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Bagdonaite I, Abdurahman S, Mirandola M, Pasqual D, Frank M, Narimatsu Y, Joshi HJ, Vakhrushev SY, Salata C, Mirazimi A, Wandall HH. Targeting host O-linked glycan biosynthesis affects Ebola virus replication efficiency and reveals differential GalNAc-T acceptor site preferences on the Ebola virus glycoprotein. J Virol 2024:e0052424. [PMID: 38757972 DOI: 10.1128/jvi.00524-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Ebola virus glycoprotein (EBOV GP) is one of the most heavily O-glycosylated viral glycoproteins, yet we still lack a fundamental understanding of the structure of its large O-glycosylated mucin-like domain and to what degree the host O-glycosylation capacity influences EBOV replication. Using tandem mass spectrometry, we identified 47 O-glycosites on EBOV GP and found similar glycosylation signatures on virus-like particle- and cell lysate-derived GP. Furthermore, we performed quantitative differential O-glycoproteomics on proteins produced in wild-type HEK293 cells and cell lines ablated for the three key initiators of O-linked glycosylation, GalNAc-T1, -T2, and -T3. The data show that 12 out of the 47 O-glycosylated sites were regulated, predominantly by GalNAc-T1. Using the glycoengineered cell lines for authentic EBOV propagation, we demonstrate the importance of O-linked glycan initiation and elongation for the production of viral particles and the titers of progeny virus. The mapped O-glycan positions and structures allowed to generate molecular dynamics simulations probing the largely unknown spatial arrangements of the mucin-like domain. The data highlight targeting GALNT1 or C1GALT1C1 as a possible way to modulate O-glycan density on EBOV GP for novel vaccine designs and tailored intervention approaches.IMPORTANCEEbola virus glycoprotein acquires its extensive glycan shield in the host cell, where it is decorated with N-linked glycans and mucin-type O-linked glycans. The latter is initiated by a family of polypeptide GalNAc-transferases that have different preferences for optimal peptide substrates resulting in a spectrum of both very selective and redundant substrates for each isoform. In this work, we map the exact locations of O-glycans on Ebola virus glycoprotein and identify subsets of sites preferentially initiated by one of the three key isoforms of GalNAc-Ts, demonstrating that each enzyme contributes to the glycan shield integrity. We further show that altering host O-glycosylation capacity has detrimental effects on Ebola virus replication, with both isoform-specific initiation and elongation playing a role. The combined structural and functional data highlight glycoengineered cell lines as useful tools for investigating molecular mechanisms imposed by specific glycans and for steering the immune responses in future vaccine designs.
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Affiliation(s)
- Ieva Bagdonaite
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Mattia Mirandola
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Denis Pasqual
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Yoshiki Narimatsu
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Hiren J Joshi
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Cristiano Salata
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Ali Mirazimi
- Public Health Agency of Sweden, Solna, Sweden
- Department of Laboratory Medicine (LABMED), Karolinska Institute, Stockholm, Sweden
- National Veterinary Institute, Uppsala, Sweden
| | - Hans H Wandall
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
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2
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Poulhazan A, Arnold AA, Mentink-Vigier F, Muszyński A, Azadi P, Halim A, Vakhrushev SY, Joshi HJ, Wang T, Warschawski DE, Marcotte I. Molecular-level architecture of Chlamydomonas reinhardtii's glycoprotein-rich cell wall. Nat Commun 2024; 15:986. [PMID: 38307857 PMCID: PMC10837150 DOI: 10.1038/s41467-024-45246-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/19/2024] [Indexed: 02/04/2024] Open
Abstract
Microalgae are a renewable and promising biomass for large-scale biofuel, food and nutrient production. However, their efficient exploitation depends on our knowledge of the cell wall composition and organization as it can limit access to high-value molecules. Here we provide an atomic-level model of the non-crystalline and water-insoluble glycoprotein-rich cell wall of Chlamydomonas reinhardtii. Using in situ solid-state and sensitivity-enhanced nuclear magnetic resonance, we reveal unprecedented details on the protein and carbohydrate composition and their nanoscale heterogeneity, as well as the presence of spatially segregated protein- and glycan-rich regions with different dynamics and hydration levels. We show that mannose-rich lower-molecular-weight proteins likely contribute to the cell wall cohesion by binding to high-molecular weight protein components, and that water provides plasticity to the cell-wall architecture. The structural insight exemplifies strategies used by nature to form cell walls devoid of cellulose or other glycan polymers.
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Affiliation(s)
- Alexandre Poulhazan
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, H2X 2J6, Canada
| | - Alexandre A Arnold
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, H2X 2J6, Canada
| | - Frederic Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32310, USA
| | - Artur Muszyński
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Adnan Halim
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Tuo Wang
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA.
| | - Dror E Warschawski
- Laboratoire des Biomolécules, LBM, CNRS UMR 7203, Sorbonne Université, École Normale Supérieure, PSL University, 75005, Paris, France.
| | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, H2X 2J6, Canada.
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3
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de Haan N, Song M, Grant OC, Ye Z, Khoder Agha F, Koed Møller Aasted M, Woods RJ, Vakhrushev SY, Wandall HH. Sensitive and Specific Global Cell Surface N-Glycoproteomics Shows Profound Differences Between Glycosylation Sites and Subcellular Components. Anal Chem 2023; 95:17328-17336. [PMID: 37956981 PMCID: PMC10688226 DOI: 10.1021/acs.analchem.3c03626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/02/2023] [Indexed: 11/21/2023]
Abstract
Cell surface glycans are essential for establishing cell communication, adhesion, and migration. However, it remains challenging to obtain cell surface-specific information about glycoconjugate structures. Acquiring this information is essential for unraveling the functional role of glycans and for exploiting them as clinical targets. To specifically analyze the N-glycoprotein forms expressed at the cell surface, we developed a C18 liquid chromatography (LC)-mass spectrometry (MS)-based glycoproteomics method in combination with highly specific cell surface protein labeling and enrichment using a biotin label. The surface-specificity of the method was validated by MS-based proteomics of subcellular component marker proteins. Using the human keratinocytes N/TERT-1 as a model system, we identified and quantified the glycosylation of hundreds of cell surface N-glycosylation sites. This approach allowed us to study the glycoforms present at the functional relevant cell surface, omitting immaturely glycosylated proteins present in the secretory pathway. Interestingly, the different stages of N-glycan processing at individual sites displayed at the cell surface were found to correlate with their accessibility for ER-residing processing enzymes, as investigated through molecular dynamics simulations. Using the new approach, we compared N-glycosylation sites of proteins expressed on the cell surface to their counterparts in a total cell lysate, showing profound differences in glycosylation between the subcellular components and indicating the relevance of the method for future studies in understanding contextual glycan functions.
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Affiliation(s)
- Noortje de Haan
- Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333, ZA, The Netherlands
| | - Ming Song
- Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Oliver C. Grant
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Zilu Ye
- Novo
Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
| | - Fawzi Khoder Agha
- Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | | | - Robert J. Woods
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Sergey Y. Vakhrushev
- Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Hans H. Wandall
- Copenhagen
Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
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4
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Rudjord-Levann AM, Ye Z, Hafkenscheid L, Horn S, Wiegertjes R, Nielsen MA, Song M, Mathiesen CB, Stoop J, Stowell S, Straten PT, Leffler H, Vakhrushev SY, Dabelsteen S, Olsen JV, Wandall HH. Galectin-1 induces a tumor-associated macrophage phenotype and upregulates indoleamine 2,3-dioxygenase-1. iScience 2023; 26:106984. [PMID: 37534161 PMCID: PMC10391608 DOI: 10.1016/j.isci.2023.106984] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/18/2023] [Accepted: 05/24/2023] [Indexed: 08/04/2023] Open
Abstract
Galectins are a group of carbohydrate-binding proteins with a presumed immunomodulatory role and an elusive function on antigen-presenting cells. Here we analyzed the expression of galectin-1 and found upregulation of galectin-1 in the extracellular matrix across multiple tumors. Performing an in-depth and dynamic proteomic and phosphoproteomic analysis of human macrophages stimulated with galectin-1, we show that galectin-1 induces a tumor-associated macrophage phenotype with increased expression of key immune checkpoint protein programmed cell death 1 ligand 1 (PD-L1/CD274) and immunomodulator indoleamine 2,3-dioxygenase-1 (IDO1). Galectin-1 induced IDO1 and its active metabolite kynurenine in a dose-dependent manner through JAK/STAT signaling. In a 3D organotypic tissue model system equipped with genetically engineered tumorigenic epithelial cells, we analyzed the cellular source of galectin-1 in the extracellular matrix and found that galectin-1 is derived from epithelial and stromal cells. Our results highlight the potential of targeting galectin-1 in immunotherapeutic treatment of human cancers.
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Affiliation(s)
- Asha M. Rudjord-Levann
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lise Hafkenscheid
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sabrina Horn
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Renske Wiegertjes
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mathias A.I. Nielsen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ming Song
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline B.K. Mathiesen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesse Stoop
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sean Stowell
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Per Thor Straten
- Center for Cancer Immune Therapy, Copenhagen University Hospital, Herlev, Denmark
| | - Hakon Leffler
- Division of Microbiology, Immunology and Glycobiology, BMC C1228b, Klinikgatan 28, Lund, Sweden
| | - Sergey Y. Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sally Dabelsteen
- Department of Oral Medicine and Pathology, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Jesper V. Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans H. Wandall
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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5
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Larsen ISB, Povolo L, Zhou L, Tian W, Mygind KJ, Hintze J, Jiang C, Hartill V, Prescott K, Johnson CA, Mullegama SV, McConkie-Rosell A, McDonald M, Hansen L, Vakhrushev SY, Schjoldager KT, Clausen H, Worzfeld T, Joshi HJ, Halim A. The SHDRA syndrome-associated gene TMEM260 encodes a protein-specific O-mannosyltransferase. Proc Natl Acad Sci U S A 2023; 120:e2302584120. [PMID: 37186866 PMCID: PMC10214176 DOI: 10.1073/pnas.2302584120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023] Open
Abstract
Mutations in the TMEM260 gene cause structural heart defects and renal anomalies syndrome, but the function of the encoded protein remains unknown. We previously reported wide occurrence of O-mannose glycans on extracellular immunoglobulin, plexin, transcription factor (IPT) domains found in the hepatocyte growth factor receptor (cMET), macrophage-stimulating protein receptor (RON), and plexin receptors, and further demonstrated that two known protein O-mannosylation systems orchestrated by the POMT1/2 and transmembrane and tetratricopeptide repeat-containing proteins 1-4 gene families were not required for glycosylation of these IPT domains. Here, we report that the TMEM260 gene encodes an ER-located protein O-mannosyltransferase that selectively glycosylates IPT domains. We demonstrate that disease-causing TMEM260 mutations impair O-mannosylation of IPT domains and that TMEM260 knockout in cells results in receptor maturation defects and abnormal growth of 3D cell models. Thus, our study identifies the third protein-specific O-mannosylation pathway in mammals and demonstrates that O-mannosylation of IPT domains serves critical functions during epithelial morphogenesis. Our findings add a new glycosylation pathway and gene to a growing group of congenital disorders of glycosylation.
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Affiliation(s)
- Ida Signe Bohse Larsen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Lorenzo Povolo
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Luping Zhou
- Faculty of Medicine, Institute of Pharmacology, University of Marburg, 35043Marburg, Germany
| | - Weihua Tian
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Kasper Johansen Mygind
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - John Hintze
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Chen Jiang
- Faculty of Medicine, Institute of Pharmacology, University of Marburg, 35043Marburg, Germany
| | - Verity Hartill
- Leeds Institute of Medical Research, University of Leeds, St James’ University Hospital, LeedsLS2 9JT, United Kingdom
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, LeedsLS7 4SA, United Kingdom
| | - Katrina Prescott
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, LeedsLS7 4SA, United Kingdom
| | - Colin A. Johnson
- Leeds Institute of Medical Research, University of Leeds, St James’ University Hospital, LeedsLS2 9JT, United Kingdom
| | | | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC27710
| | - Marie McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC27710
| | - Lars Hansen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Sergey Y. Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Katrine T. Schjoldager
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Thomas Worzfeld
- Faculty of Medicine, Institute of Pharmacology, University of Marburg, 35043Marburg, Germany
- Max-Planck-Institute for Heart and Lung Research, 61231Bad Nauheim, Germany
| | - Hiren J. Joshi
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
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6
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Sørensen DM, Büll C, Madsen TD, Lira-Navarrete E, Clausen TM, Clark AE, Garretson AF, Karlsson R, Pijnenborg JFA, Yin X, Miller RL, Chanda SK, Boltje TJ, Schjoldager KT, Vakhrushev SY, Halim A, Esko JD, Carlin AF, Hurtado-Guerrero R, Weigert R, Clausen H, Narimatsu Y. Identification of global inhibitors of cellular glycosylation. Nat Commun 2023; 14:948. [PMID: 36804936 PMCID: PMC9941569 DOI: 10.1038/s41467-023-36598-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
Small molecule inhibitors of glycosylation enzymes are valuable tools for dissecting glycan functions and potential drug candidates. Screening for inhibitors of glycosyltransferases are mainly performed by in vitro enzyme assays with difficulties moving candidates to cells and animals. Here, we circumvent this by employing a cell-based screening assay using glycoengineered cells expressing tailored reporter glycoproteins. We focused on GalNAc-type O-glycosylation and selected the GalNAc-T11 isoenzyme that selectively glycosylates endocytic low-density lipoprotein receptor (LDLR)-related proteins as targets. Our screen of a limited small molecule compound library did not identify selective inhibitors of GalNAc-T11, however, we identify two compounds that broadly inhibited Golgi-localized glycosylation processes. These compounds mediate the reversible fragmentation of the Golgi system without affecting secretion. We demonstrate how these inhibitors can be used to manipulate glycosylation in cells to induce expression of truncated O-glycans and augment binding of cancer-specific Tn-glycoprotein antibodies and to inhibit expression of heparan sulfate and binding and infection of SARS-CoV-2.
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Affiliation(s)
- Daniel Madriz Sørensen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Christian Büll
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Thomas D Madsen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Erandi Lira-Navarrete
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- The Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, 50018, Zaragoza, Spain
- Fundación ARAID, 50018, Zaragoza, Spain
| | - Thomas Mandel Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alex E Clark
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Aaron F Garretson
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Richard Karlsson
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Johan F A Pijnenborg
- Institute for Molecules and Materials, Department of Synthetic Organic Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Xin Yin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Rebecca L Miller
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Sumit K Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Thomas J Boltje
- Institute for Molecules and Materials, Department of Synthetic Organic Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Aaron F Carlin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ramon Hurtado-Guerrero
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- The Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, 50018, Zaragoza, Spain
- Fundación ARAID, 50018, Zaragoza, Spain
| | - Roberto Weigert
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark.
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark.
- GlycoDisplay ApS, Copenhagen, Denmark.
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7
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Chen YH, Tian W, Yasuda M, Ye Z, Song M, Mandel U, Kristensen C, Povolo L, Marques ARA, Čaval T, Heck AJR, Sampaio JL, Johannes L, Tsukimura T, Desnick R, Vakhrushev SY, Yang Z, Clausen H. A universal GlycoDesign for lysosomal replacement enzymes to improve circulation time and biodistribution. Front Bioeng Biotechnol 2023; 11:1128371. [PMID: 36911201 PMCID: PMC9999025 DOI: 10.3389/fbioe.2023.1128371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/06/2023] [Indexed: 03/14/2023] Open
Abstract
Currently available enzyme replacement therapies for lysosomal storage diseases are limited in their effectiveness due in part to short circulation times and suboptimal biodistribution of the therapeutic enzymes. We previously engineered Chinese hamster ovary (CHO) cells to produce α-galactosidase A (GLA) with various N-glycan structures and demonstrated that elimination of mannose-6-phosphate (M6P) and conversion to homogeneous sialylated N-glycans prolonged circulation time and improved biodistribution of the enzyme following a single-dose infusion into Fabry mice. Here, we confirmed these findings using repeated infusions of the glycoengineered GLA into Fabry mice and further tested whether this glycoengineering approach, Long-Acting-GlycoDesign (LAGD), could be implemented on other lysosomal enzymes. LAGD-engineered CHO cells stably expressing a panel of lysosomal enzymes [aspartylglucosamine (AGA), beta-glucuronidase (GUSB), cathepsin D (CTSD), tripeptidyl peptidase (TPP1), alpha-glucosidase (GAA) or iduronate 2-sulfatase (IDS)] successfully converted all M6P-containing N-glycans to complex sialylated N-glycans. The resulting homogenous glycodesigns enabled glycoprotein profiling by native mass spectrometry. Notably, LAGD extended the plasma half-life of all three enzymes tested (GLA, GUSB, AGA) in wildtype mice. LAGD may be widely applicable to lysosomal replacement enzymes to improve their circulatory stability and therapeutic efficacy.
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Affiliation(s)
- Yen-Hsi Chen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,GlycoDisplay ApS, Copenhagen, Denmark
| | - Weihua Tian
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Makiko Yasuda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Zilu Ye
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ming Song
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Lorenzo Povolo
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Tomislav Čaval
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University and Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University and Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Julio Lopes Sampaio
- Institut Curie, PSL Research University, Cellular and Chemical Biology, U1143 INSERM, UMR3666 CNRS, Paris, France
| | - Ludger Johannes
- Institut Curie, PSL Research University, Cellular and Chemical Biology, U1143 INSERM, UMR3666 CNRS, Paris, France
| | - Takahiro Tsukimura
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Functional Bioanalysis, Meiji Pharmaceutical University, Tokyo, Japan
| | - Robert Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk AS, Copenhagen, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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8
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Ye Z, Kilic G, Dabelsteen S, Marinova IN, Thøfner JF, Song M, Rudjord-Levann AM, Bagdonaite I, Vakhrushev SY, Brakebusch CH, Olsen JV, Wandall HH. Characterization of TGF-β signaling in a human organotypic skin model reveals that loss of TGF-βRII induces invasive tissue growth. Sci Signal 2022; 15:eabo2206. [DOI: 10.1126/scisignal.abo2206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Transforming growth factor–β (TGF-β) signaling regulates various aspects of cell growth and differentiation and is often dysregulated in human cancers. We combined genetic engineering of a human organotypic three-dimensional (3D) skin model with global quantitative proteomics and phosphoproteomics to dissect the importance of essential components of the TGF-β signaling pathway, including the ligands TGF-β1, TGF-β2, and TGF-β3, the receptor TGF-βRII, and the intracellular effector SMAD4. Consistent with the antiproliferative effects of TGF-β signaling, the loss of TGF-β1 or SMAD4 promoted cell cycling and delayed epidermal differentiation. The loss of TGF-βRII, which abrogates both SMAD4-dependent and SMAD4-independent downstream signaling, more strongly affected cell proliferation and differentiation than did loss of SMAD4, and it induced invasive growth. TGF-βRII knockout reduced cell-matrix interactions, and the production of matrix proteins increased the production of cancer-associated cell-cell adhesion proteins and proinflammatory mediators and increased mitogen-activated protein kinase (MAPK) signaling. Inhibiting the activation of the ERK and p38 MAPK pathways blocked the development of the invasive phenotype upon the loss of TGF-βRII. This study provides a framework for exploring TGF-β signaling pathways in human epithelial tissue homeostasis and transformation using genetic engineering, 3D tissue models, and high-throughput quantitative proteomics and phosphoproteomics.
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Affiliation(s)
- Zilu Ye
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gülcan Kilic
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Section of Oral Biology and Immunopathology, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Sally Dabelsteen
- Section of Oral Biology and Immunopathology, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Irina N. Marinova
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens F. B. Thøfner
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ming Song
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Asha M. Rudjord-Levann
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ieva Bagdonaite
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y. Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cord H. Brakebusch
- Biotech Research and Innovation Centre, Biomedical Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jesper V. Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans H. Wandall
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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9
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Nielsen MI, de Haan N, Kightlinger W, Ye Z, Dabelsteen S, Li M, Jewett MC, Bagdonaite I, Vakhrushev SY, Wandall HH. Global mapping of GalNAc-T isoform-specificities and O-glycosylation site-occupancy in a tissue-forming human cell line. Nat Commun 2022; 13:6257. [PMID: 36270990 PMCID: PMC9587226 DOI: 10.1038/s41467-022-33806-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 09/30/2022] [Indexed: 12/25/2022] Open
Abstract
Mucin-type-O-glycosylation on proteins is integrally involved in human health and disease and is coordinated by an enzyme family of 20 N-acetylgalactosaminyltransferases (GalNAc-Ts). Detailed knowledge on the biological effects of site-specific O-glycosylation is limited due to lack of information on specific glycosylation enzyme activities and O-glycosylation site-occupancies. Here we present a systematic analysis of the isoform-specific targets of all GalNAc-Ts expressed within a tissue-forming human skin cell line, and demonstrate biologically significant effects of O-glycan initiation on epithelial formation. We find over 300 unique glycosylation sites across a diverse set of proteins specifically regulated by one of the GalNAc-T isoforms, consistent with their impact on the tissue phenotypes. Notably, we discover a high variability in the O-glycosylation site-occupancy of 70 glycosylated regions of secreted proteins. These findings revisit the relevance of individual O-glycosylation sites in the proteome, and provide an approach to establish which sites drive biological functions.
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Affiliation(s)
- Mathias I. Nielsen
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Noortje de Haan
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Weston Kightlinger
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark ,grid.16753.360000 0001 2299 3507Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL 60208 USA
| | - Zilu Ye
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sally Dabelsteen
- grid.5254.60000 0001 0674 042XDepartment of Oral Medicine and Pathology, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Minyan Li
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael C. Jewett
- grid.16753.360000 0001 2299 3507Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL 60208 USA
| | - Ieva Bagdonaite
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y. Vakhrushev
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans H. Wandall
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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10
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Van Coillie J, Schulz MA, Bentlage AEH, de Haan N, Ye Z, Geerdes DM, van Esch WJE, Hafkenscheid L, Miller RL, Narimatsu Y, Vakhrushev SY, Yang Z, Vidarsson G, Clausen H. Role of N-Glycosylation in FcγRIIIa interaction with IgG. Front Immunol 2022; 13:987151. [PMID: 36189205 PMCID: PMC9524020 DOI: 10.3389/fimmu.2022.987151] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/16/2022] [Indexed: 01/09/2023] Open
Abstract
Immunoglobulins G (IgG) and their Fc gamma receptors (FcγRs) play important roles in our immune system. The conserved N-glycan in the Fc region of IgG1 impacts interaction of IgG with FcγRs and the resulting effector functions, which has led to the design of antibody therapeutics with greatly improved antibody-dependent cell cytotoxicity (ADCC) activities. Studies have suggested that also N-glycosylation of the FcγRIII affects receptor interactions with IgG, but detailed studies of the interaction of IgG1 and FcγRIIIa with distinct N-glycans have been hindered by the natural heterogeneity in N-glycosylation. In this study, we employed comprehensive genetic engineering of the N-glycosylation capacities in mammalian cell lines to express IgG1 and FcγRIIIa with different N-glycan structures to more generally explore the role of N-glycosylation in IgG1:FcγRIIIa binding interactions. We included FcγRIIIa variants of both the 158F and 158V allotypes and investigated the key N-glycan features that affected binding affinity. Our study confirms that afucosylated IgG1 has the highest binding affinity to oligomannose FcγRIIIa, a glycan structure commonly found on Asn162 on FcγRIIIa expressed by NK cells but not monocytes or recombinantly expressed FcγRIIIa.
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Affiliation(s)
- Julie Van Coillie
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Morten A. Schulz
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Arthur E. H. Bentlage
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Noortje de Haan
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Lise Hafkenscheid
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rebecca L. Miller
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- GlycoDisplay ApS, Copenhagen, Denmark
| | - Sergey Y. Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- GlycoDisplay ApS, Copenhagen, Denmark
| | - Gestur Vidarsson
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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11
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Hütte HJ, Tiemann B, Shcherbakova A, Grote V, Hoffmann M, Povolo L, Lommel M, Strahl S, Vakhrushev SY, Rapp E, Buettner FFR, Halim A, Imberty A, Bakker H. A Bacterial Mannose Binding Lectin as a Tool for the Enrichment of C- and O-Mannosylated Peptides. Anal Chem 2022; 94:7329-7338. [PMID: 35549177 DOI: 10.1021/acs.analchem.2c00742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry (MS) easily detects C-mannosylated peptides from purified proteins but not from complex biological samples. Enrichment of specific glycopeptides by lectin affinity prior to MS analysis has been widely applied to support glycopeptide identification but was until now not available for C-mannosylated peptides. Here, we used the α-mannose-specific Burkholderia cenocepacia lectin A (BC2L-A) and show that, in addition to its previously demonstrated high-mannose N-glycan binding capability, this lectin is able to retain C- and O-mannosylated peptides. Besides testing binding abilities to standard peptides, we applied BC2L-A affinity to enrich C-mannosylated peptides from complex samples of tryptic digests of HEK293 and MCF10A whole cell extracts, which led to the identification of novel C-mannosylation sites. In conclusion, BC2L-A enabled specific enrichment of C- and O-mannosylated peptides and might have superior properties over other mannose binding lectins for this purpose.
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Affiliation(s)
- Hermann J Hütte
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Birgit Tiemann
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Aleksandra Shcherbakova
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Valerian Grote
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Marcus Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Lorenzo Povolo
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Mark Lommel
- Centre for Organismal Studies (COS), Glycobiology, Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Sabine Strahl
- Centre for Organismal Studies (COS), Glycobiology, Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany.,glyXera GmbH, Brenneckestrasse 20, 39120 Magdeburg, Germany
| | - Falk F R Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Adnan Halim
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Anne Imberty
- Université Grenoble Alpes, CNRS, CERMAV, 601 rue de la chimie, 38000 Grenoble, France
| | - Hans Bakker
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
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12
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Coelho H, Rivas MDL, Grosso AS, Diniz A, Soares CO, Francisco RA, Dias JS, Compañon I, Sun L, Narimatsu Y, Vakhrushev SY, Clausen H, Cabrita EJ, Jiménez-Barbero J, Corzana F, Hurtado-Guerrero R, Marcelo F. Atomic and Specificity Details of Mucin 1 O-Glycosylation Process by Multiple Polypeptide GalNAc-Transferase Isoforms Unveiled by NMR and Molecular Modeling. JACS Au 2022; 2:631-645. [PMID: 35373202 PMCID: PMC8969996 DOI: 10.1021/jacsau.1c00529] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Indexed: 05/10/2023]
Abstract
The large family of polypeptide GalNAc-transferases (GalNAc-Ts) controls with precision how GalNAc O-glycans are added in the tandem repeat regions of mucins (e.g., MUC1). However, the structural features behind the creation of well-defined and clustered patterns of O-glycans in mucins are poorly understood. In this context, herein, we disclose the full process of MUC1 O-glycosylation by GalNAc-T2/T3/T4 isoforms by NMR spectroscopy assisted by molecular modeling protocols. By using MUC1, with four tandem repeat domains as a substrate, we confirmed the glycosylation preferences of different GalNAc-Ts isoforms and highlighted the importance of the lectin domain in the glycosylation site selection after the addition of the first GalNAc residue. In a glycosylated substrate, with yet multiple acceptor sites, the lectin domain contributes to orientate acceptor sites to the catalytic domain. Our experiments suggest that during this process, neighboring tandem repeats are critical for further glycosylation of acceptor sites by GalNAc-T2/T4 in a lectin-assisted manner. Our studies also show local conformational changes in the peptide backbone during incorporation of GalNAc residues, which might explain GalNAc-T2/T3/T4 fine specificities toward the MUC1 substrate. Interestingly, we postulate that a specific salt-bridge and the inverse γ-turn conformation of the PDTRP sequence in MUC1 are the main structural motifs behind the GalNAc-T4 specificity toward this region. In addition, in-cell analysis shows that the GalNAc-T4 isoform is the only isoform glycosylating the Thr of the immunogenic epitope PDTRP in vivo, which highlights the relevance of GalNAc-T4 in the glycosylation of this epitope. Finally, the NMR methodology established herein can be extended to other glycosyltransferases, such as C1GalT1 and ST6GalNAc-I, to determine the specificity toward complex mucin acceptor substrates.
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Affiliation(s)
- Helena Coelho
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- CIC
bioGUNE, Basque Research and Technology
Alliance (BRTA), Bizkaia
Technology Park, Building 801A, 48170 Derio, Spain
- Department
of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, Leioa 48940, Bizkaia, Spain
| | - Matilde de las Rivas
- Institute
for Biocomputation and Physics of Complex Systems (BIFI), Laboratorio
de Microscopias Avanzadas (LMA), University
of Zaragoza, Mariano
Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain
| | - Ana S. Grosso
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Diniz
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Cátia O. Soares
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Rodrigo A. Francisco
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Jorge S. Dias
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ismael Compañon
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, E-26006 Logroño, Spain
| | - Lingbo Sun
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Yoshiki Narimatsu
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Sergey Y. Vakhrushev
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Henrik Clausen
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Eurico J. Cabrita
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Basque Research and Technology
Alliance (BRTA), Bizkaia
Technology Park, Building 801A, 48170 Derio, Spain
- Department
of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, Leioa 48940, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain
- Centro de Investigacion
Biomedica En Red de Enfermedades Respiratorias, 28029 Madrid, Spain
| | - Francisco Corzana
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, E-26006 Logroño, Spain
| | - Ramon Hurtado-Guerrero
- Institute
for Biocomputation and Physics of Complex Systems (BIFI), Laboratorio
de Microscopias Avanzadas (LMA), University
of Zaragoza, Mariano
Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
- Fundación
ARAID, 50018 Zaragoza, Spain
| | - Filipa Marcelo
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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13
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de Haan N, Narimatsu Y, Koed Møller Aasted M, Larsen ISB, Marinova IN, Dabelsteen S, Vakhrushev SY, Wandall HH. In-Depth Profiling of O-Glycan Isomers in Human Cells Using C18 Nanoliquid Chromatography-Mass Spectrometry and Glycogenomics. Anal Chem 2022; 94:4343-4351. [PMID: 35245040 PMCID: PMC8928149 DOI: 10.1021/acs.analchem.1c05068] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
O-Glycosylation is an omnipresent modification
of the human proteome affecting many cellular functions, including
protein cleavage, protein folding, and cellular signaling, interactions,
and trafficking. The functions are governed by differentially regulated O-glycan types and terminal structures. It is therefore
essential to develop analytical methods that facilitate the annotation
of O-glycans in biological material. While various
successful strategies for the in-depth profiling of released O-glycans have been reported, these methods are often limitedly
accessible to the nonspecialist or challenged by the high abundance
of O-glycan structural isomers. Here, we developed
a high-throughput sample preparation approach for the nonreductive
release and characterization of O-glycans from human
cell material. Reducing-end labeling allowed efficient isomer separation
and detection using C18 nanoliquid chromatography coupled to Orbitrap
mass spectrometry. Using the method in combination with a library
of genetically glycoengineered cells displaying defined O-glycan types and structures, we were able to annotate individual O-glycan structural isomers from a complex mixture. Applying
the method in a model system of human keratinocytes, we found a wide
variety of O-glycan structures, including O-fucose, O-glucose, O-GlcNAc, and O-GalNAc glycosylation, with the latter
carrying both elongated core1 and core2 structures and varying numbers
of fucoses and sialic acids. The method, including the now well-characterized
standards, provides the opportunity to study glycomic changes in human
tissue and disease models using rather mainstream analytical equipment.
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Affiliation(s)
- Noortje de Haan
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | | | - Ida S B Larsen
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Irina N Marinova
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Sally Dabelsteen
- Department of Odontology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
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14
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Konstantinidi A, Nason R, Čaval T, Sun L, Sørensen DM, Furukawa S, Ye Z, Vincentelli R, Narimatsu Y, Vakhrushev SY, Clausen H. Exploring the glycosylation of mucins by use of O-glycodomain reporters recombinantly expressed in glycoengineered HEK293 cells. J Biol Chem 2022; 298:101784. [PMID: 35247390 PMCID: PMC8980628 DOI: 10.1016/j.jbc.2022.101784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 12/18/2022] Open
Abstract
Mucins and glycoproteins with mucin-like regions contain densely O-glycosylated domains often found in tandem repeat (TR) sequences. These O-glycodomains have traditionally been difficult to characterize because of their resistance to proteolytic digestion, and knowledge of the precise positions of O-glycans is particularly limited for these regions. Here, we took advantage of a recently developed glycoengineered cell-based platform for the display and production of mucin TR reporters with custom-designed O-glycosylation to characterize O-glycodomains derived from mucins and mucin-like glycoproteins. We combined intact mass and bottom–up site-specific analysis for mapping O-glycosites in the mucins, MUC2, MUC20, MUC21, protein P-selectin-glycoprotein ligand 1, and proteoglycan syndecan-3. We found that all the potential Ser/Thr positions in these O-glycodomains were O-glycosylated when expressed in human embryonic kidney 293 SimpleCells (Tn-glycoform). Interestingly, we found that all potential Ser/Thr O-glycosites in TRs derived from secreted mucins and most glycosites from transmembrane mucins were almost fully occupied, whereas TRs from a subset of transmembrane mucins were less efficiently processed. We further used the mucin TR reporters to characterize cleavage sites of glycoproteases StcE (secreted protease of C1 esterase inhibitor from EHEC) and BT4244, revealing more restricted substrate specificities than previously reported. Finally, we conducted a bottom–up analysis of isolated ovine submaxillary mucin, which supported our findings that mucin TRs in general are efficiently O-glycosylated at all potential glycosites. This study provides insight into O-glycosylation of mucins and mucin-like domains, and the strategies developed open the field for wider analysis of native mucins.
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Affiliation(s)
- Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rebecca Nason
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tomislav Čaval
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lingbo Sun
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Daniel M Sørensen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sanae Furukawa
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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15
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Karlsson R, Chopra P, Joshi A, Yang Z, Vakhrushev SY, Clausen TM, Painter CD, Szekeres GP, Chen YH, Sandoval DR, Hansen L, Esko JD, Pagel K, Dyer DP, Turnbull JE, Clausen H, Boons GJ, Miller RL. Dissecting structure-function of 3-O-sulfated heparin and engineered heparan sulfates. Sci Adv 2021; 7:eabl6026. [PMID: 34936441 PMCID: PMC8694587 DOI: 10.1126/sciadv.abl6026] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 11/08/2021] [Indexed: 06/01/2023]
Abstract
Heparan sulfate (HS) polysaccharides are master regulators of diverse biological processes via sulfated motifs that can recruit specific proteins. 3-O-sulfation of HS/heparin is crucial for anticoagulant activity, but despite emerging evidence for roles in many other functions, a lack of tools for deciphering structure-function relationships has hampered advances. Here, we describe an approach integrating synthesis of 3-O-sulfated standards, comprehensive HS disaccharide profiling, and cell engineering to address this deficiency. Its application revealed previously unseen differences in 3-O-sulfated profiles of clinical heparins and 3-O-sulfotransferase (HS3ST)–specific variations in cell surface HS profiles. The latter correlated with functional differences in anticoagulant activity and binding to platelet factor 4 (PF4), which underlies heparin-induced thrombocytopenia, a known side effect of heparin. Unexpectedly, cells expressing the HS3ST4 isoenzyme generated HS with potent anticoagulant activity but weak PF4 binding. The data provide new insights into 3-O-sulfate structure-function and demonstrate proof of concept for tailored cell-based synthesis of next-generation heparins.
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Affiliation(s)
- Richard Karlsson
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Pradeep Chopra
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Apoorva Joshi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
- GlycoDisplay ApS, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sergey Y. Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Thomas Mandel Clausen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chelsea D. Painter
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gergo P. Szekeres
- Freie Universitaet Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, 14195 Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Yen-Hsi Chen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
- GlycoDisplay ApS, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Daniel R. Sandoval
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lars Hansen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Jeffrey D. Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kevin Pagel
- Freie Universitaet Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, 14195 Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Douglas P. Dyer
- Wellcome Centre for Cell-Matrix Research, Geoffrey Jefferson Brain Research Centre, Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Jeremy E. Turnbull
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
- Centre for Glycobiology, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Science, and Bijvoet Center for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, Netherlands
| | - Rebecca L. Miller
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
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16
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Sun L, Konstantinidi A, Ye Z, Nason R, Zhang Y, Büll C, Kahl-Knutson B, Hansen L, Leffler H, Vakhrushev SY, Yang Z, Clausen H, Narimatsu Y. Installation of O-glycan sulfation capacities in human HEK293 cells for display of sulfated mucins. J Biol Chem 2021; 298:101382. [PMID: 34954141 PMCID: PMC8789585 DOI: 10.1016/j.jbc.2021.101382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 11/25/2022] Open
Abstract
The human genome contains at least 35 genes that encode Golgi sulfotransferases that function in the secretory pathway, where they are involved in decorating glycosaminoglycans, glycolipids, and glycoproteins with sulfate groups. Although a number of important interactions by proteins such as selectins, galectins, and sialic acid–binding immunoglobulin-like lectins are thought to mainly rely on sulfated O-glycans, our insight into the sulfotransferases that modify these glycoproteins, and in particular GalNAc-type O-glycoproteins, is limited. Moreover, sulfated mucins appear to accumulate in respiratory diseases, arthritis, and cancer. To explore further the genetic and biosynthetic regulation of sulfated O-glycans, here we expanded a cell-based glycan array in the human embryonic kidney 293 (HEK293) cell line with sulfation capacities. We stably engineered O-glycan sulfation capacities in HEK293 cells by site-directed knockin of sulfotransferase genes in combination with knockout of genes to eliminate endogenous O-glycan branching (core2 synthase gene GCNT1) and/or sialylation capacities in order to provide simplified substrates (core1 Galβ1–3GalNAcα1–O-Ser/Thr) for the introduced sulfotransferases. Expression of the galactose 3-O-sulfotransferase 2 in HEK293 cells resulted in sulfation of core1 and core2 O-glycans, whereas expression of galactose 3-O-sulfotransferase 4 resulted in sulfation of core1 only. We used the engineered cell library to dissect the binding specificity of galectin-4 and confirmed binding to the 3-O-sulfo-core1 O-glycan. This is a first step toward expanding the emerging cell-based glycan arrays with the important sulfation modification for display and production of glycoconjugates with sulfated O-glycans.
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Affiliation(s)
- Lingbo Sun
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; Medical College of Yan'an University, Yan'an University, Yan'an, 716000, Shaanxi Province, China
| | - Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Rebecca Nason
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Yuecheng Zhang
- Department of Biomedical Sciences, Faculty of Health and Society, Malmö University, Jan Waldenströms gata 25, 205 06 Malmö, Sweden
| | - Christian Büll
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Barbro Kahl-Knutson
- Department of Laboratory Medicine, Section MIG, Lund University BMC-C1228b, Klinikgatan28, 221 84 Lund, Sweden
| | - Lars Hansen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Hakon Leffler
- Department of Laboratory Medicine, Section MIG, Lund University BMC-C1228b, Klinikgatan28, 221 84 Lund, Sweden
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Zhang Yang
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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17
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Kawahara R, Chernykh A, Alagesan K, Bern M, Cao W, Chalkley RJ, Cheng K, Choo MS, Edwards N, Goldman R, Hoffmann M, Hu Y, Huang Y, Kim JY, Kletter D, Liquet B, Liu M, Mechref Y, Meng B, Neelamegham S, Nguyen-Khuong T, Nilsson J, Pap A, Park GW, Parker BL, Pegg CL, Penninger JM, Phung TK, Pioch M, Rapp E, Sakalli E, Sanda M, Schulz BL, Scott NE, Sofronov G, Stadlmann J, Vakhrushev SY, Woo CM, Wu HY, Yang P, Ying W, Zhang H, Zhang Y, Zhao J, Zaia J, Haslam SM, Palmisano G, Yoo JS, Larson G, Khoo KH, Medzihradszky KF, Kolarich D, Packer NH, Thaysen-Andersen M. Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis. Nat Methods 2021; 18:1304-1316. [PMID: 34725484 DOI: 10.1101/2021.03.14.435332] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/22/2021] [Indexed: 05/18/2023]
Abstract
Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N- and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results were variable, several high-performance glycoproteomics informatics strategies were identified. Deep analysis of the data revealed key performance-associated search parameters and led to recommendations for improved 'high-coverage' and 'high-accuracy' glycoproteomics search solutions. This study concludes that diverse software packages for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies and specifies key variables that will guide future software developments and assist informatics decision-making in glycoproteomics.
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Affiliation(s)
- Rebeca Kawahara
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Anastasia Chernykh
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Kathirvel Alagesan
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia
| | | | - Weiqian Cao
- Institutes of Biomedical Sciences, and the NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Robert J Chalkley
- UCSF, School of Pharmacy, Department of Pharmaceutical Chemistry, San Francisco, CA, USA
| | - Kai Cheng
- State University of New York, Buffalo, NY, USA
| | - Matthew S Choo
- Analytics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Nathan Edwards
- Clinical and Translational Glycoscience Research Center (CTGRC), Georgetown University, Washington, DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - Radoslav Goldman
- Clinical and Translational Glycoscience Research Center (CTGRC), Georgetown University, Washington, DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
- Department of Oncology, Georgetown University, Washington, DC, USA
| | - Marcus Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Yingwei Hu
- Department of Pathology, The Johns Hopkins University, Baltimore, MD, USA
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Jin Young Kim
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Republic of Korea
| | | | - Benoit Liquet
- Department of Mathematics and Statistics, Macquarie University, Sydney, NSW, Australia
- CNRS, Laboratoire de Mathématiques et de leurs Applications de PAU, E2S-UPPA, Pau, France
| | - Mingqi Liu
- Institutes of Biomedical Sciences, and the NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Bo Meng
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, China
| | | | - Terry Nguyen-Khuong
- Analytics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jonas Nilsson
- Proteomics Core Facility, Sahlgrenska academy, University of Gothenburg, Gothenburg, Sweden
| | - Adam Pap
- BRC, Laboratory of Proteomics Research, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gun Wook Park
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Republic of Korea
| | - Benjamin L Parker
- Department of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, University of Queensland, Queensland, QLD, Australia
| | - Josef M Penninger
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Toan K Phung
- School of Chemistry and Molecular Biosciences, University of Queensland, Queensland, QLD, Australia
| | - Markus Pioch
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
- glyXera GmbH, Magdeburg, Germany
| | - Enes Sakalli
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Miloslav Sanda
- Clinical and Translational Glycoscience Research Center (CTGRC), Georgetown University, Washington, DC, USA
- Department of Oncology, Georgetown University, Washington, DC, USA
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, University of Queensland, Queensland, QLD, Australia
| | - Nichollas E Scott
- Deparment of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
| | - Georgy Sofronov
- Department of Mathematics and Statistics, Macquarie University, Sydney, NSW, Australia
| | - Johannes Stadlmann
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hung-Yi Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Pengyuan Yang
- Institutes of Biomedical Sciences, and the NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, China
| | - Hui Zhang
- Department of Pathology, The Johns Hopkins University, Baltimore, MD, USA
| | - Yong Zhang
- State Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, China
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Joseph Zaia
- Department of Biochemistry, Boston University Medical Campus, Boston, MA, USA
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, UK
| | - Giuseppe Palmisano
- Instituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jong Shin Yoo
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
| | - Göran Larson
- Department of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kai-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Katalin F Medzihradszky
- UCSF, School of Pharmacy, Department of Pharmaceutical Chemistry, San Francisco, CA, USA
- BRC, Laboratory of Proteomics Research, Szeged, Hungary
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia
| | - Nicolle H Packer
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia.
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18
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García-García A, Serna S, Yang Z, Delso I, Taleb V, Hicks T, Artschwager R, Vakhrushev SY, Clausen H, Angulo J, Corzana F, Reichardt NC, Hurtado-Guerrero R. FUT8-Directed Core Fucosylation of N-glycans Is Regulated by the Glycan Structure and Protein Environment. ACS Catal 2021; 11:9052-9065. [PMID: 35662980 PMCID: PMC9161449 DOI: 10.1021/acscatal.1c01698] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/24/2021] [Indexed: 12/17/2022]
Abstract
FUT8 is an essential α-1,6-fucosyltransferase that fucosylates the innermost GlcNAc of N-glycans, a process called core fucosylation. In vitro, FUT8 exhibits substrate preference for the biantennary complex N-glycan oligosaccharide (G0), but the role of the underlying protein/peptide to which N-glycans are attached remains unclear. Here, we explored the FUT8 enzyme with a series of N-glycan oligosaccharides, N-glycopeptides, and an Asn-linked oligosaccharide. We found that the underlying peptide plays a role in fucosylation of paucimannose (low mannose) and high-mannose N-glycans but not for complex-type N-glycans. Using saturation transfer difference (STD) NMR spectroscopy, we demonstrate that FUT8 recognizes all sugar units of the G0 N-glycan and most of the amino acid residues (Asn-X-Thr) that serve as a recognition sequon for the oligosaccharyltransferase (OST). The largest STD signals were observed in the presence of GDP, suggesting that prior FUT8 binding to GDP-β-l-fucose (GDP-Fuc) is required for an optimal recognition of N-glycans. We applied genetic engineering of glycosylation capacities in CHO cells to evaluate FUT8 core fucosylation of high-mannose and complex-type N-glycans in cells with a panel of well-characterized therapeutic N-glycoproteins. This confirmed that core fucosylation mainly occurs on complex-type N-glycans, although clearly only at selected glycosites. Eliminating the capacity for complex-type glycosylation in cells (KO mgat1) revealed that glycosites with complex-type N-glycans when converted to high mannose lost the core Fuc. Interestingly, however, for erythropoietin that is uncommon among the tested glycoproteins in efficiently acquiring tetra-antennary N-glycans, two out of three N-glycosites obtained Fuc on the high-mannose N-glycans. An examination of the N-glycosylation sites of several protein crystal structures indicates that core fucosylation is mostly affected by the accessibility and nature of the N-glycan and not by the nature of the underlying peptide sequence. These data have further elucidated the different FUT8 acceptor substrate specificities both in vitro and in vivo in cells, revealing different mechanisms for promoting core fucosylation.
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Affiliation(s)
- Ana García-García
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain
| | - Sonia Serna
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, Donostia San Sebastián 20014, Spain
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Ignacio Delso
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Víctor Taleb
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain
| | - Thomas Hicks
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Raik Artschwager
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, Donostia San Sebastián 20014, Spain
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.,Departamento de Química Orgánica, Universidad de Sevilla, Sevilla 41012, Spain.,Instituto de Investigaciones Químicas (CSIC-US), Avda. Américo Vespucio, 49, Seville 41092, Spain
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, Logroño E-26006, Spain
| | - Niels C Reichardt
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, Donostia San Sebastián 20014, Spain.,CIBER-BBN, Paseo Miramón 182, San Sebastian 20014, Spain
| | - Ramon Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain.,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark.,Fundación ARAID, Zaragoza 50018, Spain
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19
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Mao Y, Wang S, Zhao Y, Konstantinidi A, Sun L, Ye Z, Vakhrushev SY. Systematic Evaluation of Fragmentation Methods for Unlabeled and Isobaric Mass Tag-Labeled O-Glycopeptides. Anal Chem 2021; 93:11167-11175. [PMID: 34347445 DOI: 10.1021/acs.analchem.1c01696] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Dissecting site-specific functions of O-glycosylation requires simultaneous identification and quantification of differentially expressed O-glycopeptides by mass spectrometry. However, different dissociation methods have not been systematically compared in their performance in terms of identification, glycosite localization, and quantification with isobaric labeling. Here, we conducted this comparison on highly enriched unlabeled O-glycopeptides with higher-energy collision dissociation (HCD), electron-transfer/collision-induced dissociation (ETciD), and electron transfer/higher-energy collisional dissociation (EThcD), concluding that ETciD and EThcD with optimal supplemental activation resulted in superior identification of glycopeptides and unambiguous site localizations than HCD in a database search by Sequest HT. We later described a pseudo-EThcD strategy that in silico concatenates the electron transfer dissociation spectrum with the paired HCD spectrum acquired sequentially for the same precursor ions, which combines the identification advantage of ETciD/EThcD with the superior reporter ion quality of HCD. We demonstrated its improvements in identification and quantification of isobaric mass tag-labeled O-glycopeptides and showcased the discovery of the specific glycosites of GalNAc transferase 11 (GALNT11) in HepG2 cells.
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Affiliation(s)
- Yang Mao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Guangdong Provincial Key Laboratory of Drug Non-Clinical Evaluation and Research, Guangzhou 510990, China
| | - Shengjun Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Guangdong Provincial Key Laboratory of Drug Non-Clinical Evaluation and Research, Guangzhou 510990, China
| | - Yuanqi Zhao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Lingyu Sun
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zilu Ye
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen 2200, Denmark
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20
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Nason R, Büll C, Konstantinidi A, Sun L, Ye Z, Halim A, Du W, Sørensen DM, Durbesson F, Furukawa S, Mandel U, Joshi HJ, Dworkin LA, Hansen L, David L, Iverson TM, Bensing BA, Sullam PM, Varki A, Vries ED, de Haan CAM, Vincentelli R, Henrissat B, Vakhrushev SY, Clausen H, Narimatsu Y. Display of the human mucinome with defined O-glycans by gene engineered cells. Nat Commun 2021; 12:4070. [PMID: 34210959 PMCID: PMC8249670 DOI: 10.1038/s41467-021-24366-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/08/2021] [Indexed: 02/08/2023] Open
Abstract
Mucins are a large family of heavily O-glycosylated proteins that cover all mucosal surfaces and constitute the major macromolecules in most body fluids. Mucins are primarily defined by their variable tandem repeat (TR) domains that are densely decorated with different O-glycan structures in distinct patterns, and these arguably convey much of the informational content of mucins. Here, we develop a cell-based platform for the display and production of human TR O-glycodomains (~200 amino acids) with tunable structures and patterns of O-glycans using membrane-bound and secreted reporters expressed in glycoengineered HEK293 cells. Availability of defined mucin TR O-glycodomains advances experimental studies into the versatile role of mucins at the interface with pathogenic microorganisms and the microbiome, and sparks new strategies for molecular dissection of specific roles of adhesins, glycoside hydrolases, glycopeptidases, viruses and other interactions with mucin TRs as highlighted by examples.
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Affiliation(s)
- Rebecca Nason
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Büll
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lingbo Sun
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wenjuan Du
- Section Virology, Division of Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, CL, Utrecht, the Netherlands
| | - Daniel M Sørensen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fabien Durbesson
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Sanae Furukawa
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leo Alexander Dworkin
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Hansen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leonor David
- Institute of Molecular Pathology and Immunology of the University of Porto/I3S, Porto, Portugal.,Medical Faculty of the University of Porto, Porto, Portugal
| | - Tina M Iverson
- Departments of Pharmacology and Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Barbara A Bensing
- Department of Medicine, The San Francisco Veterans Affairs Medical Center, and the University of California, San Francisco, CA, USA
| | - Paul M Sullam
- Department of Medicine, The San Francisco Veterans Affairs Medical Center, and the University of California, San Francisco, CA, USA
| | - Ajit Varki
- The Glycobiology Research and Training Center, and the Department of Cellular and Molecular Medicine, University of California, San Diego, CA, USA
| | - Erik de Vries
- Section Virology, Division of Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, CL, Utrecht, the Netherlands
| | - Cornelis A M de Haan
- Section Virology, Division of Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, CL, Utrecht, the Netherlands
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Bernard Henrissat
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark. .,GlycoDisplay ApS, Copenhagen, Denmark.
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21
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Čaval T, de Haan N, Konstantinidi A, Vakhrushev SY. Quantitative characterization of O-GalNAc glycosylation. Curr Opin Struct Biol 2021. [PMID: 33508547 DOI: 10.1016/jsbi.2020.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
O-GalNAc type glycosylation is an abundant and complex protein modification. Recent developments in mass spectrometry resulted in significant success in quantitative analysis of O-GalNAc glycosylation. The analysis of released O-GalNAc type glycans expanded our horizons of understanding the glycome of various biological models. The site-specific analysis of glycosylation micro-heterogeneity of purified proteins opened perspectives for the improved design of glycoprotein therapeutics. Advanced gene editing and chemical technologies applied to O-glycoproteomics enabled to identify O-GalNAc glycosylation at unprecedented depth. Progress in the analysis of intact glycoproteins under native and reduced conditions enabled the monitoring of glycosylation proteoform variants. Despite of the astonishing results in quantitative O-GalNAc glycoproteomics, site-specific mapping of the full O-GalNAc structural repertoire in complex samples is yet a long way off. Here, we summarize the most common quantitative strategies in O-GalNAc glycoproteomics, review recent progress and discuss benefits and limitations of the various approaches in the field.
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Affiliation(s)
- Tomislav Čaval
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Noortje de Haan
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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22
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Akan I, Halim A, Vakhrushev SY, Clausen H, Hanover JA. Drosophila O-GlcNAcase Mutants Reveal an Expanded Glycoproteome and Novel Growth and Longevity Phenotypes. Cells 2021; 10:cells10051026. [PMID: 33925313 PMCID: PMC8145559 DOI: 10.3390/cells10051026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/19/2021] [Accepted: 04/25/2021] [Indexed: 12/17/2022] Open
Abstract
The reversible posttranslational O-GlcNAc modification of serine or threonine residues of intracellular proteins is involved in many cellular events from signaling cascades to epigenetic and transcriptional regulation. O-GlcNAcylation is a conserved nutrient-dependent process involving two enzymes, with O-GlcNAc transferase (OGT) adding O-GlcNAc and with O-GlcNAcase (OGA) removing it in a manner that’s protein- and context-dependent. O-GlcNAcylation is essential for epigenetic regulation of gene expression through its action on Polycomb and Trithorax and COMPASS complexes. However, the important role of O-GlcNAc in adult life and health span has been largely unexplored, mainly due the lack of available model systems. Cataloging the O-GlcNAc proteome has proven useful in understanding the biology of this modification in vivo. In this study, we leveraged a recently developed oga knockout fly mutant to identify the O-GlcNAcylated proteins in adult Drosophilamelanogaster. The adult O-GlcNAc proteome revealed many proteins related to cell and organismal growth, development, differentiation, and epigenetics. We identified many O-GlcNAcylated proteins that play a role in increased growth and decreased longevity, including HCF, SIN3A, LOLA, KISMET, ATX2, SHOT, and FOXO. Interestingly, oga mutant flies are larger and have a shorter life span compared to wild type flies, suggesting increased O-GlcNAc results in increased growth. Our results suggest that O-GlcNAc alters the function of many proteins related to transcription, epigenetic modification and signaling pathways that regulate growth rate and longevity. Therefore, our findings highlight the importance of O-GlcNAc in growth and life span in adult Drosophila.
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Affiliation(s)
- Ilhan Akan
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark; (A.H.); (S.Y.V.); (H.C.)
| | - Sergey Y. Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark; (A.H.); (S.Y.V.); (H.C.)
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark; (A.H.); (S.Y.V.); (H.C.)
| | - John A. Hanover
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
- Correspondence:
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23
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Bagdonaite I, Thompson AJ, Wang X, Søgaard M, Fougeroux C, Frank M, Diedrich JK, Yates JR, Salanti A, Vakhrushev SY, Paulson JC, Wandall HH. Site-Specific O-Glycosylation Analysis of SARS-CoV-2 Spike Protein Produced in Insect and Human Cells. Viruses 2021; 13:v13040551. [PMID: 33806155 PMCID: PMC8064498 DOI: 10.3390/v13040551] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 12/22/2022] Open
Abstract
Enveloped viruses hijack not only the host translation processes, but also its glycosylation machinery, and to a variable extent cover viral surface proteins with tolerogenic host-like structures. SARS-CoV-2 surface protein S presents as a trimer on the viral surface and is covered by a dense shield of N-linked glycans, and a few O-glycosites have been reported. The location of O-glycans is controlled by a large family of initiating enzymes with variable expression in cells and tissues and hence is difficult to predict. Here, we used our well-established O-glycoproteomic workflows to map the precise positions of O-linked glycosylation sites on three different entities of protein S—insect cell or human cell-produced ectodomains, or insect cell derived receptor binding domain (RBD). In total 25 O-glycosites were identified, with similar patterns in the two ectodomains of different cell origin, and a distinct pattern of the monomeric RBD. Strikingly, 16 out of 25 O-glycosites were located within three amino acids from known N-glycosites. However, O-glycosylation was primarily found on peptides that were unoccupied by N-glycans, and otherwise had low overall occupancy. This suggests possible complementary functions of O-glycans in immune shielding and negligible effects of O-glycosylation on subunit vaccine design for SARS-CoV-2.
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Affiliation(s)
- Ieva Bagdonaite
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark;
- Correspondence: (I.B.); (H.H.W.)
| | - Andrew J. Thompson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (A.J.T.); (X.W.); (J.K.D.); (J.R.Y.III); (J.C.P.)
| | - Xiaoning Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (A.J.T.); (X.W.); (J.K.D.); (J.R.Y.III); (J.C.P.)
| | - Max Søgaard
- ExpreS2ion Biotechnologies, SCION-DTU Science Park, 2970 Hørsholm, Denmark;
| | - Cyrielle Fougeroux
- Centre for Medical Parasitology at Department of Immunology and Microbiology, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, 2200 Copenhagen, Denmark; (C.F.); (A.S.)
- AdaptVac Aps, 2970 Hørsholm, Denmark
| | | | - Jolene K. Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (A.J.T.); (X.W.); (J.K.D.); (J.R.Y.III); (J.C.P.)
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (A.J.T.); (X.W.); (J.K.D.); (J.R.Y.III); (J.C.P.)
| | - Ali Salanti
- Centre for Medical Parasitology at Department of Immunology and Microbiology, University of Copenhagen and Department of Infectious Diseases, Copenhagen University Hospital, 2200 Copenhagen, Denmark; (C.F.); (A.S.)
| | - Sergey Y. Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - James C. Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (A.J.T.); (X.W.); (J.K.D.); (J.R.Y.III); (J.C.P.)
| | - Hans H. Wandall
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark;
- Correspondence: (I.B.); (H.H.W.)
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24
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Čaval T, de Haan N, Konstantinidi A, Vakhrushev SY. Quantitative characterization of O-GalNAc glycosylation. Curr Opin Struct Biol 2021; 68:135-141. [PMID: 33508547 DOI: 10.1016/j.sbi.2020.12.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/26/2020] [Accepted: 12/29/2020] [Indexed: 12/16/2022]
Abstract
O-GalNAc type glycosylation is an abundant and complex protein modification. Recent developments in mass spectrometry resulted in significant success in quantitative analysis of O-GalNAc glycosylation. The analysis of released O-GalNAc type glycans expanded our horizons of understanding the glycome of various biological models. The site-specific analysis of glycosylation micro-heterogeneity of purified proteins opened perspectives for the improved design of glycoprotein therapeutics. Advanced gene editing and chemical technologies applied to O-glycoproteomics enabled to identify O-GalNAc glycosylation at unprecedented depth. Progress in the analysis of intact glycoproteins under native and reduced conditions enabled the monitoring of glycosylation proteoform variants. Despite of the astonishing results in quantitative O-GalNAc glycoproteomics, site-specific mapping of the full O-GalNAc structural repertoire in complex samples is yet a long way off. Here, we summarize the most common quantitative strategies in O-GalNAc glycoproteomics, review recent progress and discuss benefits and limitations of the various approaches in the field.
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Affiliation(s)
- Tomislav Čaval
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Noortje de Haan
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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25
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Ye Z, Vakhrushev SY. The Role of Data-Independent Acquisition for Glycoproteomics. Mol Cell Proteomics 2021; 20:100042. [PMID: 33372048 PMCID: PMC8724878 DOI: 10.1074/mcp.r120.002204] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/26/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Data-independent acquisition (DIA) is now an emerging method in bottom–up proteomics and capable of achieving deep proteome coverage and accurate label-free quantification. However, for post-translational modifications, such as glycosylation, DIA methodology is still in the early stage of development. The full characterization of glycoproteins requires site-specific glycan identification as well as subsequent quantification of glycan structures at each site. The tremendous complexity of glycosylation represents a significant analytical challenge in glycoproteomics. This review focuses on the development and perspectives of DIA methodology for N- and O-linked glycoproteomics and posits that DIA-based glycoproteomics could be a method of choice to address some of the challenging aspects of glycoproteomics. First, the current challenges in glycoproteomics and the basic principles of DIA are briefly introduced. DIA-based glycoproteomics is then summarized and described into four aspects based on the actual samples. Finally, we discussed the important challenges and future perspectives in the field. We believe that DIA can significantly facilitate glycoproteomic studies and contribute to the development of future advanced tools and approaches in the field of glycoproteomics. Protein glycosylation and challenges in glycoproteomics. Data-independent acquisition for deglycosylated and intact N-linked glycopeptides. Unbiased screening of oxonium ions from all glycopeptide precursors. Glyco–data-independent acquisition on mucin-type O-glycopeptides.
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Affiliation(s)
- Zilu Ye
- Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen N, Denmark.
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26
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Madsen TD, Hansen LH, Hintze J, Ye Z, Jebari S, Andersen DB, Joshi HJ, Ju T, Goetze JP, Martin C, Rosenkilde MM, Holst JJ, Kuhre RE, Goth CK, Vakhrushev SY, Schjoldager KT. An atlas of O-linked glycosylation on peptide hormones reveals diverse biological roles. Nat Commun 2020; 11:4033. [PMID: 32820167 PMCID: PMC7441158 DOI: 10.1038/s41467-020-17473-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 07/02/2020] [Indexed: 12/17/2022] Open
Abstract
Peptide hormones and neuropeptides encompass a large class of bioactive peptides that regulate physiological processes like anxiety, blood glucose, appetite, inflammation and blood pressure. Here, we execute a focused discovery strategy to provide an extensive map of O-glycans on peptide hormones. We find that almost one third of the 279 classified peptide hormones carry O-glycans. Many of the identified O-glycosites are conserved and are predicted to serve roles in proprotein processing, receptor interaction, biodistribution and biostability. We demonstrate that O-glycans positioned within the receptor binding motifs of members of the neuropeptide Y and glucagon families modulate receptor activation properties and substantially extend peptide half-lives. Our study highlights the importance of O-glycosylation in the biology of peptide hormones, and our map of O-glycosites in this large class of biomolecules serves as a discovery platform for an important class of molecules with potential opportunities for drug designs.
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Affiliation(s)
- Thomas D Madsen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Lasse H Hansen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.,Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100, Copenhagen O, Denmark
| | - John Hintze
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Shifa Jebari
- Biofisika Institute (UPV/EHU, CSIC), Departamento de Bioquímica, Universidad del País Vasco, Bilbao, 48080, Spain
| | - Daniel B Andersen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Tongzhong Ju
- Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Jens P Goetze
- Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100, Copenhagen O, Denmark.,Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Cesar Martin
- Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Mette M Rosenkilde
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Jens J Holst
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Rune E Kuhre
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Christoffer K Goth
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.
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27
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Dabelsteen S, Pallesen EMH, Marinova IN, Nielsen MI, Adamopoulou M, Rømer TB, Levann A, Andersen MM, Ye Z, Thein D, Bennett EP, Büll C, Moons SJ, Boltje T, Clausen H, Vakhrushev SY, Bagdonaite I, Wandall HH. Essential Functions of Glycans in Human Epithelia Dissected by a CRISPR-Cas9-Engineered Human Organotypic Skin Model. Dev Cell 2020; 54:669-684.e7. [PMID: 32710848 PMCID: PMC7497784 DOI: 10.1016/j.devcel.2020.06.039] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/07/2020] [Accepted: 06/29/2020] [Indexed: 12/26/2022]
Abstract
The glycome undergoes characteristic changes during histogenesis and organogenesis, but our understanding of the importance of select glycan structures for tissue formation and homeostasis is incomplete. Here, we present a human organotypic platform that allows genetic dissection of cellular glycosylation capacities and systematic interrogation of the roles of distinct glycan types in tissue formation. We used CRISPR-Cas9 gene targeting to generate a library of 3D organotypic skin tissues that selectively differ in their capacity to produce glycan structures on the main types of N- and O-linked glycoproteins and glycolipids. This tissue library revealed distinct changes in skin formation associated with a loss of features for all tested glycoconjugates. The organotypic skin model provides phenotypic cues for the distinct functions of glycoconjugates and serves as a unique resource for further genetic dissection and identification of the specific structural features involved. The strategy is also applicable to other organotypic tissue models. Glycosphingolipids tune cell signaling and impact epithelial barrier formation Complex N-glycans govern wound healing and lamellar body functions in human skin Core-1 O-glycans are essential for cell-cell adhesion and human tissue differentiation Notch O-fucosylation and O-glucosylation have distinct roles in human tissue formation
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Affiliation(s)
- Sally Dabelsteen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark; Department of Oral Pathology, School of Dentistry, University of Copenhagen, Denmark
| | - Emil M H Pallesen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Irina N Marinova
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mathias I Nielsen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Maria Adamopoulou
- Department of Oral Pathology, School of Dentistry, University of Copenhagen, Denmark
| | - Troels B Rømer
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Asha Levann
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel M Andersen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - David Thein
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christian Büll
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sam J Moons
- Institute for Molecules and Materials, Nijmegen 6525 AJ, the Netherlands
| | - Thomas Boltje
- Institute for Molecules and Materials, Nijmegen 6525 AJ, the Netherlands
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ieva Bagdonaite
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
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28
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Bagdonaite I, Pallesen EM, Ye Z, Vakhrushev SY, Marinova IN, Nielsen MI, Kramer SH, Pedersen SF, Joshi HJ, Bennett EP, Dabelsteen S, Wandall HH. O-glycan initiation directs distinct biological pathways and controls epithelial differentiation. EMBO Rep 2020; 21:e48885. [PMID: 32329196 PMCID: PMC7271655 DOI: 10.15252/embr.201948885] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 03/03/2020] [Accepted: 03/16/2020] [Indexed: 12/17/2022] Open
Abstract
Post-translational modifications (PTMs) greatly expand the function and potential for regulation of protein activity, and O-glycosylation is among the most abundant and diverse PTMs. Initiation of O-GalNAc glycosylation is regulated by 20 distinct GalNAc-transferases (GalNAc-Ts), and deficiencies in individual GalNAc-Ts are associated with human disease, causing subtle but distinct phenotypes in model organisms. Here, we generate a set of isogenic keratinocyte cell lines lacking either of the three dominant and differentially expressed GalNAc-Ts. Through the ability of keratinocytes to form epithelia, we investigate the phenotypic consequences of the loss of individual GalNAc-Ts. Moreover, we probe the cellular responses through global transcriptomic, differential glycoproteomic, and differential phosphoproteomic analyses. We demonstrate that loss of individual GalNAc-T isoforms causes distinct epithelial phenotypes through their effect on specific biological pathways; GalNAc-T1 targets are associated with components of the endomembrane system, GalNAc-T2 targets with cell-ECM adhesion, and GalNAc-T3 targets with epithelial differentiation. Thus, GalNAc-T isoforms serve specific roles during human epithelial tissue formation.
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Affiliation(s)
- Ieva Bagdonaite
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Emil Mh Pallesen
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Irina N Marinova
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mathias I Nielsen
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Signe H Kramer
- Cell Biology and Physiology, Department of Science, University of Copenhagen, Copenhagen, Denmark
| | - Stine F Pedersen
- Cell Biology and Physiology, Department of Science, University of Copenhagen, Copenhagen, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.,School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Sally Dabelsteen
- School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Institute of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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29
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Hansen LH, Madsen TD, Goth CK, Clausen H, Chen Y, Dzoyashvili N, Iyer SR, Sangaralingham SJ, Burnett JC, Rehfeld JF, Vakhrushev SY, Schjoldager KT, Goetze JP. Correction: Discovery of O-glycans on atrial natriuretic peptide (ANP) that affect both its proteolytic degradation and potency at its cognate receptor. J Biol Chem 2019; 294:18516. [PMID: 31784477 DOI: 10.1074/jbc.aac119.011661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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30
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Narimatsu Y, Joshi HJ, Schjoldager KT, Hintze J, Halim A, Steentoft C, Nason R, Mandel U, Bennett EP, Clausen H, Vakhrushev SY. Exploring Regulation of Protein O-Glycosylation in Isogenic Human HEK293 Cells by Differential O-Glycoproteomics. Mol Cell Proteomics 2019; 18:1396-1409. [PMID: 31040225 PMCID: PMC6601209 DOI: 10.1074/mcp.ra118.001121] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 03/26/2019] [Indexed: 02/04/2023] Open
Abstract
Most proteins trafficking the secretory pathway of metazoan cells will acquire GalNAc-type O-glycosylation. GalNAc-type O-glycosylation is differentially regulated in cells by the expression of a repertoire of up to twenty genes encoding polypeptide GalNAc-transferase isoforms (GalNAc-Ts) that initiate O-glycosylation. These GalNAc-Ts orchestrate the positions and patterns of O-glycans on proteins in coordinated, but poorly understood ways - guided partly by the kinetic properties and substrate specificities of their catalytic domains, as well as by modulatory effects of their unique GalNAc-binding lectin domains. Here, we provide the hereto most comprehensive characterization of nonredundant contributions of individual GalNAc-T isoforms to the O-glycoproteome of the human HEK293 cell using quantitative differential O-glycoproteomics on a panel of isogenic HEK293 cells with knockout of GalNAc-T genes (GALNT1, T2, T3, T7, T10, or T11). We confirm that a major part of the O-glycoproteome is covered by redundancy, whereas distinct O-glycosite subsets are covered by nonredundant GalNAc-T isoform-specific functions. We demonstrate that the GalNAc-T7 and T10 isoforms function in follow-up of high-density O-glycosylated regions, and that GalNAc-T11 has highly restricted functions and essentially only serves the low-density lipoprotein-related receptors in linker regions (C6XXXTC1) between the ligand-binding repeats.
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Affiliation(s)
- Yoshiki Narimatsu
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
| | - Hiren J Joshi
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Katrine T Schjoldager
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - John Hintze
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Adnan Halim
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Catharina Steentoft
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Rebecca Nason
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Ulla Mandel
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Eric P Bennett
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- From the ‡Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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31
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Narimatsu Y, Joshi HJ, Nason R, Van Coillie J, Karlsson R, Sun L, Ye Z, Chen YH, Schjoldager KT, Steentoft C, Furukawa S, Bensing BA, Sullam PM, Thompson AJ, Paulson JC, Büll C, Adema GJ, Mandel U, Hansen L, Bennett EP, Varki A, Vakhrushev SY, Yang Z, Clausen H. An Atlas of Human Glycosylation Pathways Enables Display of the Human Glycome by Gene Engineered Cells. Mol Cell 2019; 75:394-407.e5. [PMID: 31227230 DOI: 10.1016/j.molcel.2019.05.017] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 02/08/2019] [Accepted: 05/10/2019] [Indexed: 11/29/2022]
Abstract
The structural diversity of glycans on cells-the glycome-is vast and complex to decipher. Glycan arrays display oligosaccharides and are used to report glycan hapten binding epitopes. Glycan arrays are limited resources and present saccharides without the context of other glycans and glycoconjugates. We used maps of glycosylation pathways to generate a library of isogenic HEK293 cells with combinatorially engineered glycosylation capacities designed to display and dissect the genetic, biosynthetic, and structural basis for glycan binding in a natural context. The cell-based glycan array is self-renewable and reports glycosyltransferase genes required (or blocking) for interactions through logical sequential biosynthetic steps, which is predictive of structural glycan features involved and provides instructions for synthesis, recombinant production, and genetic dissection strategies. Broad utility of the cell-based glycan array is demonstrated, and we uncover higher order binding of microbial adhesins to clustered patches of O-glycans organized by their presentation on proteins.
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Affiliation(s)
- Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark.
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Rebecca Nason
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Julie Van Coillie
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Richard Karlsson
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Lingbo Sun
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Yen-Hsi Chen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Catharina Steentoft
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Sanae Furukawa
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Barbara A Bensing
- Department of Medicine, The San Francisco Veterans Affairs Medical Center, and the University of California, San Francisco, San Francisco, CA 94121, USA
| | - Paul M Sullam
- Department of Medicine, The San Francisco Veterans Affairs Medical Center, and the University of California, San Francisco, San Francisco, CA 94121, USA
| | - Andrew J Thompson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christian Büll
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark; Radiotherapy and OncoImmunology Laboratory, Department of Radiotherapy, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Gosse J Adema
- Radiotherapy and OncoImmunology Laboratory, Department of Radiotherapy, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Lars Hansen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Eric Paul Bennett
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Ajit Varki
- The Glycobiology Research and Training Center and the Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Zhang Yang
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark.
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32
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Hansen LH, Madsen TD, Goth CK, Clausen H, Chen Y, Dzhoyashvili N, Iyer SR, Sangaralingham SJ, Burnett JC, Rehfeld JF, Vakhrushev SY, Schjoldager KT, Goetze JP. Discovery of O-glycans on atrial natriuretic peptide (ANP) that affect both its proteolytic degradation and potency at its cognate receptor. J Biol Chem 2019; 294:12567-12578. [PMID: 31186350 DOI: 10.1074/jbc.ra119.008102] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/03/2019] [Indexed: 12/11/2022] Open
Abstract
Atrial natriuretic peptide (ANP) is a peptide hormone that in response to atrial stretch is secreted from atrial myocytes into the circulation, where it stimulates vasodilatation and natriuresis. ANP is an important biomarker of heart failure where low plasma concentrations exclude cardiac dysfunction. ANP is a member of the natriuretic peptide (NP) family, which also includes the B-type natriuretic peptide (BNP) and the C-type natriuretic peptide. The proforms of these hormones undergo processing to mature peptides, and for proBNP, this process has previously been demonstrated to be regulated by O-glycosylation. It has been suggested that proANP also may undergo post-translational modifications. Here, we conducted a targeted O-glycoproteomics approach to characterize O-glycans on NPs and demonstrate that all NP members can carry O-glycans. We identified four O-glycosites in proANP in the porcine heart, and surprisingly, two of these were located on the mature bioactive ANP itself. We found that one of these glycans is located within a conserved sequence motif of the receptor-binding region, suggesting that O-glycans may serve a function beyond intracellular processing and maturation. We also identified an O-glycoform of proANP naturally occurring in human circulation. We demonstrated that site-specific O-glycosylation shields bioactive ANP from proteolytic degradation and modifies potency at its cognate receptor in vitro Furthermore, we showed that ANP O-glycosylation attenuates acute renal and cardiovascular ANP actions in vivo The discovery of novel glycosylated ANP proteoforms reported here significantly improves our understanding of cardiac endocrinology and provides important insight into the etiology of heart failure.
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Affiliation(s)
- Lasse H Hansen
- Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, 9 Blegdamsvej, 2100 Copenhagen, Denmark,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Thomas Daugbjerg Madsen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Christoffer K Goth
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Yang Chen
- Cardiorenal Research Laboratory, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota 55905
| | - Nina Dzhoyashvili
- Cardiorenal Research Laboratory, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota 55905
| | - Seethalakshmi R Iyer
- Cardiorenal Research Laboratory, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota 55905
| | - S Jeson Sangaralingham
- Cardiorenal Research Laboratory, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota 55905
| | - John C Burnett
- Cardiorenal Research Laboratory, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota 55905
| | - Jens F Rehfeld
- Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, 9 Blegdamsvej, 2100 Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jens P Goetze
- Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen, 9 Blegdamsvej, 2100 Copenhagen, Denmark .,Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 3 Blegdamsvej, 2200 Copenhagen, Denmark
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33
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Freitas D, Balmaña M, Poças J, Campos D, Osório H, Konstantinidi A, Vakhrushev SY, Magalhães A, Reis CA. Different isolation approaches lead to diverse glycosylated extracellular vesicle populations. J Extracell Vesicles 2019; 8:1621131. [PMID: 31236201 PMCID: PMC6571546 DOI: 10.1080/20013078.2019.1621131] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 04/17/2019] [Accepted: 05/03/2019] [Indexed: 12/18/2022] Open
Abstract
Extracellular vesicles (EVs) are a heterogeneous group of small secreted particles involved in intercellular communication and mediating a broad spectrum of biological functions. EVs cargo is composed of a large repertoire of molecules, including glycoconjugates. Herein, we report the first study on the impact of the isolation strategy on the EV populations’ glycosylation profile. The use of different state-of-the-art protocols, namely differential ultracentrifugation (UC), total exosome isolation (TEI), OptiPrepTM density gradient (ODG) and size exclusion chromatography (SEC) resulted in EV populations displaying different sets of glycoconjugates. The EV populations obtained by UC, ODG and SEC methods displayed similar protein and glycan profiles, whereas TEI methodology isolated the most distinct EV population. In addition, ODG and SEC isolation protocols provided an enhanced EV glycoproteins detection. Remarkably, proteins displaying the tumour-associated glycan sialyl-Tn (STn) were identified as packaged cargo into EVs independently of the isolation methodology. STn carrying EV samples isolated by UC, ODG and SEC presented a considerable set of cancer-related proteins that were not detected in EVs isolated by TEI. Our work demonstrates the impact of using different isolation methodologies in the populations of EVs that are obtained, with consequences in the glycosylation profile of the isolated population. Furthermore, our results highlight the importance of selecting adequate EV isolation protocols and cell culture conditions to determine the structural and functional complexity of the EV glycoconjugates.
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Affiliation(s)
- Daniela Freitas
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,IPATIMUP -Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Meritxell Balmaña
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,IPATIMUP -Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Juliana Poças
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,IPATIMUP -Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Diana Campos
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,IPATIMUP -Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Hugo Osório
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,IPATIMUP -Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ana Magalhães
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,IPATIMUP -Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Celso A Reis
- i3S-Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.,IPATIMUP -Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
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34
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Wang S, Mao Y, Narimatsu Y, Ye Z, Tian W, Goth CK, Lira-Navarrete E, Pedersen NB, Benito-Vicente A, Martin C, Uribe KB, Hurtado-Guerrero R, Christoffersen C, Seidah NG, Nielsen R, Christensen EI, Hansen L, Bennett EP, Vakhrushev SY, Schjoldager KT, Clausen H. Site-specific O-glycosylation of members of the low-density lipoprotein receptor superfamily enhances ligand interactions. J Biol Chem 2019; 294:8349. [PMID: 31127061 DOI: 10.1074/jbc.aac119.009121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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35
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Steentoft C, Fuhrmann M, Battisti F, Van Coillie J, Madsen TD, Campos D, Halim A, Vakhrushev SY, Joshi HJ, Schreiber H, Mandel U, Narimatsu Y. A strategy for generating cancer-specific monoclonal antibodies to aberrant O-glycoproteins: identification of a novel dysadherin-Tn antibody. Glycobiology 2019; 29:307-319. [PMID: 30726901 PMCID: PMC6430981 DOI: 10.1093/glycob/cwz004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/18/2019] [Accepted: 01/24/2019] [Indexed: 12/25/2022] Open
Abstract
Successful application of potent antibody-based T-cell engaging immunotherapeutic strategies is currently limited mainly to hematological cancers. One major reason is the lack of well-characterized antigens on solid tumors with sufficient cancer specific expression. Aberrantly O-glycosylated proteins contain promising cancer-specific O-glycopeptide epitopes suitable for immunotherapeutic applications, but currently only few examples of such antibody epitopes have been identified. We previously showed that chimeric antigen receptor T-cells directed towards aberrantly O-glycosylated MUC1 can control malignant growth in a mouse model. Here, we present a discovery platform for the generation of cancer-specific monoclonal antibodies targeting aberrant O-glycoproteins. The strategy is based on cancer cell lines engineered to homogeneously express the truncated Tn O-glycoform, the so-called SimpleCells. We used SimpleCells of different cancer origin to elicit monoclonal antibodies with selectivity for aberrant O-glycoproteins. For validation we selected and characterized one monoclonal antibody (6C5) directed to a Tn-glycopeptide in dysadherin (FXYD5), known to be upregulated in cancer and promote metastasis. While dysadherin is widely expressed also in normal cells, we demonstrated that the 6C5 epitope is specifically expressed in cancer.
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Affiliation(s)
- Catharina Steentoft
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Max Fuhrmann
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Federico Battisti
- Department of Experimental Medicine, “Sapienza” University of Rome, Viale Regina Elena 324 Rome, Italy
| | - Julie Van Coillie
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Thomas D Madsen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Diana Campos
- Instituto de Investigação e Inovação e Saúde, Universidade do Porto, Rua Júlio Amaral de Carvalho 45, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Júlio Amaral de Carvalho 45, Porto, Portugal
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Hans Schreiber
- Department of Pathology, Committee on Immunology, Committee on Cancer Biology, The University of Chicago, 5841 S. Maryland Avenue, Chicago, IL, USA
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
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36
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Valoskova K, Biebl J, Roblek M, Emtenani S, Gyoergy A, Misova M, Ratheesh A, Reis-Rodrigues P, Shkarina K, Larsen ISB, Vakhrushev SY, Clausen H, Siekhaus DE. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. eLife 2019; 8:e41801. [PMID: 30910009 PMCID: PMC6435326 DOI: 10.7554/elife.41801] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/11/2019] [Indexed: 12/29/2022] Open
Abstract
Aberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva's vertebrate ortholog, MFSD1, rescues the minerva mutant's migration and T-antigen glycosylation defects. We thus identify a key conserved regulator that orchestrates O-glycosylation on a protein subset to activate a program governing migration steps important for both development and cancer metastasis.
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Affiliation(s)
| | - Julia Biebl
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Marko Roblek
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Shamsi Emtenani
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Attila Gyoergy
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Michaela Misova
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Aparna Ratheesh
- Institute of Science and Technology AustriaKlosterneuburgAustria
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical SchoolUniversity of WarwickCoventryUnited Kingdom
| | | | | | - Ida Signe Bohse Larsen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Daria E Siekhaus
- Institute of Science and Technology AustriaKlosterneuburgAustria
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37
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Hintze J, Ye Z, Narimatsu Y, Madsen TD, Joshi HJ, Goth CK, Linstedt A, Bachert C, Mandel U, Bennett EP, Vakhrushev SY, Schjoldager KT. Probing the contribution of individual polypeptide GalNAc-transferase isoforms to the O-glycoproteome by inducible expression in isogenic cell lines. J Biol Chem 2018; 293:19064-19077. [PMID: 30327431 PMCID: PMC6295722 DOI: 10.1074/jbc.ra118.004516] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/04/2018] [Indexed: 12/25/2022] Open
Abstract
The GalNAc-type O-glycoproteome is orchestrated by a large family of polypeptide GalNAc-transferase isoenzymes (GalNAc-Ts) with partially overlapping contributions to the O-glycoproteome besides distinct nonredundant functions. Increasing evidence indicates that individual GalNAc-Ts co-regulate and fine-tune specific protein functions in health and disease, and deficiencies in individual GALNT genes underlie congenital diseases with distinct phenotypes. Studies of GalNAc-T specificities have mainly been performed with in vitro enzyme assays using short peptide substrates, but recently quantitative differential O-glycoproteomics of isogenic cells with and without GALNT genes has enabled a more unbiased exploration of the nonredundant contributions of individual GalNAc-Ts. Both approaches suggest that fairly small subsets of O-glycosites are nonredundantly regulated by specific GalNAc-Ts, but how these isoenzymes orchestrate regulation among competing redundant substrates is unclear. To explore this, here we developed isogenic cell model systems with Tet-On inducible expression of two GalNAc-T genes, GALNT2 and GALNT11, in a knockout background in HEK293 cells. Using quantitative O-glycoproteomics with tandem-mass-tag (TMT) labeling, we found that isoform-specific glycosites are glycosylated in a dose-dependent manner and that induction of GalNAc-T2 or -T11 produces discrete glycosylation effects without affecting the major part of the O-glycoproteome. These results support previous findings indicating that individual GalNAc-T isoenzymes can serve in fine-tuned regulation of distinct protein functions.
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Affiliation(s)
- John Hintze
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Zilu Ye
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Yoshiki Narimatsu
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Thomas Daugbjerg Madsen
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Hiren J Joshi
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Christoffer K Goth
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Adam Linstedt
- the Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Collin Bachert
- the Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Ulla Mandel
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Eric P Bennett
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Sergey Y Vakhrushev
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
| | - Katrine T Schjoldager
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark and
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38
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Schulz MA, Tian W, Mao Y, Van Coillie J, Sun L, Larsen JS, Chen YH, Kristensen C, Vakhrushev SY, Clausen H, Yang Z. Glycoengineering design options for IgG1 in CHO cells using precise gene editing. Glycobiology 2018; 28:542-549. [PMID: 29596681 DOI: 10.1093/glycob/cwy022] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/26/2018] [Indexed: 12/11/2022] Open
Abstract
Precise gene editing technologies are providing new opportunities to stably engineer host cells for recombinant production of therapeutic glycoproteins with different glycan structures. The glycosylation of recombinant therapeutics has long been a focus for both quality and consistency of products and for optimizing and improving pharmacokinetic properties as well as bioactivity. Structures of glycans on therapeutic glycoproteins are important for circulation, biodistribution and bioactivity. In particular, the latter has been demonstrated for therapeutic IgG1 antibodies where the core α1,6Fucose on the conserved N-glycan at Asn297 have remarkable dampening effects on antibody effector functions. We previously explored precise gene engineering and design options for N-glycosylation in CHO cells, and here we focus on engineering options possible for N-glycans on human IgG1. We demonstrate stable precise gene engineering of rather homogenous biantennary N-glycans with and without galactose (G0F, G2F) as well as the α2,6-linked monosialylated (G2FS1) glycoform. We were unable to introduce substantial disialylated glycoforms. Instead we engineered a novel monoantennary homogeneous N-glycan design with complete α2,6-linked sialic acid capping. All N-glycoforms may be engineered with and without core α1,6Fucose. The stably engineered design options enable production of human IgG antibodies with an array of distinct glycoforms for testing and selection of optimal design for different therapeutic applications.
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Affiliation(s)
- Morten A Schulz
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Weihua Tian
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Yang Mao
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Julie Van Coillie
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Lingbo Sun
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Joachim S Larsen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Yen-Hsi Chen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Claus Kristensen
- GlycoDisplay ApS, Blegdamsvej 3, Building 07-10-85, Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark.,GlycoDisplay ApS, Blegdamsvej 3, Building 07-10-85, Copenhagen N, Denmark
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39
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Narimatsu H, Kaji H, Vakhrushev SY, Clausen H, Zhang H, Noro E, Togayachi A, Nagai-Okatani C, Kuno A, Zou X, Cheng L, Tao SC, Sun Y. Current Technologies for Complex Glycoproteomics and Their Applications to Biology/Disease-Driven Glycoproteomics. J Proteome Res 2018; 17:4097-4112. [PMID: 30359034 DOI: 10.1021/acs.jproteome.8b00515] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Glycoproteomics is an important recent advance in the field of glycoscience. In glycomics, glycan structures are comprehensively analyzed after glycans are released from glycoproteins. However, a major limitation of glycomics is the lack of insight into glycoprotein functions. The Biology/Disease-driven Human Proteome Project has a particular focus on biological and medical applications. Glycoproteomics technologies aimed at obtaining a comprehensive understanding of intact glycoproteins, i.e., the kind of glycan structures that are attached to particular amino acids and proteins, have been developed. This Review focuses on the recent progress of the technologies and their applications. First, the methods for large-scale identification of both N- and O-glycosylated proteins are summarized. Next, the progress of analytical methods for intact glycopeptides is outlined. MS/MS-based methods were developed for improving the sensitivity and speed of the mass spectrometer, in parallel with the software for complex spectrum assignment. In addition, a unique approach to identify intact glycopeptides using MS1-based accurate masses is introduced. Finally, as an advance of glycomics, two approaches to provide the spatial distribution of glycans in cells are described, i.e., MS imaging and lectin microarray. These methods allow rapid glycomic profiling of different types of biological samples and thus facilitate glycoproteomics.
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Affiliation(s)
- Hisashi Narimatsu
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Hiroyuki Kaji
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics , University of Copenhagen , Blegdamsvej 3 , Copenhagen 2200 , Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics , University of Copenhagen , Blegdamsvej 3 , Copenhagen 2200 , Denmark
| | - Hui Zhang
- Center for Biomarker Discovery and Translation , Johns Hopkins University , 400 North Broadway , Baltimore , Maryland 21205 , United States
| | - Erika Noro
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Akira Togayachi
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Chiaki Nagai-Okatani
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Atsushi Kuno
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan
| | - Xia Zou
- Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono , Tsukuba , Ibaraki 305-8568 , Japan.,Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| | - Li Cheng
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
| | - Yangyang Sun
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education) , Shanghai Jiao Tong University , 800 Dong Chuan Road , Minhang , Shanghai 200240 , P.R. China
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40
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Bagdonaite I, Vakhrushev SY, Joshi HJ, Wandall HH. Viral glycoproteomes: technologies for characterization and outlook for vaccine design. FEBS Lett 2018; 592:3898-3920. [PMID: 29961944 DOI: 10.1002/1873-3468.13177] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/13/2018] [Accepted: 06/26/2018] [Indexed: 12/27/2022]
Abstract
It has long been known that surface proteins of most enveloped viruses are covered with glycans. It has furthermore been demonstrated that glycosylation is essential for propagation and immune evasion for many viruses. The recent development of high-resolution mass spectrometry techniques has enabled identification not only of the precise structures but also the positions of such post-translational modifications on viruses, revealing substantial differences in extent of glycosylation and glycan maturation for different classes of viruses. In-depth characterization of glycosylation and other post-translational modifications of viral envelope glycoproteins is essential for rational design of vaccines and antivirals. In this Review, we provide an overview of techniques used to address viral glycosylation and summarize information on glycosylation of enveloped viruses representing ongoing public health challenges. Furthermore, we discuss how knowledge on glycosylation can be translated to means to prevent and combat viral infections.
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Affiliation(s)
- Ieva Bagdonaite
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Denmark
| | - Hiren J Joshi
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Denmark
| | - Hans H Wandall
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Denmark
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41
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de Las Rivas M, Coelho H, Diniz A, Lira-Navarrete E, Compañón I, Jiménez-Barbero J, Schjoldager KT, Bennett EP, Vakhrushev SY, Clausen H, Corzana F, Marcelo F, Hurtado-Guerrero R. Structural Analysis of a GalNAc-T2 Mutant Reveals an Induced-Fit Catalytic Mechanism for GalNAc-Ts. Chemistry 2018; 24:8382-8392. [PMID: 29601100 DOI: 10.1002/chem.201800701] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Indexed: 02/02/2023]
Abstract
The family of polypeptide N-acetylgalactosamine (GalNAc) transferases (GalNAc-Ts) orchestrates the initiating step of mucin-type protein O-glycosylation by transfer of GalNAc moieties to serine and threonine residues in proteins. Deficiencies and dysregulation of GalNAc-T isoenzymes are related to different diseases. Recently, it has been demonstrated that an inactive GalNAc-T2 mutant (F104S), which is not located at the active site, induces low levels of high-density lipoprotein cholesterol (HDL-C) in humans. Herein, the molecular basis for F104S mutant inactivation has been deciphered. Saturation transfer difference NMR spectroscopy experiments demonstrate that the mutation induces loss of binding to peptide substrates. Analysis of the crystal structure of the F104S mutant bound to UDP-GalNAc (UDP=uridine diphosphate), combined with molecular dynamics (MD) simulations, has revealed that the flexible loop is disordered and displays larger conformational changes in the mutant enzyme than that in the wild-type (WT) enzyme. 19 F NMR spectroscopy experiments reveal that the WT enzyme only reaches the active state in the presence of UDP-GalNAc, which provides compelling evidence that GalNAc-T2 adopts a UDP-GalNAc-dependent induced-fit mechanism. The F104S mutation precludes the enzyme from achieving the active conformation and concomitantly binding peptide substrates. This study provides new insights into the catalytic mechanism of the large family of GalNAc-Ts and how these enzymes orchestrate protein O-glycosylation.
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Affiliation(s)
- Matilde de Las Rivas
- Instituto de Biocomputación y Fisica de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50018, Zaragoza, Spain
| | - Helena Coelho
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170, Derio, Spain
- Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940, Leioa, Bizkaia, Spain
| | - Ana Diniz
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Erandi Lira-Navarrete
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Ismael Compañón
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006, Logroño, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170, Derio, Spain
- Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940, Leioa, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009, Bilbao, Spain
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006, Logroño, Spain
| | - Filipa Marcelo
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Ramon Hurtado-Guerrero
- Instituto de Biocomputación y Fisica de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50018, Zaragoza, Spain
- Fundación ARAID, 50018, Zaragoza, Spain
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42
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King SL, Goth CK, Eckhard U, Joshi HJ, Haue AD, Vakhrushev SY, Schjoldager KT, Overall CM, Wandall HH. TAILS N-terminomics and proteomics reveal complex regulation of proteolytic cleavage by O-glycosylation. J Biol Chem 2018; 293:7629-7644. [PMID: 29593093 PMCID: PMC5961060 DOI: 10.1074/jbc.ra118.001978] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/27/2018] [Indexed: 12/31/2022] Open
Abstract
Proteolytic processing is an irreversible post-translational modification functioning as a ubiquitous regulator of cellular activity. Protease activity is tightly regulated via control of gene expression, enzyme and substrate compartmentalization, zymogen activation, enzyme inactivation, and substrate availability. Emerging evidence suggests that proteolysis can also be regulated by substrate glycosylation and that glycosylation of individual sites on a substrate can decrease or, in rare cases, increase its sensitivity to proteolysis. Here, we investigated the relationship between site-specific, mucin-type (or GalNAc-type) O-glycosylation and proteolytic cleavage of extracellular proteins. Using in silico analysis, we found that O-glycosylation and cleavage sites are significantly associated with each other. We then used a positional proteomic strategy, terminal amine isotopic labeling of substrates (TAILS), to map the in vivo cleavage sites in HepG2 SimpleCells with and without one of the key initiating GalNAc transferases, GalNAc-T2, and after treatment with exogenous matrix metalloproteinase 9 (MMP9) or neutrophil elastase. Surprisingly, we found that loss of GalNAc-T2 not only increased cleavage, but also decreased cleavage across a broad range of other substrates, including key regulators of the protease network. We also found altered processing of several central regulators of lipid homeostasis, including apolipoprotein B and the phospholipid transfer protein, providing new clues to the previously reported link between GALNT2 and lipid homeostasis. In summary, we show that loss of GalNAc-T2 O-glycosylation leads to a general decrease in cleavage and that GalNAc-T2 O-glycosylation affects key regulators of the cellular proteolytic network, including multiple members of the serpin family.
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Affiliation(s)
- Sarah L King
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Christoffer K Goth
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Ulrich Eckhard
- the Centre for Blood Research, Department of Oral Biological and Medical Sciences, Faculty of Dentistry, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hiren J Joshi
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Amalie D Haue
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Sergey Y Vakhrushev
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Katrine T Schjoldager
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
| | - Christopher M Overall
- the Centre for Blood Research, Department of Oral Biological and Medical Sciences, Faculty of Dentistry, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hans H Wandall
- From the Department of Cellular and Molecular Medicine, Centre for Glycomics, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark and
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43
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Wang S, Mao Y, Narimatsu Y, Ye Z, Tian W, Goth CK, Lira-Navarrete E, Pedersen NB, Benito-Vicente A, Martin C, Uribe KB, Hurtado-Guerrero R, Christoffersen C, Seidah NG, Nielsen R, Christensen EI, Hansen L, Bennett EP, Vakhrushev SY, Schjoldager KT, Clausen H. Site-specific O-glycosylation of members of the low-density lipoprotein receptor superfamily enhances ligand interactions. J Biol Chem 2018; 293:7408-7422. [PMID: 29559555 DOI: 10.1074/jbc.m117.817981] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 02/27/2018] [Indexed: 11/06/2022] Open
Abstract
The low-density lipoprotein receptor (LDLR) and related receptors are important for the transport of diverse biomolecules across cell membranes and barriers. Their functions are especially relevant for cholesterol homeostasis and diseases, including neurodegenerative and kidney disorders. Members of the LDLR-related protein family share LDLR class A (LA) repeats providing binding properties for lipoproteins and other biomolecules. We previously demonstrated that short linker regions between these LA repeats contain conserved O-glycan sites. Moreover, we found that O-glycan modifications at these sites are selectively controlled by the GalNAc-transferase isoform, GalNAc-T11. However, the effects of GalNAc-T11-mediated O-glycosylation on LDLR and related receptor localization and function are unknown. Here, we characterized O-glycosylation of LDLR-related proteins and identified conserved O-glycosylation sites in the LA linker regions of VLDLR, LRP1, and LRP2 (Megalin) from both cell lines and rat organs. Using a panel of gene-edited isogenic cell line models, we demonstrate that GalNAc-T11-mediated LDLR and VLDLR O-glycosylation is not required for transport and cell-surface expression and stability of these receptors but markedly enhances LDL and VLDL binding and uptake. Direct ELISA-based binding assays with truncated LDLR constructs revealed that O-glycosylation increased affinity for LDL by ∼5-fold. The molecular basis for this observation is currently unknown, but these findings open up new avenues for exploring the roles of LDLR-related proteins in disease.
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Affiliation(s)
- Shengjun Wang
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Yang Mao
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Weihua Tian
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Christoffer K Goth
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Erandi Lira-Navarrete
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Nis B Pedersen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Asier Benito-Vicente
- Biofisika Institute, Centro Superior de Investigaciones Cientificas (CSIC), Universidad del Pais Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), and Departamento de Bioquimica, Universidad del Pais Vasco, 48080 Bilbao, Spain
| | - Cesar Martin
- Biofisika Institute, Centro Superior de Investigaciones Cientificas (CSIC), Universidad del Pais Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), and Departamento de Bioquimica, Universidad del Pais Vasco, 48080 Bilbao, Spain
| | - Kepa B Uribe
- Biofisika Institute, Centro Superior de Investigaciones Cientificas (CSIC), Universidad del Pais Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), and Departamento de Bioquimica, Universidad del Pais Vasco, 48080 Bilbao, Spain
| | - Ramon Hurtado-Guerrero
- The Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-Instituto de Química Física Rocasolano (IQFR), CSIC Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, 50009 Zaragoza, Spain
| | - Christina Christoffersen
- Department of Clinical Biochemistry, Rigshospitalet and Department of Biomedical Sciences, University of Copenhagen, Copenhagen 2100, Denmark
| | - Nabil G Seidah
- Clinical Research Institute of Montreal, University of Montreal, Montreal, Quebec H2W 1R7, Canada
| | - Rikke Nielsen
- Department of Biomedicine, Aarhus University, DK-8000 Aarhus, Denmark
| | | | - Lars Hansen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
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44
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Lackman JJ, Goth CK, Halim A, Vakhrushev SY, Clausen H, Petäjä-Repo UE. Site-specific O-glycosylation of N-terminal serine residues by polypeptide GalNAc-transferase 2 modulates human δ-opioid receptor turnover at the plasma membrane. Cell Signal 2018; 42:184-193. [PMID: 29097258 DOI: 10.1016/j.cellsig.2017.10.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 12/21/2022]
Abstract
G protein-coupled receptors (GPCRs) are an important protein family of signalling receptors that govern a wide variety of physiological functions. The capacity to transmit extracellular signals and the extent of cellular response are largely determined by the amount of functional receptors at the cell surface that is subject to complex and fine-tuned regulation. Here, we demonstrate that the cell surface expression level of an inhibitory GPCR, the human δ-opioid receptor (hδOR) involved in pain and mood regulation, is modulated by site-specific N-acetylgalactosamine (GalNAc) -type O-glycosylation. Importantly, we identified one out of the 20 polypeptide GalNAc-transferase isoforms, GalNAc-T2, as the specific regulator of O-glycosylation of Ser6, Ser25 and Ser29 in the N-terminal ectodomain of the receptor. This was demonstrated by in vitro glycosylation assays using peptides corresponding to the hδOR N-terminus, Vicia villosa lectin affinity purification of receptors expressed in HEK293 SimpleCells capable of synthesizing only truncated O-glycans, GalNAc-T edited cell line model systems, and site-directed mutagenesis of the putative O-glycosylation sites. Interestingly, a single-nucleotide polymorphism, at residue 27 (F27C), was found to alter O-glycosylation of the receptor in efficiency as well as in glycosite usage. Furthermore, flow cytometry and cell surface biotinylation assays using O-glycan deficient CHO-ldlD cells revealed that the absence of O-glycans results in decreased receptor levels at the plasma membrane due to enhanced turnover. In addition, mutation of the identified O-glycosylation sites led to a decrease in the number of ligand-binding competent receptors and impaired agonist-mediated inhibition of cyclic AMP accumulation in HEK293 cells. Thus, site-specific O-glycosylation by a selected GalNAc-T isoform can increase the stability of a GPCR, in a process that modulates the constitutive turnover and steady-state levels of functional receptors at the cell surface.
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MESH Headings
- Acetylgalactosamine/chemistry
- Acetylgalactosamine/metabolism
- Amino Acid Sequence
- Animals
- CHO Cells
- Cell Line, Tumor
- Cell Membrane/chemistry
- Cell Membrane/metabolism
- Chromatography, Affinity/methods
- Cricetulus
- Cyclic AMP/metabolism
- Glycosylation
- HEK293 Cells
- Hep G2 Cells
- Humans
- Mutagenesis, Site-Directed
- N-Acetylgalactosaminyltransferases/genetics
- N-Acetylgalactosaminyltransferases/metabolism
- Neurons/cytology
- Neurons/metabolism
- Peptides/chemical synthesis
- Peptides/metabolism
- Plant Lectins/chemistry
- Polymorphism, Single Nucleotide
- Protein Processing, Post-Translational
- Protein Stability
- Receptors, Opioid, delta/chemistry
- Receptors, Opioid, delta/genetics
- Receptors, Opioid, delta/metabolism
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Sequence Alignment
- Serine/metabolism
- Polypeptide N-acetylgalactosaminyltransferase
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Affiliation(s)
- Jarkko J Lackman
- Medical Research Center Oulu, Research Unit of Biomedicine, University of Oulu, FI-90014 Oulu, Finland
| | - Christoffer K Goth
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Ulla E Petäjä-Repo
- Medical Research Center Oulu, Research Unit of Biomedicine, University of Oulu, FI-90014 Oulu, Finland.
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45
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Joshi HJ, Jørgensen A, Schjoldager KT, Halim A, Dworkin LA, Steentoft C, Wandall HH, Clausen H, Vakhrushev SY. GlycoDomainViewer: a bioinformatics tool for contextual exploration of glycoproteomes. Glycobiology 2017; 28:131-136. [DOI: 10.1093/glycob/cwx104] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/07/2017] [Indexed: 11/13/2022] Open
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46
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Lavrsen K, Dabelsteen S, Vakhrushev SY, Levann AMR, Haue AD, Dylander A, Mandel U, Hansen L, Frödin M, Bennett EP, Wandall HH. De novo expression of human polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6) in colon adenocarcinoma inhibits the differentiation of colonic epithelium. J Biol Chem 2017; 293:1298-1314. [PMID: 29187600 DOI: 10.1074/jbc.m117.812826] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/27/2017] [Indexed: 12/25/2022] Open
Abstract
Aberrant expression of O-glycans is a hallmark of epithelial cancers. Mucin-type O-glycosylation is initiated by a large family of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (GalNAc-Ts) that target different proteins and are differentially expressed in cells and organs. Here, we investigated the expression patterns of all of the GalNAc-Ts in colon cancer by analyzing transcriptomic data. We found that GalNAc-T6 was highly up-regulated in colon adenocarcinomas but absent in normal-appearing adjacent colon tissue. These results were verified by immunohistochemistry, suggesting that GalNAc-T6 plays a role in colon carcinogenesis. To investigate the function of GalNAc-T6 in colon cancer, we used precise gene targeting to produce isogenic colon cancer cell lines with a knockout/rescue system for GALNT6 GalNAc-T6 expression was associated with a cancer-like, dysplastic growth pattern, whereas GALNT6 knockout cells showed a more normal differentiation pattern, reduced proliferation, normalized cell-cell adhesion, and formation of crypts in tissue cultures. O-Glycoproteomic analysis of the engineered cell lines identified a small set of GalNAc-T6-specific targets, suggesting that this isoform has unique cellular functions. In support of this notion, the genetically and functionally closely related GalNAc-T3 homolog did not show compensatory functionality for effects observed for GalNAc-T6. Taken together, these data strongly suggest that aberrant GalNAc-T6 expression and site-specific glycosylation is involved in oncogenic transformation.
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Affiliation(s)
- Kirstine Lavrsen
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Sally Dabelsteen
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Sergey Y Vakhrushev
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Asha M R Levann
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Amalie Dahl Haue
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - August Dylander
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Ulla Mandel
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Lars Hansen
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Morten Frödin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK 2200, Copenhagen N, Denmark
| | - Eric P Bennett
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Hans H Wandall
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
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47
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Hansen LH, Darkner S, Svendsen JH, Henningsen K, Pehrson S, Chen X, Vakhrushev SY, Schjoldager KT, Goetze JP. Chromogranin A in the mammalian heart: expression without secretion. Biomark Med 2017; 11:541-545. [PMID: 28685598 DOI: 10.2217/bmm-2017-0052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To investigate whether chromogranin A (CgA) is secreted from the heart into circulation. MATERIALS & METHODS Porcine cardiac tissue was analyzed for the presence of CgA-derived glycopeptides using a global O-glycoproteomic strategy. Blood was sampled from the femoral vein, right atrium, coronary sinus and the left atrium from patients with predominantly atrial disease. The local concentration of proatrial natriuretic peptide and CgA was measured with immunoassays. RESULTS We identified CgA-derived glycopeptides exclusively in the atrial tissue. Proatrial natriuretic peptide is secreted from the heart (coronary sinus [795 pmol/l] vs left atrium [678 pmol/l]; p < 0.01) whereas no CgA gradient across the heart could be established (p = 0.6366). CONCLUSION The cardiac atria express but do not secrete CgA into circulation in patients with atrial disease.
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Affiliation(s)
- Lasse H Hansen
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Stine Darkner
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jesper H Svendsen
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Kristoffer Henningsen
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Steen Pehrson
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Xu Chen
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jens P Goetze
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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48
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Larsen ISB, Narimatsu Y, Joshi HJ, Yang Z, Harrison OJ, Brasch J, Shapiro L, Honig B, Vakhrushev SY, Clausen H, Halim A. Mammalian O-mannosylation of cadherins and plexins is independent of protein O-mannosyltransferases 1 and 2. J Biol Chem 2017; 292:11586-11598. [PMID: 28512129 DOI: 10.1074/jbc.m117.794487] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Indexed: 11/06/2022] Open
Abstract
Protein O-mannosylation is found in yeast and metazoans, and a family of conserved orthologous protein O-mannosyltransferases is believed to initiate this important post-translational modification. We recently discovered that the cadherin superfamily carries O-linked mannose (O-Man) glycans at highly conserved residues in specific extracellular cadherin domains, and it was suggested that the function of E-cadherin was dependent on the O-Man glycans. Deficiencies in enzymes catalyzing O-Man biosynthesis, including the two human protein O-mannosyltransferases, POMT1 and POMT2, underlie a subgroup of congenital muscular dystrophies designated α-dystroglycanopathies, because deficient O-Man glycosylation of α-dystroglycan disrupts laminin interaction with α-dystroglycan and the extracellular matrix. To explore the functions of O-Man glycans on cadherins and protocadherins, we used a combinatorial gene-editing strategy in multiple cell lines to evaluate the role of the two POMTs initiating O-Man glycosylation and the major enzyme elongating O-Man glycans, the protein O-mannose β-1,2-N-acetylglucosaminyltransferase, POMGnT1. Surprisingly, O-mannosylation of cadherins and protocadherins does not require POMT1 and/or POMT2 in contrast to α-dystroglycan, and moreover, the O-Man glycans on cadherins are not elongated. Thus, the classical and evolutionarily conserved POMT O-mannosylation pathway is essentially dedicated to α-dystroglycan and a few other proteins, whereas a novel O-mannosylation process in mammalian cells is predicted to serve the large cadherin superfamily and other proteins.
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Affiliation(s)
- Ida Signe Bohse Larsen
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark, and
| | - Yoshiki Narimatsu
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark, and
| | - Hiren Jitendra Joshi
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark, and
| | - Zhang Yang
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark, and
| | | | - Julia Brasch
- the Department of Biochemistry and Molecular Biophysics
| | - Lawrence Shapiro
- the Department of Biochemistry and Molecular Biophysics.,Zuckerman Mind Brain Behavior Institute, Department of Systems Biology, and
| | - Barry Honig
- the Department of Biochemistry and Molecular Biophysics.,Zuckerman Mind Brain Behavior Institute, Department of Systems Biology, and.,Howard Hughes Medical Institute Columbia University, New York, New York 10032
| | - Sergey Y Vakhrushev
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark, and
| | - Henrik Clausen
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark, and
| | - Adnan Halim
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark, and
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49
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Khetarpal SA, Schjoldager KT, Christoffersen C, Raghavan A, Edmondson AC, Reutter HM, Ahmed B, Ouazzani R, Peloso GM, Vitali C, Zhao W, Somasundara AVH, Millar JS, Park Y, Fernando G, Livanov V, Choi S, Noé E, Patel P, Ho SP, Kirchgessner TG, Wandall HH, Hansen L, Bennett EP, Vakhrushev SY, Saleheen D, Kathiresan S, Brown CD, Abou Jamra R, LeGuern E, Clausen H, Rader DJ. Loss of Function of GALNT2 Lowers High-Density Lipoproteins in Humans, Nonhuman Primates, and Rodents. Cell Metab 2016; 24:234-45. [PMID: 27508872 PMCID: PMC5663192 DOI: 10.1016/j.cmet.2016.07.012] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 04/14/2016] [Accepted: 07/20/2016] [Indexed: 02/01/2023]
Abstract
Human genetics studies have implicated GALNT2, encoding GalNAc-T2, as a regulator of high-density lipoprotein cholesterol (HDL-C) metabolism, but the mechanisms relating GALNT2 to HDL-C remain unclear. We investigated the impact of homozygous GALNT2 deficiency on HDL-C in humans and mammalian models. We identified two humans homozygous for loss-of-function mutations in GALNT2 who demonstrated low HDL-C. We also found that GALNT2 loss of function in mice, rats, and nonhuman primates decreased HDL-C. O-glycoproteomics studies of a human GALNT2-deficient subject validated ANGPTL3 and ApoC-III as GalNAc-T2 targets. Additional glycoproteomics in rodents identified targets influencing HDL-C, including phospholipid transfer protein (PLTP). GALNT2 deficiency reduced plasma PLTP activity in humans and rodents, and in mice this was rescued by reconstitution of hepatic Galnt2. We also found that GALNT2 GWAS SNPs associated with reduced HDL-C also correlate with lower hepatic GALNT2 expression. These results posit GALNT2 as a direct modulator of HDL metabolism across mammals.
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Affiliation(s)
- Sumeet A Khetarpal
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Institute of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark.
| | - Christina Christoffersen
- Department of Clinical Biochemistry, Rigshospitalet and Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Avanthi Raghavan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew C Edmondson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Heiko M Reutter
- Institute of Human Genetics, University of Bonn, Bonn 53012, Germany; Department of Neonatology and Pediatric Intensive Care, University of Bonn, Bonn 53012, Germany
| | - Bouhouche Ahmed
- Research Team on Neurodegenerative Diseases, Medical School and Pharmacy, Mohammed V University, 10100 Rabat, Morocco
| | - Reda Ouazzani
- Neurophysiology Division, Hospital of Specialities, CHIS Ibn Sina, 6402 Rabat, Morocco
| | - Gina M Peloso
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Cecilia Vitali
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wei Zhao
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amritha Varshini Hanasoge Somasundara
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John S Millar
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - YoSon Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gayani Fernando
- Department of Cardiovascular Drug Discovery, Bristol-Myers Squibb, Pennington, NJ 08534, USA
| | - Valentin Livanov
- Department of Applied Genomics, Bristol-Myers Squibb, Pennington, NJ 08534, USA
| | - Seungbum Choi
- Gacheon Cardiovascular Research Institute, Gachon University, 21565 Incheon, Korea
| | - Eric Noé
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, and AP-HP, Department of Genetics, Pitié-La Salpêtrière Hospital, 75013 Paris, France
| | - Pritesh Patel
- Department of Applied Genomics, Bristol-Myers Squibb, Pennington, NJ 08534, USA
| | - Siew Peng Ho
- Department of Applied Genomics, Bristol-Myers Squibb, Pennington, NJ 08534, USA
| | - Todd G Kirchgessner
- Department of Cardiovascular Drug Discovery, Bristol-Myers Squibb, Pennington, NJ 08534, USA
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Institute of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Lars Hansen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Institute of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Institute of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Institute of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Danish Saleheen
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN Cambridge, UK; Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Centre for Non-Communicable Diseases, 75300 Karachi, Pakistan
| | - Sekar Kathiresan
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Christopher D Brown
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, 04103 Leipzig, Germany; Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Eric LeGuern
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, Inserm U 1127, CNRS UMR 7225, ICM, and AP-HP, Department of Genetics, Pitié-La Salpêtrière Hospital, 75013 Paris, France
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Institute of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Bagdonaite I, Nordén R, Joshi HJ, King SL, Vakhrushev SY, Olofsson S, Wandall HH. Global Mapping of O-Glycosylation of Varicella Zoster Virus, Human Cytomegalovirus, and Epstein-Barr Virus. J Biol Chem 2016; 291:12014-28. [PMID: 27129252 DOI: 10.1074/jbc.m116.721746] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Indexed: 12/27/2022] Open
Abstract
Herpesviruses are among the most complex and widespread viruses, infection and propagation of which depend on envelope proteins. These proteins serve as mediators of cell entry as well as modulators of the immune response and are attractive vaccine targets. Although envelope proteins are known to carry glycans, little is known about the distribution, nature, and functions of these modifications. This is particularly true for O-glycans; thus we have recently developed a "bottom up" mass spectrometry-based technique for mapping O-glycosylation sites on herpes simplex virus type 1. We found wide distribution of O-glycans on herpes simplex virus type 1 glycoproteins and demonstrated that elongated O-glycans were essential for the propagation of the virus. Here, we applied our proteome-wide discovery platform for mapping O-glycosites on representative and clinically significant members of the herpesvirus family: varicella zoster virus, human cytomegalovirus, and Epstein-Barr virus. We identified a large number of O-glycosites distributed on most envelope proteins in all viruses and further demonstrated conserved patterns of O-glycans on distinct homologous proteins. Because glycosylation is highly dependent on the host cell, we tested varicella zoster virus-infected cell lysates and clinically isolated virus and found evidence of consistent O-glycosites. These results present a comprehensive view of herpesvirus O-glycosylation and point to the widespread occurrence of O-glycans in regions of envelope proteins important for virus entry, formation, and recognition by the host immune system. This knowledge enables dissection of specific functional roles of individual glycosites and, moreover, provides a framework for design of glycoprotein vaccines with representative glycosylation.
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Affiliation(s)
- Ieva Bagdonaite
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark and
| | - Rickard Nordén
- the Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Hiren J Joshi
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark and
| | - Sarah L King
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark and
| | - Sergey Y Vakhrushev
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark and
| | - Sigvard Olofsson
- the Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, 413 45 Gothenburg, Sweden
| | - Hans H Wandall
- From the Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark and
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