1
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Chen S, Xie Y, Alvarez MR, Sheng Y, Bouchibti Y, Chang V, Lebrilla CB. Quantitative Glycan-Protein Cross-Linking Mass Spectrometry Using Enrichable Linkers Reveals Extensive Glycan-Mediated Protein Interaction Networks. Anal Chem 2025; 97:1584-1593. [PMID: 39805041 PMCID: PMC11780575 DOI: 10.1021/acs.analchem.4c04134] [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: 08/05/2024] [Revised: 12/19/2024] [Accepted: 01/03/2025] [Indexed: 01/16/2025]
Abstract
Protein-protein interactions in the cell membrane are typically mediated by glycans, with terminal sialic acid often involved in these interactions. To probe the nature of the interactions, we developed quantitative cross-linking methods involving the glycans of the glycoproteins and the polypeptide moieties of proteins. We designed and synthesized biotinylated enrichable cross-linkers that were click-tagged to metabolically incorporate azido-sialic acid on cell surface glycans to allow cross-linking of the azido-glycans with lysine residues on proximal polypeptides. The glycopeptide-peptide cross-links (GPx) were enriched using biotin groups through affinity purification with streptavidin resin beads. Workflows using two linkers, one photocleavable and the other disulfide, were developed and applied to reveal the sialic acid-mediated cell-surface protein networks of PNT2 (prostate) cells. Glycopeptide-peptide pairs were identified, with 12000 GPx linked by sialylated glycoforms revealing interactions between source glycoproteins and nearly 700 target proteins. Protein-protein interactions were characterized by as many as 40 peptide pairs, and the extent of the interactions between proteins was prioritized by the number of GPx. Quantitation was performed by counting the number of GPx that identify the protein pairs. Abundant membrane proteins such as ITGB1 yielded an interactome consisting of around 400 other proteins, which were ranked from the most extensive interaction, having the largest number of GPx, to at least one. The interactome was further confirmed separately by published databases. This tool will enhance our understanding of glycosylation on protein-protein interactions and provide new potential targets for therapeutics.
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Affiliation(s)
- Siyu Chen
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Yixuan Xie
- Department
of Chemistry, University of California, Davis, California 95616, United States
- State
Key Laboratory of Genetic Engineering, Greater Bay Area Institute
of Precision Medicine (Guangzhou), School of Life Sciences and Institutes
of Biomedical Sciences, Fudan University, Shanghai, 200438, China
| | | | - Ying Sheng
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Yasmine Bouchibti
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Vincent Chang
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Carlito B. Lebrilla
- Department
of Chemistry, University of California, Davis, California 95616, United States
- Department
of Biochemistry, University of California, Davis, California 95616, United States
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2
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Chen L, Li Y, Guo Y, Wang G, Feng N, Sun J, Zhong Y, Yao Y, Ding L, Ju H. Two-Level Spatially Localized Proximity Labeling for Cross-Biological-Hierarchy Measurement and Manipulation. Angew Chem Int Ed Engl 2025:e202421448. [PMID: 39805739 DOI: 10.1002/anie.202421448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Revised: 12/31/2024] [Accepted: 01/13/2025] [Indexed: 01/16/2025]
Abstract
Proximity labeling (PL) has emerged as a powerful technique for the in situ elucidation of biomolecular interaction networks. However, PL methods generally rely on single-biological-hierarchy control of spatial localization at the labeling site, which limits their application in multi-tiered biological systems. Here, we introduced another enzymatic reaction upstream of an enzyme-based PL reaction and targeted the two enzymes to markers indicating different biological hierarchies, establishing a two-level spatially localized proximity labeling (P2L) platform for in situ molecular measurement and manipulation. Using the cellular- and glycan-level as the hierarchical models, we demonstrated the ability of P2L to efficiently execute a two-step logic operation and to discriminate target cells with different levels of glycosylation within mixed cell populations. By mounting clickable handles via P2L, we reprogrammed the robust covalent assembly of cells at designated sites. The combination of P2L with proteomics led to the profiling of the protein microenvironment of specific glycans on target cells, revealing changes in tumor-cell-surface interactions under immune pressure from a glycan perspective. P2L provides not only a solution for revealing the heterogeneity of biological systems, but also new insights in the fields of intelligent logic computation, enzyme engineering, tissue engineering, etc.
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Affiliation(s)
- Liusheng Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yiran Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yuna Guo
- School of Clinical and Basic Medical Sciences, Shandong First Medical University, Jinan, 250117, China
| | - Guyu Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Nan Feng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jiahui Sun
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yihong Zhong
- College of Chemistry and Materials, Jiangxi Normal University, Nanchang, 330022, China
| | - Yunyan Yao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), ChemBioMed Interdisciplinary Research Center, Nanjing University, Nanjing, 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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3
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Liu X, Yi L, Lin Z, Chen S, Wang S, Sheng Y, Lebrilla CB, Garcia BA, Xie Y. Metabolic Control of Glycosylation Forms for Establishing Glycan-Dependent Protein Interaction Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.30.621210. [PMID: 39554187 PMCID: PMC11565926 DOI: 10.1101/2024.10.30.621210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Protein-protein interactions (PPIs) provide essential insights into the complex molecular mechanisms and signaling pathways within cells that regulate development and disease-related phenotypes. However, for membrane proteins, the impact of various forms of glycosylation has often been overlooked in PPI studies. In this study, we introduce a novel approach, glycan-dependent affinity purification followed by mass spectrometry (GAP-MS), to assess variations in PPIs for any glycoprotein of interest under different glycosylation conditions. As a proof of principle, we selected four glycoproteins-BSG, CD44, EGFR, and SLC3A2-as baits to compare their co-purified partners across five metabolically controlled glycan conditions. The findings demonstrate the capability of GAP-MS to identify PPIs influenced by altered glycosylation states, establishing a foundation for systematically exploring the Glycan-Dependent Protein Interactome (GDPI) for other glycoproteins of interest.
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Affiliation(s)
- Xingyu Liu
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Li Yi
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Siyu Chen
- Department of Chemistry, University of California, Davis, Davis, California, United States
| | - Shunyang Wang
- Department of Chemistry, University of California, Davis, Davis, California, United States
| | - Ying Sheng
- Department of Chemistry, University of California, Davis, Davis, California, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, Davis, California, United States
- Department of Biochemistry, University of California, Davis, Davis, California, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Yixuan Xie
- State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
- Department of Chemistry, University of California, Davis, Davis, California, United States
- Lead contact
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4
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Alvarez MRS, Moreno PG, Grijaldo-Alvarez SJB, Yadlapati A, Zhou Q, Narciso MP, Completo GC, Nacario RC, Rabajante JF, Heralde FM, Lebrilla CB. The effects of immortalization on the N-glycome and proteome of CDK4-transformed lung cancer cells. Glycobiology 2024; 34:cwae030. [PMID: 38579012 PMCID: PMC11041852 DOI: 10.1093/glycob/cwae030] [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: 02/22/2024] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024] Open
Abstract
Biological experiments are often conducted in vitro using immortalized cells due to their accessibility and ease of propagation compared to primary cells and live animals. However, immortalized cells may present different proteomic and glycoproteomic characteristics from the primary cell source due to the introduction of genes that enhance proliferation (e.g. CDK4) or enable telomere lengthening. To demonstrate the changes in phenotype upon CDK4-transformation, we performed LC-MS/MS glycomic and proteomic characterizations of a human lung cancer primary cell line (DTW75) and a CDK4-transformed cell line (GL01) derived from DTW75. We observed that the primary and CDK4-transformed cells expressed significantly different levels of sialylated, fucosylated, and sialofucosylated N-glycans. Specifically, the primary cells expressed higher levels of hybrid- and complex-type sialylated N-glycans, while CDK4-transformed cells expressed higher levels of complex-type fucosylated and sialofucosylated N-glycans. Further, we compared the proteomic differences between the cell lines and found that CDK4-transformed cells expressed higher levels of RNA-binding and adhesion proteins. Further, we observed that the CDK4-transformed cells changed N-glycosylation after 31 days in cell culture, with a decrease in high-mannose and increase in fucosylated, sialylated, and sialofucosylated N-glycans. Identifying these changes between primary and CDK4-transformed cells will provide useful insight when adapting cell lines that more closely resemble in vivo physiological conditions.
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Affiliation(s)
- Michael Russelle S Alvarez
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California, 95616, USA
| | - Patrick Gabriel Moreno
- Molecular Diagnostics and Cellular Therapeutics Laboratory, Lung Center of the Philippines, Quezon City, 1100, Philippines
| | - Sheryl Joyce B Grijaldo-Alvarez
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California, 95616, USA
- Institute of Chemistry, College of Arts and Sciences, University of the Philippines Los Baños, 4031, Philippines
| | - Anirudh Yadlapati
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California, 95616, USA
| | - Qingwen Zhou
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California, 95616, USA
| | - Michelle P Narciso
- Institute of Mathematical Sciences and Physics, College of Arts and Sciences, University of the Philippines Los Baños, 4031, Philippines
| | - Gladys Cherisse Completo
- Institute of Chemistry, College of Arts and Sciences, University of the Philippines Los Baños, 4031, Philippines
| | - Ruel C Nacario
- Institute of Chemistry, College of Arts and Sciences, University of the Philippines Los Baños, 4031, Philippines
| | - Jomar F Rabajante
- Institute of Mathematical Sciences and Physics, College of Arts and Sciences, University of the Philippines Los Baños, 4031, Philippines
| | - Francisco M Heralde
- Molecular Diagnostics and Cellular Therapeutics Laboratory, Lung Center of the Philippines, Quezon City, 1100, Philippines
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, 1000, Philippines
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California, 95616, USA
- Department of Chemistry, Biochemistry, Molecular, Cellular and Developmental Biology Group, University of California, Davis, 1 Shields Avenue, Davis, California, 95616, USA
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5
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Xie Y, Chen S, Alvarez MR, Sheng Y, Li Q, Maverakis E, Lebrilla CB. Protein oxidation of fucose environments (POFE) reveals fucose-protein interactions. Chem Sci 2024; 15:5256-5267. [PMID: 38577366 PMCID: PMC10988611 DOI: 10.1039/d3sc06432h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/03/2024] [Indexed: 04/06/2024] Open
Abstract
Cell membrane glycoproteins are generally highly fucosylated and sialylated, and post-translational modifications play important roles in the proteins' functions of signaling, binding and cellular processing. For these reasons, methods for measuring sialic acid-mediated protein-protein interactions have been developed. However, determining the role of fucose in these interactions has been limited by technological barriers that have thus far hindered the ability to characterize and observe fucose-mediated protein-protein interactions. Herein, we describe a method to metabolically label mammalian cells with modified fucose, which incorporates a bioorthogonal group into cell membrane glycoproteins thereby enabling the characterization of cell-surface fucose interactome. Copper-catalyzed click chemistry was used to conjugate a proximity labeling probe, azido-FeBABE. Following the addition of hydrogen peroxide (H2O2), the fucose-azido-FeBABE catalyzed the formation of hydroxyl radicals, which in turn oxidized the amino acids in the proximity of the labeled fucose residue. The oxidized peptides were identified using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Variations in degree of protein oxidation were obtained with different H2O2 reaction times yielding the acquisition of spatial information of the fucose-interacting proteins. In addition, specific glycoprotein-protein interactions were constructed for Galectin-3 (LEG3) and Galectin-3-binding protein (LG3BP) illustrating the further utility of the method. This method identifies new fucose binding partners thereby enhancing our understanding of the cell glycocalyx.
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Affiliation(s)
- Yixuan Xie
- Department of Chemistry, University of California, Davis Davis California USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine St. Louis Missouri 63110 USA
| | - Siyu Chen
- Department of Chemistry, University of California, Davis Davis California USA
| | | | - Ying Sheng
- Department of Chemistry, University of California, Davis Davis California USA
| | - Qiongyu Li
- Department of Chemistry, University of California, Davis Davis California USA
| | - Emanual Maverakis
- Department of Dermatology, University of California, Davis Sacramento California USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis Davis California USA
- Department of Biochemistry, University of California, Davis Davis California USA
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6
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Milione RR, Schell BB, Douglas CJ, Seath CP. Creative approaches using proximity labeling to gain new biological insights. Trends Biochem Sci 2024; 49:224-235. [PMID: 38160064 PMCID: PMC10939868 DOI: 10.1016/j.tibs.2023.12.005] [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: 09/19/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
At its most fundamental level, life is a collection of synchronized cellular processes driven by interactions among biomolecules. Proximity labeling has emerged as a powerful technique to capture these interactions in native settings, revealing previously unexplored elements of biology. This review highlights recent developments in proximity labeling, focusing on methods that push the fundamental technologies beyond the classic bait-prey paradigm, such as RNA-protein interactions, ligand/small-molecule-protein interactions, cell surface protein interactions, and subcellular protein trafficking. The advancement of proximity labeling methods to address different biological problems will accelerate our understanding of the complex biological systems that make up life.
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Affiliation(s)
- Ryan R Milione
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Bin-Bin Schell
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Cameron J Douglas
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Ciaran P Seath
- Skaggs Graduate School of Chemical and Biological Sciences, 120 Scripps Way, Jupiter, FL 33458, USA; Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, 120 Scripps Way, Jupiter, FL 33458, USA.
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7
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Kuliesiute U, Joseph K, Straehle J, Madapusi Ravi V, Kueckelhaus J, Kada Benotmane J, Zhang J, Vlachos A, Beck J, Schnell O, Neniskyte U, Heiland DH. Sialic acid metabolism orchestrates transcellular connectivity and signaling in glioblastoma. Neuro Oncol 2023; 25:1963-1975. [PMID: 37288604 PMCID: PMC10628944 DOI: 10.1093/neuonc/noad101] [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: 11/02/2022] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND In glioblastoma (GBM), the effects of altered glycocalyx are largely unexplored. The terminal moiety of cell coating glycans, sialic acid, is of paramount importance for cell-cell contacts. However, sialic acid turnover in gliomas and its impact on tumor networks remain unknown. METHODS We streamlined an experimental setup using organotypic human brain slice cultures as a framework for exploring brain glycobiology, including metabolic labeling of sialic acid moieties and quantification of glycocalyx changes. By live, 2-photon and high-resolution microscopy we have examined morphological and functional effects of altered sialic acid metabolism in GBM. By calcium imaging we investigated the effects of the altered glycocalyx on a functional level of GBM networks. RESULTS The visualization and quantitative analysis of newly synthesized sialic acids revealed a high rate of de novo sialylation in GBM cells. Sialyltrasferases and sialidases were highly expressed in GBM, indicating that significant turnover of sialic acids is involved in GBM pathology. Inhibition of either sialic acid biosynthesis or desialylation affected the pattern of tumor growth and lead to the alterations in the connectivity of glioblastoma cells network. CONCLUSIONS Our results indicate that sialic acid is essential for the establishment of GBM tumor and its cellular network. They highlight the importance of sialic acid for glioblastoma pathology and suggest that dynamics of sialylation have the potential to be targeted therapeutically.
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Affiliation(s)
- Ugne Kuliesiute
- Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Freiburg, Germany
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- VU LSC-EMBL Partnership for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Kevin Joseph
- Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Freiburg, Germany
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center Brain Links Brain Tools, University of Freiburg, Freiburg, Germany
| | - Jakob Straehle
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Vidhya Madapusi Ravi
- Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Freiburg, Germany
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center Brain Links Brain Tools, University of Freiburg, Freiburg, Germany
| | - Jan Kueckelhaus
- Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Freiburg, Germany
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center Brain Links Brain Tools, University of Freiburg, Freiburg, Germany
| | - Jasim Kada Benotmane
- Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Freiburg, Germany
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center Brain Links Brain Tools, University of Freiburg, Freiburg, Germany
| | - Junyi Zhang
- Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Freiburg, Germany
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center Brain Links Brain Tools, University of Freiburg, Freiburg, Germany
| | - Andreas Vlachos
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center Brain Links Brain Tools, University of Freiburg, Freiburg, Germany
- Center for Basics in Neuromodulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Juergen Beck
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Oliver Schnell
- Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Freiburg, Germany
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
| | - Urte Neniskyte
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- VU LSC-EMBL Partnership for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Dieter Henrik Heiland
- Microenvironment and Immunology Research Laboratory, Medical Center, University of Freiburg, Freiburg, Germany
- Department of Neurosurgery, Medical Center, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Freiburg University, Freiburg, Germany
- Department of Neurological Surgery, Lou and Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Comprehensive Cancer Center Freiburg (CCCF), Faculty of Medicine and Medical Center—University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner siteFreiburg
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8
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Le B, Zhu K, Brown C, Reid B, Cressman A, Zhao M, Fierro FA. Reducing Sialylation Enhances Electrotaxis of Corneal Epithelial Cells. Int J Mol Sci 2023; 24:14327. [PMID: 37762630 PMCID: PMC10531958 DOI: 10.3390/ijms241814327] [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: 08/25/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Corneal wound healing is a complex biological process that integrates a host of different signals to coordinate cell behavior. Upon wounding, there is the generation of an endogenous wound electric field that serves as a powerful cue to guide cell migration. Concurrently, the corneal epithelium reduces sialylated glycoforms, suggesting that sialylation plays an important role during electrotaxis. Here, we show that pretreating human telomerase-immortalized corneal epithelial (hTCEpi) cells with a sialyltransferase inhibitor, P-3FAX-Neu5Ac (3F-Neu5Ac), improves electrotaxis by enhancing directionality, but not speed. This was recapitulated using Kifunensine, which inhibits cleavage of mannoses and therefore precludes sialylation on N-glycans. We also identified that 3F-Neu5Ac enhanced the responsiveness of the hTCEpi cell population to the electric field and that pretreated hTCEpi cells showed increased directionality even at low voltages. Furthermore, when we increased sialylation using N-azidoacetylmannosamine-tetraacylated (Ac4ManNAz), hTCEpi cells showed a decrease in both speed and directionality. Importantly, pretreating enucleated eyes with 3F-Neu5Ac significantly improved re-epithelialization in an ex vivo model of a corneal injury. Finally, we show that in hTCEpi cells, sialylation is increased by growth factor deprivation and reduced by PDGF-BB. Taken together, our results suggest that during corneal wound healing, reduced sialylated glycoforms enhance electrotaxis and re-epithelialization, potentially opening new avenues to promote corneal wound healing.
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Affiliation(s)
- Bryan Le
- Department of Ophthalmology, University of California, Davis, CA 95616, USA; (B.L.); (M.Z.)
| | - Kan Zhu
- Department of Ophthalmology, University of California, Davis, CA 95616, USA; (B.L.); (M.Z.)
| | - Chelsea Brown
- Department of Ophthalmology, University of California, Davis, CA 95616, USA; (B.L.); (M.Z.)
| | - Brian Reid
- Department of Ophthalmology, University of California, Davis, CA 95616, USA; (B.L.); (M.Z.)
| | - Amin Cressman
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA 95817, USA
| | - Min Zhao
- Department of Ophthalmology, University of California, Davis, CA 95616, USA; (B.L.); (M.Z.)
| | - Fernando A. Fierro
- Department of Cell Biology and Human Anatomy, University of California, Davis, CA 95817, USA
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9
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Huang X, Han Y, Li J, Tang M, Qing G. Sensitive and specific detection of saccharide species based on fluorescence: update from 2016. Anal Bioanal Chem 2023:10.1007/s00216-023-04703-w. [PMID: 37119357 PMCID: PMC10148015 DOI: 10.1007/s00216-023-04703-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/01/2023]
Abstract
Increasing evidence supports the critical role of saccharides in various pathophysiological steps of tumor progression, where they regulate tumor proliferation, invasion, hematogenic metastasis, and angiogenesis. The identification and recognition of these saccharides provide a solid foundation for the development of targeted drug preparations, which are however not fully understood due to their complex and similar structures. In order to achieve fluorescence sensing of saccharides, extensive research has been conducted to design molecular probes and nanoparticles made of different materials. This paper aims to provide in-depth discussion of three main topics that cover the current status of the carbohydrate sensing based on the fluorescence sensing mechanism, including a phenylboronic acid-based sensing platform, non-boronic acid entities, as well as an enzyme-based sensing platform. It also highlights efforts made to understand the recognition mechanisms and improve the sensing properties of these systems. Finally, we present the challenge of achieving high selectivity and sensitivity recognition of saccharides, and suggest possible future avenues for exploration.
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Affiliation(s)
- Xiaohuan Huang
- Hubei Key Laboratory of Pollutant Analysis and Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Ying Han
- Hubei Key Laboratory of Pollutant Analysis and Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Junrong Li
- Hubei Key Laboratory of Pollutant Analysis and Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Mingliang Tang
- College of Life Sciences, Wuhan University, 299 Bayi Road, Wuhan, 430072, People's Republic of China
| | - Guangyan Qing
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, People's Republic of China.
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10
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Čaval T, Alisson-Silva F, Schwarz F. Roles of glycosylation at the cancer cell surface: opportunities for large scale glycoproteomics. Theranostics 2023; 13:2605-2615. [PMID: 37215580 PMCID: PMC10196828 DOI: 10.7150/thno.81760] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Cell surface glycosylation has a variety of functions, and its dysregulation in cancer contributes to impaired signaling, metastasis and the evasion of the immune responses. Recently, a number of glycosyltransferases that lead to altered glycosylation have been linked to reduced anti-tumor immune responses: B3GNT3, which is implicated in PD-L1 glycosylation in triple negative breast cancer, FUT8, through fucosylation of B7H3, and B3GNT2, which confers cancer resistance to T cell cytotoxicity. Given the increased appreciation of the relevance of protein glycosylation, there is a critical need for the development of methods that allow for an unbiased interrogation of cell surface glycosylation status. Here we provide an overview of the broad changes in glycosylation at the surface of cancer cell and describe selected examples of receptors with aberrant glycosylation leading to functional changes, with emphasis on immune checkpoint inhibitors, growth-promoting and growth-arresting receptors. Finally, we posit that the field of glycoproteomics has matured to an extent where large-scale profiling of intact glycopeptides from the cell surface is feasible and is poised for discovery of new actionable targets against cancer.
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11
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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: 4.5] [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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12
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Reeves AE, Huang ML. Proximity labeling technologies to illuminate glycan-protein interactions. Curr Opin Chem Biol 2023; 72:102233. [PMID: 36493526 PMCID: PMC9870929 DOI: 10.1016/j.cbpa.2022.102233] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022]
Abstract
Glycosylation is a ubiquitous post-translational modification read by glycan-binding proteins (GBP) to encode important functions, but a robust understanding of these interactions and their consequences can be challenging to uncover. Glycan-GBP interactions are transient and weak, making them difficult to capture, and glycosylation is dynamic and heterogenous, necessitating study in native cellular environments to identify endogenous ligands. Proximity labeling, an experimental innovation that labels biomolecules close to a protein of interest, has recently emerged as a powerful strategy to overcome these limitations, allowing interactors to be tagged in cells for subsequent enrichment and identification by mass spectrometry-based proteomics. We will describe this nascent technique and discuss its applications in the last five years with different GBP classes, including Siglecs, galectins, and non-human lectins.
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Affiliation(s)
- Abigail E Reeves
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Mia L Huang
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
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13
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Zhou Q, Alvarez MRS, Solakyildirim K, Tena J, Serrano LMN, Lam M, Nguyen C, Tobias F, Hummon AB, Nacario RC, Lebrilla CB. Multi-glycomic analysis of spheroid glycocalyx differentiates 2- and 3-dimensional cell models. Glycobiology 2023; 33:2-16. [PMID: 36345209 PMCID: PMC9829041 DOI: 10.1093/glycob/cwac075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/10/2022] [Accepted: 09/26/2022] [Indexed: 11/09/2022] Open
Abstract
A multi-glycomic method for characterizing the glycocalyx was employed to identify the difference between 2-dimensional (2D) and 3-dimensional (3D) culture models with two human colorectal cancer cell lines, HCT116 and HT29. 3D cell cultures are considered more representative of cancer due to their ability to mimic the microenvironment found in tumors. For this reason, they have become an important tool in cancer research. Cell-cell interactions increase in 3D models compared to 2D, indeed significant glycomic changes were observed for each cell line. Analyses included the N-glycome, O-glycome, glycolipidome, glycoproteome, and proteome providing the most extensive characterization of the glycocalyx between 3D and 2D thus far. The different glycoconjugates were affected in different ways. In the N-glycome, the 3D cells increased in high-mannose glycosylation and in core fucosylation. Glycolipids increased in sialylation. Specific glycoproteins were found to increase in the 3D cell, elucidating the pathways that are affected between the two models. The results show large structural and biological changes between the 2 models suggesting that the 2 are indeed very different potentially affecting individual outcomes in the study of diseases.
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Affiliation(s)
- Qingwen Zhou
- Department of Chemistry, University of California, Davis, CA, United States
| | - Michael Russelle S Alvarez
- Department of Chemistry, University of California, Davis, CA, United States
- Institute of Chemistry, University of the Philippines Los Banos, Los Banos, Laguna, Philippines
| | - Kemal Solakyildirim
- Department of Chemistry, University of California, Davis, CA, United States
- Department of Chemistry, Erzincan Binali Yildirim University, Erzincan, Turkey
| | - Jennyfer Tena
- Department of Chemistry, University of California, Davis, CA, United States
| | - Luster Mae N Serrano
- Institute of Chemistry, University of the Philippines Los Banos, Los Banos, Laguna, Philippines
| | - Matthew Lam
- Department of Chemistry, University of California, Davis, CA, United States
| | - Cynthia Nguyen
- Department of Chemistry, University of California, Davis, CA, United States
| | - Fernando Tobias
- Department of Chemistry and Biochemistry, The Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, The Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States
| | - Ruel C Nacario
- Institute of Chemistry, University of the Philippines Los Banos, Los Banos, Laguna, Philippines
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, CA, United States
- Department of Chemistry, Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, CA, United States
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14
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Theyab A, Alsharif KF, Alzahrani KJ, Oyouni AAA, Hawsawi YM, Algahtani M, Alghamdi S, Alshammary AF. New insight into strategies used to develop long-acting G-CSF biologics for neutropenia therapy. Front Oncol 2023; 12:1026377. [PMID: 36686781 PMCID: PMC9850083 DOI: 10.3389/fonc.2022.1026377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023] Open
Abstract
Over the last 20 years, granulocyte colony-stimulating factors (G-CSFs) have become the major therapeutic option for the treatment of patients with neutropenia. Most of the current G-CSFs require daily injections, which are inconvenient and expensive for patients. Increased understanding of G-CSFs' structure, expression, and mechanism of clearance has been very instrumental in the development of new generations of long-acting G-CSFs with improved efficacy. Several approaches to reducing G-CSF clearance via conjugation techniques have been investigated. PEGylation, glycosylation, polysialylation, or conjugation with immunoglobulins or albumins have successfully increased G-CSFs' half-lives. Pegfilgrastim (Neulasta) has been successfully approved and marketed for the treatment of patients with neutropenia. The rapidly expanding market for G-CSFs has increased demand for G-CSF biosimilars. Therefore, the importance of this review is to highlight the principle, elimination's route, half-life, clearance, safety, benefits, and limitations of different strategies and techniques used to increase the half-life of biotherapeutic G-CSFs. Understanding these strategies will allow for a new treatment with more competitive manufacturing and lower unit costs compared with that of Neulasta.
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Affiliation(s)
- Abdulrahman Theyab
- Department of Laboratory and Blood Bank, Security Forces Hospital, Makkah, Saudi Arabia,College of Medicine, Al-Faisal University, Riyadh, Saudi Arabia,*Correspondence: Abdulrahman Theyab, ; Khalaf F. Alsharif,
| | - Khalaf F. Alsharif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia,*Correspondence: Abdulrahman Theyab, ; Khalaf F. Alsharif,
| | - Khalid J. Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | | | - Yousef MohammedRabaa Hawsawi
- College of Medicine, Al-Faisal University, Riyadh, Saudi Arabia,Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Mohammad Algahtani
- Department of Laboratory and Blood Bank, Security Forces Hospital, Makkah, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Amal F. Alshammary
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
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15
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Guo Y, Jia W, Yang J, Zhan X. Cancer glycomics offers potential biomarkers and therapeutic targets in the framework of 3P medicine. Front Endocrinol (Lausanne) 2022; 13:970489. [PMID: 36072925 PMCID: PMC9441633 DOI: 10.3389/fendo.2022.970489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022] Open
Abstract
Glycosylation is one of the most important post-translational modifications (PTMs) in a protein, and is the most abundant and diverse biopolymer in nature. Glycans are involved in multiple biological processes of cancer initiation and progression, including cell-cell interactions, cell-extracellular matrix interactions, tumor invasion and metastasis, tumor angiogenesis, and immune regulation. As an important biomarker, tumor-associated glycosylation changes have been extensively studied. This article reviews recent advances in glycosylation-based biomarker research, which is useful for cancer diagnosis and prognostic assessment. Truncated O-glycans, sialylation, fucosylation, and complex branched structures have been found to be the most common structural patterns in malignant tumors. In recent years, immunochemical methods, lectin recognition-based methods, mass spectrometry (MS)-related methods, and fluorescence imaging-based in situ methods have greatly promoted the discovery and application potentials of glycomic and glycoprotein biomarkers in various cancers. In particular, MS-based proteomics has significantly facilitated the comprehensive research of extracellular glycoproteins, increasing our understanding of their critical roles in regulating cellular activities. Predictive, preventive and personalized medicine (PPPM; 3P medicine) is an effective approach of early prediction, prevention and personalized treatment for different patients, and it is known as the new direction of medical development in the 21st century and represents the ultimate goal and highest stage of medical development. Glycosylation has been revealed to have new diagnostic, prognostic, and even therapeutic potentials. The purpose of glycosylation analysis and utilization of biology is to make a fundamental change in health care and medical practice, so as to lead medical research and practice into a new era of 3P medicine.
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Affiliation(s)
- Yuna Guo
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Wenshuang Jia
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Jingru Yang
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
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16
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Griffin ME, Hsieh-Wilson LC. Tools for mammalian glycoscience research. Cell 2022; 185:2657-2677. [PMID: 35809571 PMCID: PMC9339253 DOI: 10.1016/j.cell.2022.06.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 10/17/2022]
Abstract
Cellular carbohydrates or glycans are critical mediators of biological function. Their remarkably diverse structures and varied activities present exciting opportunities for understanding many areas of biology. In this primer, we discuss key methods and recent breakthrough technologies for identifying, monitoring, and manipulating glycans in mammalian systems.
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Affiliation(s)
- Matthew E Griffin
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Microbiology and Immunology, Scripps Research, La Jolla, CA 92037, USA
| | - Linda C Hsieh-Wilson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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17
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Huang Y, Zhai G, Li Y, Han Y, Chen C, Lu C, Zhang K. Deciphering the Interactome of Histone Marks in Living Cells via Genetic Code Expansion Combined with Proximity Labeling. Anal Chem 2022; 94:10705-10714. [PMID: 35862615 DOI: 10.1021/acs.analchem.2c01042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deciphering the endogenous interactors of histone post-translational modifications (hPTMs, also called histone marks) is essential to understand the mechanisms of epigenetic regulation. However, most of the analytical methods to determine hPTM interactomes are in vitro settings, lacking interrogating native chromatin. Although lysine crotonylation (Kcr) has recently been considered an important hPTM for the regulation of gene transcription, the interactors of Kcr still remain to be explored. Herein, we present a general approach relying upon a genetic code expansion system, APEX2 (engineered peroxidase)-mediated proximity labeling, and quantitative proteomics to profile interactomes of the selected hPTMs in living cells. We genetically fused APEX2 to the recombinant histone H3 with a crotonyl lysine inserted site specifically to generate APEX2-H3K9cr that incorporated into native chromatin. Upon activation, APEX2 triggered in vivo biotin labeling of H3K9cr interactors that can then be enriched with streptavidin beads and identified by mass spectrometry. Proteomic analysis further revealed the endogenous interactomes of H3K9cr and confirmed the reliability of the method. Moreover, DPF2 was identified as a candidate interactor, and the binding interaction of DPF2 to H3K9c was further characterized and verified. This study provides a novel strategy for the identification of hPTM interactomes in living cells, and we envision that this is key to elucidating epigenetic regulatory pathways.
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Affiliation(s)
- Yepei Huang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Micro-environment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Guijin Zhai
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yanan Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yue Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Chen Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Congcong Lu
- College of Life Sciences, Nankai University, Tianjin 300070, China
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Micro-environment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
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18
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Sheng Y, Vinjamuri A, Alvarez MRS, Xie Y, McGrath M, Chen S, Barboza M, Frieman M, Lebrilla CB. Host Cell Glycocalyx Remodeling Reveals SARS-CoV-2 Spike Protein Glycomic Binding Sites. Front Mol Biosci 2022; 9:799703. [PMID: 35372520 PMCID: PMC8964299 DOI: 10.3389/fmolb.2022.799703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/31/2022] [Indexed: 12/12/2022] Open
Abstract
Glycans on the host cell membrane and viral proteins play critical roles in pathogenesis. Highly glycosylated epithelial cells represent the primary boundary separating embedded host tissues from pathogens within the respiratory and intestinal tracts. SARS-CoV-2, the causative agent for the COVID-19 pandemic, reaches into the respiratory tract. We found purified human milk oligosaccharides (HMOs) inhibited the viral binding on cells. Spike (S) protein receptor binding domain (RBD) binding to host cells were partly blocked by co-incubation with exogenous HMOs, most by 2-6-sialyl-lactose (6'SL), supporting the notion that HMOs can function as decoys in defense against SARS-Cov2. To investigate the effect of host cell glycocalyx on viral adherence, we metabolically modified and confirmed with glycomic methods the cell surface glycome to enrich specific N-glycan types including those containing sialic acids, fucose, mannose, and terminal galactose. Additionally, Immunofluorescence studies demonstrated that the S protein preferentially binds to terminal sialic acids with α-(2,6)-linkages. Furthermore, site-specific glycosylation of S protein RBD and its human receptor ACE2 were characterized using LC-MS/MS. We then performed molecular dynamics calculations on the interaction complex to further explore the interactive complex between ACE2 and the S protein. The results showed that hydrogen bonds mediated the interactions between ACE2 glycans and S protein with desialylated glycans forming significantly fewer hydrogen bonds. These results supported a mechanism where the virus binds initially to glycans on host cells preferring α-(2,6)-sialic acids and finds ACE2 and with the proper orientation infects the cell.
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Affiliation(s)
- Ying Sheng
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- The Biochemistry, Molecular, Cellular and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, Davis, CA, United States
| | - Anita Vinjamuri
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | | | - Yixuan Xie
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | - Marisa McGrath
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Siyu Chen
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | - Mariana Barboza
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Matthew Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- The Biochemistry, Molecular, Cellular and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, Davis, CA, United States
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19
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Li Q, Xie Y, Rice R, Maverakis E, Lebrilla CB. A proximity labeling method for protein–protein interactions on cell membrane. Chem Sci 2022; 13:6028-6038. [PMID: 35685794 PMCID: PMC9132088 DOI: 10.1039/d1sc06898a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/29/2022] [Indexed: 01/02/2023] Open
Abstract
Modified catalytic antibodies targeting specific antigens are employed to investigate protein interactions and antigen interaction sites.
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Affiliation(s)
- Qiongyu Li
- Department of Chemistry, University of California Davis, Davis, California, USA
| | - Yixuan Xie
- Department of Chemistry, University of California Davis, Davis, California, USA
| | - Rachel Rice
- Department of Chemistry, University of California Davis, Davis, California, USA
| | - Emanual Maverakis
- Department of Dermatology, School of Medicine, University of California Davis, Davis, California, USA
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California Davis, Davis, California, USA
- Department of Biochemistry, University of California Davis, Davis, California, USA
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20
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Pan X, Vachet RW. MEMBRANE PROTEIN STRUCTURES AND INTERACTIONS FROM COVALENT LABELING COUPLED WITH MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2022; 41:51-69. [PMID: 33145813 PMCID: PMC8093322 DOI: 10.1002/mas.21667] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 05/31/2023]
Abstract
Membrane proteins are incredibly important biomolecules because they mediate interactions between a cell's external and internal environment. Obtaining information about membrane protein structure and interactions is thus important for understanding these essential biomolecules. Compared with the analyses of water-soluble proteins, the structural analysis of membrane proteins is more challenging owing to their unique chemical properties and the presence of lipid components that are necessary to solubilize them. The combination of covalent labeling (CL) and mass spectrometry (MS) has recently been applied with great success to study membrane protein structure and interactions. These studies have demonstrated the many advantages that CL-MS methods have over other traditional biophysical techniques. In this review, we discuss both amino acid-specific and non-specific labeling approaches and the special considerations needed to address the unique challenges associated with interrogating membrane proteins. This review highlights the aspects of this approach that require special care to be applied correctly and provides a comprehensive review of the membrane protein systems that have been studied by CL-MS. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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21
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McKenzie-Coe A, Montes NS, Jones LM. Hydroxyl Radical Protein Footprinting: A Mass Spectrometry-Based Structural Method for Studying the Higher Order Structure of Proteins. Chem Rev 2021; 122:7532-7561. [PMID: 34633178 DOI: 10.1021/acs.chemrev.1c00432] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hydroxyl radical protein footprinting (HRPF) coupled to mass spectrometry has been successfully used to investigate a plethora of protein-related questions. The method, which utilizes hydroxyl radicals to oxidatively modify solvent-accessible amino acids, can inform on protein interaction sites and regions of conformational change. Hydroxyl radical-based footprinting was originally developed to study nucleic acids, but coupling the method with mass spectrometry has enabled the study of proteins. The method has undergone several advancements since its inception that have increased its utility for more varied applications such as protein folding and the study of biotherapeutics. In addition, recent innovations have led to the study of increasingly complex systems including cell lysates and intact cells. Technological advances have also increased throughput and allowed for better control of experimental conditions. In this review, we provide a brief history of the field of HRPF and detail recent innovations and applications in the field.
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Affiliation(s)
- Alan McKenzie-Coe
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Nicholas S Montes
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
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22
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Gutierrez-Reyes CD, Jiang P, Atashi M, Bennett A, Yu A, Peng W, Zhong J, Mechref Y. Advances in mass spectrometry-based glycoproteomics: An update covering the period 2017-2021. Electrophoresis 2021; 43:370-387. [PMID: 34614238 DOI: 10.1002/elps.202100188] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/30/2021] [Accepted: 09/25/2021] [Indexed: 12/23/2022]
Abstract
Protein glycosylation is one of the most common posttranslational modifications, and plays an essential role in a wide range of biological processes such as immune response, intercellular signaling, inflammation, host-pathogen interaction, and protein stability. Glycoproteomics is a proteomics subfield dedicated to identifying and characterizing the glycans and glycoproteins in a given cell or tissue. Aberrant glycosylation has been associated with various diseases such as Alzheimer's disease, viral infections, inflammation, immune deficiencies, congenital disorders, and cancers. However, glycoproteomic analysis remains challenging because of the low abundance, site-specific heterogeneity, and poor ionization efficiency of glycopeptides during LC-MS analyses. Therefore, the development of sensitive and accurate approaches to efficiently characterize protein glycosylation is crucial. Methods such as metabolic labeling, enrichment, and derivatization of glycopeptides, coupled with different mass spectrometry techniques and bioinformatics tools, have been developed to achieve sophisticated levels of quantitative and qualitative analyses of glycoproteins. This review attempts to update the recent developments in the field of glycoproteomics reported between 2017 and 2021.
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Affiliation(s)
| | - Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Andrew Bennett
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Jieqiang Zhong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
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23
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Zhou Q, Xie Y, Lam M, Lebrilla CB. N-Glycomic Analysis of the Cell Shows Specific Effects of Glycosyl Transferase Inhibitors. Cells 2021; 10:cells10092318. [PMID: 34571967 PMCID: PMC8465854 DOI: 10.3390/cells10092318] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
Glycomic profiling methods were used to determine the effect of metabolic inhibitors on glycan production. These inhibitors are commonly used to alter the cell surface glycosylation. However, structural analysis of the released glycans has been limited. In this research, the cell membranes were enriched and the glycans were released to obtain the N-glycans of the glycocalyx. Glycomic analysis using liquid chromatography–mass spectrometry (LC–MS) with a PGC chip column was used to profile the structures in the cell membrane. Glycans of untreated cells were compared to glycans of cells treated with inhibitors, including kifunensine, which inhibits the formation of complex- and hybrid-type structures, 2,4,7,8,9-Penta-O-acetyl-N-acetyl-3-fluoro-b-d-neuraminic acid methyl ester for sialylated glycans, 2-deoxy-2-fluorofucose, and 6-alkynyl fucose for fucosylated glycans. Kifunensine was the most effective, converting nearly 95% of glycans to high mannose types. The compound 6-alkynyl fucose inhibited some fucosylation but also incorporated into the glycan structure. Proteomic analysis of the enriched membrane for the four inhibitors showed only small changes in the proteome accompanied by large changes in the N-glycome for Caco-2. Future works may use these inhibitors to study the cellular behavior associated with the alteration of glycosylation in various biological systems, e.g., viral and bacterial infection, drug binding, and cell–cell interactions.
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Affiliation(s)
- Qingwen Zhou
- Department of Chemistry, University of California, Davis, CA 95616, USA; (Q.Z.); (Y.X.); (M.L.)
| | - Yixuan Xie
- Department of Chemistry, University of California, Davis, CA 95616, USA; (Q.Z.); (Y.X.); (M.L.)
| | - Matthew Lam
- Department of Chemistry, University of California, Davis, CA 95616, USA; (Q.Z.); (Y.X.); (M.L.)
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, CA 95616, USA; (Q.Z.); (Y.X.); (M.L.)
- Department of Biochemistry, University of California, Davis, CA 95616, USA
- Correspondence:
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24
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UDP-glucose pyrophosphorylase 2, a regulator of glycogen synthesis and glycosylation, is critical for pancreatic cancer growth. Proc Natl Acad Sci U S A 2021; 118:2103592118. [PMID: 34330832 PMCID: PMC8346792 DOI: 10.1073/pnas.2103592118] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
UDP-glucose pyrophosphorylase 2 (UGP2), the enzyme that synthesizes uridine diphosphate (UDP)-glucose, rests at the convergence of multiple metabolic pathways, however, the role of UGP2 in tumor maintenance and cancer metabolism remains unclear. Here, we identify an important role for UGP2 in the maintenance of pancreatic ductal adenocarcinoma (PDAC) growth in both in vitro and in vivo tumor models. We found that transcription of UGP2 is directly regulated by the Yes-associated protein 1 (YAP)-TEA domain transcription factor (TEAD) complex, identifying UGP2 as a bona fide YAP target gene. Loss of UGP2 leads to decreased intracellular glycogen levels and defects in N-glycosylation targets that are important for the survival of PDACs, including the epidermal growth factor receptor (EGFR). These critical roles of UGP2 in cancer maintenance, metabolism, and protein glycosylation may offer insights into therapeutic options for otherwise intractable PDACs.
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25
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Xie Y, Chen S, Li Q, Sheng Y, Alvarez MR, Reyes J, Xu G, Solakyildirim K, Lebrilla CB. Glycan-protein cross-linking mass spectrometry reveals sialic acid-mediated protein networks on cell surfaces. Chem Sci 2021; 12:8767-8777. [PMID: 34257876 PMCID: PMC8246274 DOI: 10.1039/d1sc00814e] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/17/2021] [Indexed: 12/15/2022] Open
Abstract
A cross-linking method is developed to elucidate glycan-mediated interactions between membrane proteins through sialic acids. The method provides information on previously unknown extensive glycomic interactions on cell membranes. The vast majority of membrane proteins are glycosylated with complicated glycan structures attached to the polypeptide backbone. Glycan-protein interactions are fundamental elements in many cellular events. Although significant advances have been made to identify protein-protein interactions in living cells, only modest advances have been made on glycan-protein interactions. Mechanistic elucidation of glycan-protein interactions has thus far remained elusive. Therefore, we developed a cross-linking mass spectrometry (XL-MS) workflow to directly identify glycan-protein interactions on the cell membrane using liquid chromatography-mass spectrometry (LC-MS). This method involved incorporating azido groups on cell surface glycans through biosynthetic pathways, followed by treatment of cell cultures with a synthesized reagent, N-hydroxysuccinimide (NHS)-cyclooctyne, which allowed the cross-linking of the sialic acid azides on glycans with primary amines on polypeptide backbones. The coupled peptide-glycan-peptide pairs after cross-linking were identified using the latest techniques in glycoproteomic and glycomic analyses and bioinformatics software. With this approach, information on the site of glycosylation, the glycoform, the source protein, and the target protein of the cross-linked pair were obtained. Glycoprotein-protein interactions involving unique glycoforms on the PNT2 cell surface were identified using the optimized and validated method. We built the GPX network of the PNT2 cell line and further investigated the biological roles of different glycan structures within protein complexes. Furthermore, we were able to build glycoprotein-protein complex models for previously unexplored interactions. The method will advance our future understanding of the roles of glycans in protein complexes on the cell surface.
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Affiliation(s)
- Yixuan Xie
- Department of Chemistry, University of California Davis California USA
| | - Siyu Chen
- Department of Chemistry, University of California Davis California USA
| | - Qiongyu Li
- Department of Chemistry, University of California Davis California USA
| | - Ying Sheng
- Department of Chemistry, Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California Davis California USA
| | | | - Joeriggo Reyes
- Marine Science Institute, University of the Philippines Diliman Quezon City Philippines
| | - Gege Xu
- Department of Chemistry, University of California Davis California USA
| | - Kemal Solakyildirim
- Department of Chemistry, University of California Davis California USA.,Department of Chemistry, Erzincan Binali Yildirim University Erzincan Turkey
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis California USA.,Department of Biochemistry, University of California Davis California USA
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26
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Sun F, Suttapitugsakul S, Wu R. Unraveling the surface glycoprotein interaction network by integrating chemical crosslinking with MS-based proteomics. Chem Sci 2021; 12:2146-2155. [PMID: 34163979 PMCID: PMC8179341 DOI: 10.1039/d0sc06327d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The cell plasma membrane provides a highly interactive platform for the information transfer between the inside and outside of cells. The surface glycoprotein interaction network is extremely important in many extracellular events, and aberrant protein interactions are closely correlated with various diseases including cancer. Comprehensive analysis of cell surface protein interactions will deepen our understanding of the collaborations among surface proteins to regulate cellular activity. In this work, we developed a method integrating chemical crosslinking, an enzymatic reaction, and MS-based proteomics to systematically characterize proteins interacting with surface glycoproteins, and then constructed the surfaceome interaction network. Glycans covalently bound to proteins were employed as “baits”, and proteins that interact with surface glycoproteins were connected using chemical crosslinking. Glycans on surface glycoproteins were oxidized with galactose oxidase (GAO) and sequentially surface glycoproteins together with their interactors (“prey”) were enriched through hydrazide chemistry. In combination with quantitative proteomics, over 300 proteins interacting with surface glycoproteins were identified. Many important domains related to extracellular events were found on these proteins. Based on the protein–protein interaction database, we constructed the interaction network among the identified proteins, in which the hub proteins play more important roles in the interactome. Through analysis of crosslinked peptides, specific interactors were identified for glycoproteins on the cell surface. The newly developed method can be extensively applied to study glycoprotein interactions on the cell surface, including the dynamics of the surfaceome interactions in cells with external stimuli. Proteins interacting with glycoproteins on the cell surface were systematically characterized by integrating chemical crosslinking, enzymatic oxidation, and MS-based proteomics. The surface glycoprotein interaction network was then constructed.![]()
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Affiliation(s)
- Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology Atlanta Georgia 30332 USA +1-404-894-7452 +1-404-385-1515
| | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology Atlanta Georgia 30332 USA +1-404-894-7452 +1-404-385-1515
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology Atlanta Georgia 30332 USA +1-404-894-7452 +1-404-385-1515
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27
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Xie Y, Sheng Y, Li Q, Ju S, Reyes J, Lebrilla CB. Determination of the glycoprotein specificity of lectins on cell membranes through oxidative proteomics. Chem Sci 2020; 11:9501-9512. [PMID: 34094216 PMCID: PMC8162070 DOI: 10.1039/d0sc04199h] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/13/2020] [Indexed: 12/25/2022] Open
Abstract
The cell membrane is composed of a network of glycoconjugates including glycoproteins and glycolipids that presents a dense matrix of carbohydrates playing critical roles in many biological processes. Lectin-based technology has been widely used to characterize glycoconjugates in tissues and cell lines. However, their specificity toward their putative glycan ligand and sensitivity in situ have been technologically difficult to study. Additionally, because they recognize primarily glycans, the underlying glycoprotein targets are generally not known. In this study, we employed lectin proximity oxidative labeling (Lectin PROXL) to identify cell surface glycoproteins that contain glycans that are recognized by lectins. Commonly used lectins were modified with a probe to produce hydroxide radicals in the proximity of the labeled lectins. The underlying polypeptides of the glycoproteins recognized by the lectins are oxidized and identified by the standard proteomic workflow. As a result, approximately 70% of identified glycoproteins were oxidized in situ by all the lectin probes, while only 5% of the total proteins were oxidized. The correlation between the glycosites and oxidation sites demonstrated the effectiveness of the lectin probes. The specificity and sensitivity of each lectin were determined using site-specific glycan information obtained through glycomic and glycoproteomic analyses. Notably, the sialic acid-binding lectins and the fucose-binding lectins had higher specificity and sensitivity compared to other lectins, while those that were specific to high mannose glycans have poor sensitivity and specificity. This method offers an unprecedented view of the interactions of lectins with specific glycoproteins as well as protein networks that are mediated by specific glycan types on cell membranes.
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Affiliation(s)
- Yixuan Xie
- Department of Chemistry, University of California Davis Davis California USA
| | - Ying Sheng
- Department of Chemistry, Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California Davis Davis California USA
| | - Qiongyu Li
- Department of Chemistry, University of California Davis Davis California USA
| | - Seunghye Ju
- Department of Chemistry, University of California Davis Davis California USA
| | - Joe Reyes
- Marine Science Institute, University of the Philippines Diliman Quezon City Philippines
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis Davis California USA
- Department of Biochemistry, University of California Davis Davis California USA
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28
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Li Q, Xie Y, Wong M, Barboza M, Lebrilla CB. Comprehensive structural glycomic characterization of the glycocalyxes of cells and tissues. Nat Protoc 2020; 15:2668-2704. [PMID: 32681150 PMCID: PMC11790333 DOI: 10.1038/s41596-020-0350-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 05/01/2020] [Indexed: 01/10/2023]
Abstract
The glycocalyx comprises glycosylated proteins and lipids and fcorms the outermost layer of cells. It is involved in fundamental inter- and intracellular processes, including non-self-cell and self-cell recognition, cell signaling, cellular structure maintenance, and immune protection. Characterization of the glycocalyx is thus essential to understanding cell physiology and elucidating its role in promoting health and disease. This protocol describes how to comprehensively characterize the glycocalyx N-glycans and O-glycans of glycoproteins, as well as intact glycolipids in parallel, using the same enriched membrane fraction. Profiling of the glycans and the glycolipids is performed using nanoflow liquid chromatography-mass spectrometry (nanoLC-MS). Sample preparation, quantitative LC-tandem MS (LC-MS/MS) analysis, and data processing methods are provided. In addition, we discuss glycoproteomic analysis that yields the site-specific glycosylation of membrane proteins. To reduce the amount of sample needed, N-glycan, O-glycan, and glycolipid analyses are performed on the same enriched fraction, whereas glycoproteomic analysis is performed on a separate enriched fraction. The sample preparation process takes 2-3 d, whereas the time spent on instrumental and data analyses could vary from 1 to 5 d for different sample sizes. This workflow is applicable to both cell and tissue samples. Systematic changes in the glycocalyx associated with specific glycoforms and glycoconjugates can be monitored with quantitation using this protocol. The ability to quantitate individual glycoforms and glycoconjugates will find utility in a broad range of fundamental and applied clinical studies, including glycan-based biomarker discovery and therapeutics.
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Affiliation(s)
- Qiongyu Li
- Department of Chemistry, University of California, Davis, Davis, California, USA
| | - Yixuan Xie
- Department of Chemistry, University of California, Davis, Davis, California, USA
| | - Maurice Wong
- Department of Chemistry, University of California, Davis, Davis, California, USA
| | - Mariana Barboza
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, Davis, California, USA.
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA.
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29
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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30
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Tong M, Smeekens JM, Xiao H, Wu R. Systematic quantification of the dynamics of newly synthesized proteins unveiling their degradation pathways in human cells. Chem Sci 2020; 11:3557-3568. [PMID: 34109028 PMCID: PMC8152571 DOI: 10.1039/c9sc06479f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/09/2020] [Indexed: 12/29/2022] Open
Abstract
Proteins are continuously synthesized during cell growth and proliferation. At the same time, excessive and misfolded proteins have to be degraded, otherwise they are a burden to cells. Protein degradation is essential to maintain proteostasis in cells, and dysfunction of protein degradation systems results in numerous diseases such as cancer and neurodegenerative diseases. Despite the importance of protein degradation, the degradation pathways of many proteins remain to be explored. Here, we comprehensively investigated the degradation of newly synthesized proteins in human cells by integrating metabolic labeling, click chemistry, and multiplexed proteomics, and systematic and quantitative analysis of newly synthesized proteins first revealed the degradation pathways of many proteins. Bioinformatic analysis demonstrates that proteins degraded through two major pathways have distinct properties and functions. Proteins degraded through the ubiquitin-proteasome pathway contain more disordered structures, whereas those through the autophagy-lysosome pathway have significantly higher hydrophobicity. Systematic and quantitative investigation of the dynamics of newly synthesized proteins provides unprecedented and valuable information about protein degradation, which leads to a better understanding of protein properties and cellular activities.
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Affiliation(s)
- Ming Tong
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology Atlanta Georgia 30332 USA +1-404-894-7452 +1-404-385-1515
| | - Johanna M Smeekens
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology Atlanta Georgia 30332 USA +1-404-894-7452 +1-404-385-1515
| | - Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology Atlanta Georgia 30332 USA +1-404-894-7452 +1-404-385-1515
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology Atlanta Georgia 30332 USA +1-404-894-7452 +1-404-385-1515
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31
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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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32
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Liu G, Jia L, Xing G. Probing Sialidases or Siglecs with Sialic Acid Analogues, Clusters and Precursors. ASIAN J ORG CHEM 2019. [DOI: 10.1002/ajoc.201900618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Guang‐jian Liu
- College of ChemistryBeijing Normal University Beijing 100875 P.R. China
| | - Li‐yan Jia
- College of ChemistryBeijing Normal University Beijing 100875 P.R. China
| | - Guo‐wen Xing
- College of ChemistryBeijing Normal University Beijing 100875 P.R. China
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33
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Han J, Huang X, Liu H, Wang J, Xiong C, Nie Z. Laser cleavable probes for in situ multiplexed glycan detection by single cell mass spectrometry. Chem Sci 2019; 10:10958-10962. [PMID: 32190253 PMCID: PMC7066667 DOI: 10.1039/c9sc03912k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022] Open
Abstract
A single-cell MS approach for multiplexed glycan detection to investigate the relationship between drug resistance and glycans at a single-cell level and quantify multiple glycans, overcoming the limit of low ionization efficiency of glycans.
Glycans binding on the cell surface through glycosylation play a key role in controlling various cellular processes, and glycan analysis at a single-cell level is necessary to study cellular heterogeneity and diagnose diseases in the early stage. Herein, we synthesized a series of laser cleavable probes, which could sensitively detect glycans on single cells and tissues by laser desorption ionization mass spectrometry (LDI-MS). This multiplexed and quantitative glycan detection was applied to evaluate the alterations of four types of glycans on breast cancer cells and drug-resistant cancer cells at a single-cell level, indicating that drug resistance may be related to the upregulation of glycan with a β-d-galactoside (Galβ) group and Neu5Aca2-6Gal(NAc)-R. Moreover, the glycan spatial distribution in cancerous and paracancerous human tissues was also demonstrated by MS imaging, showing that glycans are overexpressed in cancerous tissues. Therefore, this single-cell MS approach exhibits promise for application in studying glycan functions which are essential for clinical biomarker discovery and diagnosis of related diseases.
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Affiliation(s)
- Jing Han
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China . ; .,University of the Chinese Academy of Sciences , Beijing 100049 , China
| | - Xi Huang
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China . ;
| | - Huihui Liu
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China . ;
| | - Jiyun Wang
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China . ;
| | - Caiqiao Xiong
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China . ;
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Analytical Chemistry for Living Biosystems , Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , China . ; .,University of the Chinese Academy of Sciences , Beijing 100049 , China.,National Center for Mass Spectrometry in Beijing , Beijing 100049 , China
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34
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Li Q, Xie Y, Wong M, Lebrilla CB. Characterization of Cell Glycocalyx with Mass Spectrometry Methods. Cells 2019; 8:E882. [PMID: 31412618 PMCID: PMC6721671 DOI: 10.3390/cells8080882] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 02/06/2023] Open
Abstract
The cell membrane plays an important role in protecting the cell from its extracellular environment. As such, extensive work has been devoted to studying its structure and function. Crucial intercellular processes, such as signal transduction and immune protection, are mediated by cell surface glycosylation, which is comprised of large biomolecules, including glycoproteins and glycosphingolipids. Because perturbations in glycosylation could result in dysfunction of cells and are related to diseases, the analysis of surface glycosylation is critical for understanding pathogenic mechanisms and can further lead to biomarker discovery. Different mass spectrometry-based techniques have been developed for glycan analysis, ranging from highly specific, targeted approaches to more comprehensive profiling studies. In this review, we summarized the work conducted for extensive analysis of cell membrane glycosylation, particularly those employing liquid chromatography with mass spectrometry (LC-MS) in combination with various sample preparation techniques.
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Affiliation(s)
- Qiongyu Li
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Yixuan Xie
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Maurice Wong
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, CA 95616, USA.
- Department of Biochemistry, University of California, Davis, CA 95616, USA.
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