformation of the surfaceome during chondrogenic differentiation and phenotypic changes during OA development.
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23
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Joost S, Mikkat S, Wille M, Schümann A, Schmitt O. Membrane Protein Identification in Rodent Brain Tissue Samples and Acute Brain Slices. Cells 2019; 8:cells8050423. [PMID: 31072038 PMCID: PMC6562397 DOI: 10.3390/cells8050423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 02/07/2023] Open
Abstract
Acute brain slices are a sample format for electrophysiology, disease modeling, and organotypic cultures. Proteome analyses based on mass spectrometric measurements are seldom used on acute slices, although they offer high-content protein analyses and explorative approaches. In neuroscience, membrane proteins are of special interest for proteome-based analysis as they are necessary for metabolic, electrical, and signaling functions, including myelin maintenance and regeneration. A previously published protocol for the enrichment of plasma membrane proteins based on aqueous two-phase polymer systems followed by mass spectrometric protein identification was adjusted to the small sample size of single acute murine slices from newborn animals and the reproducibility of the results was analyzed. For this, plasma membrane proteins of 12 acute slice samples from six animals were enriched and analyzed by liquid chromatography-mass spectrometry. A total of 1161 proteins were identified, of which 369 were assigned to membranes. Protein abundances showed high reproducibility between samples. The plasma membrane protein separation protocol can be applied to single acute slices despite the low sample size and offers a high yield of identifiable proteins. This is not only the prerequisite for proteome analysis of organotypic slice cultures but also allows for the analysis of small-sized isolated brain regions at the proteome level.
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Affiliation(s)
- Sarah Joost
- Institute of Anatomy, University Medical Center Rostock, 18057 Rostock, Germany.
| | - Stefan Mikkat
- Core Facility Proteome Analysis, University Medical Center Rostock, 18057 Rostock, Germany.
| | - Michael Wille
- Institute of Anatomy, University Medical Center Rostock, 18057 Rostock, Germany.
| | - Antje Schümann
- Institute of Anatomy, University Medical Center Rostock, 18057 Rostock, Germany.
| | - Oliver Schmitt
- Institute of Anatomy, University Medical Center Rostock, 18057 Rostock, Germany.
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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: 22] [Impact Index Per Article: 4.4] [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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Kánová E, Jiménez-Munguía I, Majerová P, Tkáčová Z, Bhide K, Mertinková P, Pulzová L, Kováč A, Bhide M. Deciphering the Interactome of Neisseria meningitidis With Human Brain Microvascular Endothelial Cells. Front Microbiol 2018; 9:2294. [PMID: 30319591 PMCID: PMC6168680 DOI: 10.3389/fmicb.2018.02294] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 09/07/2018] [Indexed: 11/16/2022] Open
Abstract
Neisseria meningitidis is able to translocate the blood-brain barrier and cause meningitis. Bacterial translocation is a crucial step in the onset of neuroinvasion that involves interactions between pathogen surface proteins and host cells receptors. In this study, we applied a systematic workflow to recover and identify proteins of N. meningitidis that may interact with human brain microvascular endothelial cells (hBMECs). Biotinylated proteome of N. meningitidis was incubated with hBMECs, interacting proteins were recovered by affinity purification and identified by SWATH-MS. Interactome of N. meningitidis comprised of 41 potentially surface exposed proteins. These were assigned into groups based on their probability to interact with hBMECs: high priority candidates (21 outer membrane proteins), medium priority candidates (14 inner membrane proteins) and low priority candidates (six secretory proteins). Ontology analysis provided information for 17 out of 41 surface proteins. Based on the series of bioinformatic analyses and literature review, five surface proteins (adhesin MafA1, major outer membrane protein P.IB, putative adhesin/invasion, putative lipoprotein and membrane lipoprotein) were selected and their recombinant forms were produced for experimental validation of interaction with hBMECs by ELISA and immunocytochemistry. All candidates showed interaction with hBMECs. In this study, we present a high-throughput approach to generate a dataset of plausible meningococcal ligands followed by systematic bioinformatic pipeline to categorize the proteins for experimental validation.
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Affiliation(s)
- Evelína Kánová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Irene Jiménez-Munguía
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Petra Majerová
- Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovakia
| | - Zuzana Tkáčová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Katarína Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Patrícia Mertinková
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Lucia Pulzová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Andrej Kováč
- Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovakia
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia.,Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovakia
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26
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Integrated proteomic analysis of tumor necrosis factor α and interleukin 1β-induced endothelial inflammation. J Proteomics 2018; 192:89-101. [PMID: 30153514 DOI: 10.1016/j.jprot.2018.08.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/15/2018] [Accepted: 08/23/2018] [Indexed: 12/11/2022]
Abstract
The vascular endothelium provides a unique interaction plane for plasma proteins and leukocytes in inflammation. The pro-inflammatory cytokines Tumor Necrosis Factor α (TNFα) and interleukin 1β (IL-1β) have a profound effect on endothelial cells, which includes increased levels of adhesion molecules and a disrupted barrier function. To assess the endothelial response to these cytokines at the protein level, we evaluated changes in the whole proteome, cell surface proteome and phosphoproteome after 24 h of cytokine treatment. The effects of TNFα and IL-1β on endothelial cells were strikingly similar and included changes in proteins not previously associated with endothelial inflammation. Temporal profiling revealed time-dependent proteomic changes, including a limited number of early responsive proteins such as adhesion receptors ICAM1 and SELE. In addition, this approach uncovered a greater number of late responsive proteins, including proteins related to self-antigen peptide presentation, and a transient increase in ferritin. Peptide-based cell surface proteomics revealed extensive changes at the cell surface, which were in agreement with the whole proteome. In addition, site-specific changes within ITGA5 and ICAM1 were detected. Combined, our integrated proteomic data provide detailed information on endothelial inflammation, emphasize the role of the extracellular matrix therein, and include potential targets for therapeutic intervention. SIGNIFICANCE: Pro-inflammatory cytokines induce the expression of cell adhesion molecules in vascular endothelial cells. These molecules mediate the adhesion and migration of immune cells across the vessel wall, which is a key process to resolve infections in the underlying tissue. Dysregulation of endothelial inflammation can contribute to vascular diseases and the vascular endothelium is therefore an attractive target to control inflammation. Current strategies targeting endothelial adhesion molecules, including PECAM, CD99, ICAM1 and VCAM1 do not completely prevent transmigration. To identify additional therapeutic targets, we mapped the endothelial proteome after pro-inflammatory cytokine treatment. In addition to the whole proteome, we assessed the surface proteome to focus on cell adhesion molecules, and the phosphoproteome to uncover protein activation states. Here, we present an integrated overview of affected processes which further improves our understanding of endothelial inflammation and may eventually aid in therapeutic intervention of imbalanced inflammation.
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27
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Özkan Küçük NE, Şanal E, Tan E, Mitchison T, Özlü N. Labeling Carboxyl Groups of Surface-Exposed Proteins Provides an Orthogonal Approach for Cell Surface Isolation. J Proteome Res 2018; 17:1784-1793. [PMID: 29651847 DOI: 10.1021/acs.jproteome.7b00825] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Quantitative profiling of cell surface proteins is critically important for the understanding of cell-cell communication, signaling, tissue development, and homeostasis. Traditional proteomics methods are challenging for cell surface proteins due to their hydrophobic nature and low abundance, necessitating alternative methods to efficiently identify and quantify this protein group. Here we established carboxyl-reactive biotinylation for selective and efficient biotinylation and isolation of surface-exposed proteins of living cells. We assessed the efficiency of carboxyl-reactive biotinylation for plasma membrane proteins by comparing it with a well-established protocol, amine-reactive biotinylation, using SILAC (stable isotope labeling in cell culture). Our results show that carboxyl-reactive biotinylation of cell surface proteins is both more selective and more efficient than amine-reactive biotinylation. We conclude that it is a useful approach, which is partially orthogonal to amine-reactive biotinylation, allowing us to cast a wider net for a comprehensive profiling of cell surface proteins.
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Affiliation(s)
- Nazlı E Özkan Küçük
- Department of Molecular Biology and Genetics , Koç University , Istanbul 34450 , Turkey
| | - Erdem Şanal
- Department of Molecular Biology and Genetics , Koç University , Istanbul 34450 , Turkey
| | - Edwin Tan
- Department of Systems Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Timothy Mitchison
- Department of Systems Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Nurhan Özlü
- Department of Molecular Biology and Genetics , Koç University , Istanbul 34450 , Turkey
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Jiménez-Munguía I, Pulzova L, Kanova E, Tomeckova Z, Majerova P, Bhide K, Comor L, Sirochmanova I, Kovac A, Bhide M. Proteomic and bioinformatic pipeline to screen the ligands of S. pneumoniae interacting with human brain microvascular endothelial cells. Sci Rep 2018; 8:5231. [PMID: 29588455 PMCID: PMC5869694 DOI: 10.1038/s41598-018-23485-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 03/14/2018] [Indexed: 01/17/2023] Open
Abstract
The mechanisms by which Streptococcus pneumoniae penetrates the blood-brain barrier (BBB), reach the CNS and causes meningitis are not fully understood. Adhesion of bacterial cells on the brain microvascular endothelial cells (BMECs), mediated through protein-protein interactions, is one of the crucial steps in translocation of bacteria across BBB. In this work, we proposed a systematic workflow for identification of cell wall associated ligands of pneumococcus that might adhere to the human BMECs. The proteome of S. pneumoniae was biotinylated and incubated with BMECs. Interacting proteins were recovered by affinity purification and identified by data independent acquisition (DIA). A total of 44 proteins were identified from which 22 were found to be surface-exposed. Based on the subcellular location, ontology, protein interactive analysis and literature review, five ligands (adhesion lipoprotein, endo-β-N-acetylglucosaminidase, PhtA and two hypothetical proteins, Spr0777 and Spr1730) were selected to validate experimentally (ELISA and immunocytochemistry) the ligand-BMECs interaction. In this study, we proposed a high-throughput approach to generate a dataset of plausible bacterial ligands followed by systematic bioinformatics pipeline to categorize the protein candidates for experimental validation. The approach proposed here could contribute in the fast and reliable screening of ligands that interact with host cells.
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Affiliation(s)
- Irene Jiménez-Munguía
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic
| | - Lucia Pulzova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic
| | - Evelina Kanova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic
| | - Zuzana Tomeckova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic
| | - Petra Majerova
- Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Katarina Bhide
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic
| | - Lubos Comor
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic
| | - Ivana Sirochmanova
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic
| | - Andrej Kovac
- Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovak Republic.
- Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovak Republic.
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29
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Kuhlmann L, Cummins E, Samudio I, Kislinger T. Cell-surface proteomics for the identification of novel therapeutic targets in cancer. Expert Rev Proteomics 2018; 15:259-275. [DOI: 10.1080/14789450.2018.1429924] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Laura Kuhlmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Emma Cummins
- The Centre for Drug Research and Development, Division of Biologics, Vancouver, Canada
| | - Ismael Samudio
- The Centre for Drug Research and Development, Division of Biologics, Vancouver, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
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30
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Fechter P. Mapping Changes in Cell Surface Protein Expression Through Selective Labeling of Live Cells. Methods Mol Biol 2018; 1737:119-127. [PMID: 29484591 DOI: 10.1007/978-1-4939-7634-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
ncRNAs are key players in the adaptation of bacteria to new environments, by modulating the composition of the membrane upon changes in the environment. Nevertheless, monitoring the changes in surface protein expression is still a challenge, since these proteins are present in low abundance, and are difficult to extract. Here is described a method to easily, reproducibly, and specifically enrich total protein extracts in surface proteins. This method comprises a direct labeling of surface proteins on living cells using fluorescent dyes, followed by total protein extraction and subsequent separation of these extracts by 2D gel electrophoresis.
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Affiliation(s)
- Pierre Fechter
- UMR7242 Biotechnologie et Signalisation Cellulaire, CNRS, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, Université de Strasbourg, Illkirch-Graffenstaden, France.
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31
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Loke I, Østergaard O, Heegaard NHH, Packer NH, Thaysen-Andersen M. Paucimannose-Rich N-glycosylation of Spatiotemporally Regulated Human Neutrophil Elastase Modulates Its Immune Functions. Mol Cell Proteomics 2017; 16:1507-1527. [PMID: 28630087 PMCID: PMC5546201 DOI: 10.1074/mcp.m116.066746] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 06/04/2017] [Indexed: 12/22/2022] Open
Abstract
Human neutrophil elastase (HNE) is an important N-glycosylated serine protease in the innate immune system, but the structure and immune-modulating functions of HNE N-glycosylation remain undescribed. Herein, LC-MS/MS-based glycan, glycopeptide and glycoprotein profiling were utilized to first determine the heterogeneous N-glycosylation of HNE purified from neutrophil lysates and then from isolated neutrophil granules of healthy individuals. The spatiotemporal expression of HNE during neutrophil activation and the biological importance of its N-glycosylation were also investigated using immunoblotting, cell surface capture, native MS, receptor interaction, protease inhibition, and bacteria growth assays. Site-specific HNE glycoprofiling demonstrated that unusual paucimannosidic N-glycans, particularly Manα1,6Manβ1,4GlcNAcβ1,4(Fucα1,6)GlcNAcβ, predominantly occupied Asn124 and Asn173. The equally unusual core fucosylated monoantenna complex-type N-sialoglycans also decorated these two fully occupied sites. In contrast, the mostly unoccupied Asn88 carried nonfucosylated paucimannosidic N-glycans probably resulting from low glycosylation site solvent accessibility. Asn185 was not glycosylated. Subcellular- and site-specific glycoprofiling showed highly uniform N-glycosylation of HNE residing in distinct neutrophil compartments. Stimulation-induced cell surface mobilization demonstrated a spatiotemporal regulation, but not cell surface-specific glycosylation signatures, of HNE in activated human neutrophils. The three glycosylation sites of HNE were located distal to the active site indicating glycan functions other than interference with HNE enzyme activity. Functionally, the paucimannosidic HNE glycoforms displayed preferential binding to human mannose binding lectin compared with the HNE sialoglycoforms, suggesting a glycoform-dependent involvement of HNE in complement activation. The heavily N-glycosylated HNE protease inhibitor, α1-antitrypsin, displayed concentration-dependent complex formation and preferred glycoform-glycoform interactions with HNE. Finally, both enzymatically active HNE and isolated HNE N-glycans demonstrated low micromolar concentration-dependent growth inhibition of clinically-relevant Pseudomonas aeruginosa, suggesting some bacteriostatic activity is conferred by the HNE N-glycans. Taken together, these observations support that the unusual HNE N-glycosylation, here reported for the first time, is involved in modulating multiple immune functions central to inflammation and infection.
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Affiliation(s)
- Ian Loke
- From the ‡Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ole Østergaard
- §Department of Autoimmunology and Biomarkers, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Niels H H Heegaard
- §Department of Autoimmunology and Biomarkers, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Nicolle H Packer
- From the ‡Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Morten Thaysen-Andersen
- From the ‡Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia;
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32
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Glisovic-Aplenc T, Gill S, Spruce LA, Smith IR, Fazelinia H, Shestova O, Ding H, Tasian SK, Aplenc R, Seeholzer SH. Improved surfaceome coverage with a label-free nonaffinity-purified workflow. Proteomics 2017; 17. [PMID: 28116781 DOI: 10.1002/pmic.201600344] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 01/05/2017] [Accepted: 01/19/2017] [Indexed: 01/17/2023]
Abstract
The proteins of the cellular plasma membrane (PM) perform important functions relating to homeostasis and intercellular communication. Due to its overall low cellular abundance, amphipathic character, and low membrane-to-cytoplasm ratio, the PM proteome has been challenging to isolate and characterize, and is poorly represented in standard LC-MS/MS analyses. In this study, we employ sucrose gradient ultracentrifugation for the enrichment of the PM proteome, without chemical labeling and affinity purification, together with GeLCMS and use subsequent bioinformatics tools to select proteins associated with the PM/cell surface, herein referred to as the surfaceome. Using this methodology, we identify over 1900 cell surface associated proteins in a human acute myeloid leukemia cell line. These surface proteins comprise almost 50% of all detected cellular proteins, a number that substantially exceeds the depth of coverage in previously published studies describing the leukemia surfaceome.
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Affiliation(s)
- Tina Glisovic-Aplenc
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Saar Gill
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Lynn A Spruce
- Protein and Proteomics Core Facility, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Ian R Smith
- Protein and Proteomics Core Facility, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Hossein Fazelinia
- Protein and Proteomics Core Facility, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Olga Shestova
- Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Hua Ding
- Protein and Proteomics Core Facility, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Sarah K Tasian
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Richard Aplenc
- Division of Oncology, Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Steven H Seeholzer
- Protein and Proteomics Core Facility, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
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