1
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Shu T, Zhang Y, Sun T, Zhu Y. Polypeptide N-Acetylgalactosaminyl transferase 14 is a novel mediator in pancreatic β-cell function and growth. Mol Cell Endocrinol 2024; 591:112269. [PMID: 38763428 DOI: 10.1016/j.mce.2024.112269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/25/2024] [Accepted: 05/10/2024] [Indexed: 05/21/2024]
Abstract
Polypeptide N-Acetylgalactosaminyl transferase 14 (GALNT14) plays important roles in cancer progression and chemotherapy response. Here, we show that GALNT14 is highly expressed in pancreatic β cells and regulates β cell function and growth. We found that the expression level of Ganlt14 was significantly decreased in the primary islets from three rodent type-2 diabetic models. Single-Cell sequencing defined that Galnt14 was mainly expressed in β cells of mouse islets. Galnt14 knockout (G14KO) INS-1 cell line, constructed by using CRISPR/Cas9 technology were growth normal, but showed blunt shape, and increased basal insulin secretion. Combined proteomics and glycoproteomics demonstrated that G14KO altered cell-to-cell junctions, communication, and adhesion. Insulin receptor (IR) and IGF1-1R were indirectly confirmed for GALNT14 substrates, contributed to diminished IGF1-induced p-AKT levels and cell growth in G14KO cells. Overall, this study uncovers that GALNT14 is a novel modulator in regulating β cells biology, providing a missing link of β cells O-glycosylation to diabetes development.
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Affiliation(s)
- Tingting Shu
- Department of Central Laboratory, Geriatric Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210024, China
| | - Yan Zhang
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China; Department of Clinical Laboratory, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Tong Sun
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Yunxia Zhu
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, 211166, China.
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2
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Safferthal M, Bechtella L, Zappe A, Vos GM, Pagel K. Labeling of Mucin-Type O-Glycans for Quantification Using Liquid Chromatography and Fluorescence Detection. ACS MEASUREMENT SCIENCE AU 2024; 4:223-230. [PMID: 38645579 PMCID: PMC11027200 DOI: 10.1021/acsmeasuresciau.3c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 04/23/2024]
Abstract
O-glycosylation is a common post-translational modification that is essential for the defensive properties of mucus barriers. Incomplete and altered O-glycosylation is often linked to severe diseases, such as cancer, cystic fibrosis, and chronic obstructive pulmonary disease. Originating from a nontemplate-driven biosynthesis, mucin-type O-glycan structures are very complex. They are often present as heterogeneous mixtures containing multiple isomers. Therefore, the analysis of complex O-glycan mixtures usually requires hyphenation of orthogonal techniques such as liquid chromatography (LC), ion mobility spectrometry, and mass spectrometry (MS). However, MS-based techniques are mainly qualitative. Moreover, LC separation of O-glycans often lacks reproducibility and requires sophisticated data treatment and analysis. Here we present a mucin-type O-glycomics analysis workflow that utilizes hydrophilic interaction liquid chromatography for separation and fluorescence labeling for detection and quantification. In combination with mass spectrometry, a detailed analysis on the relative abundance of specific mucin-type O-glycan compositions and features, such as fucose, sialic acids, and sulfates, is performed. Furthermore, the average number of monosaccharide units of O-glycans in different samples was determined. To demonstrate universal applicability, the method was tested on mucins from different tissue types and mammals, such as bovine submaxillary mucins, porcine gastric mucins, and human milk mucins. To account for day-to-day retention time shifts in O-glycan separations and increase the comparability between different instruments and laboratories, we included fluorescently labeled dextran ladders in our workflow. In addition, we set up a library of glucose unit values for all identified O-glycans, which can be used to simplify the identification process of glycans in future analyses.
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Affiliation(s)
- Marc Safferthal
- Fritz
Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Biology, Chemistry, Pharmacy, Freie Universität
Berlin, Altensteinstraße
23a, 14195 Berlin, Germany
| | - Leïla Bechtella
- Fritz
Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Biology, Chemistry, Pharmacy, Freie Universität
Berlin, Altensteinstraße
23a, 14195 Berlin, Germany
| | - Andreas Zappe
- Fritz
Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Biology, Chemistry, Pharmacy, Freie Universität
Berlin, Altensteinstraße
23a, 14195 Berlin, Germany
| | - Gaël M. Vos
- Fritz
Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Biology, Chemistry, Pharmacy, Freie Universität
Berlin, Altensteinstraße
23a, 14195 Berlin, Germany
| | - Kevin Pagel
- Fritz
Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
- Department
of Biology, Chemistry, Pharmacy, Freie Universität
Berlin, Altensteinstraße
23a, 14195 Berlin, Germany
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3
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Chernykh A, Abrahams JL, Grant OC, Kambanis L, Sumer-Bayraktar Z, Ugonotti J, Kawahara R, Corcilius L, Payne RJ, Woods RJ, Thaysen-Andersen M. Position-specific N- and O-glycosylation of the reactive center loop impacts neutrophil elastase-mediated proteolysis of corticosteroid-binding globulin. J Biol Chem 2024; 300:105519. [PMID: 38042488 PMCID: PMC10784704 DOI: 10.1016/j.jbc.2023.105519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/04/2023] Open
Abstract
Corticosteroid-binding globulin (CBG) delivers anti-inflammatory cortisol to inflamed tissues through proteolysis of an exposed reactive center loop (RCL) by neutrophil elastase (NE). We previously demonstrated that RCL-localized Asn347-linked N-glycans impact NE proteolysis, but a comprehensive structure-function characterization of the RCL glycosylation is still required to better understand CBG glycobiology. Herein, we first performed RCL-centric glycoprofiling of serum-derived CBG to elucidate the Asn347-glycans and then used molecular dynamics simulations to study their impact on NE proteolysis. Importantly, we also identified O-glycosylation (di/sialyl T) across four RCL sites (Thr338/Thr342/Thr345/Ser350) of serum CBG close to the NE-targeted Val344-Thr345 cleavage site. A restricted N- and O-glycan co-occurrence pattern on the RCL involving exclusively Asn347 and Thr338 glycosylation was experimentally observed and supported in silico by modeling of a CBG-GalNAc-transferase (GalNAc-T) complex with various RCL glycans. GalNAc-T2 and GalNAc-T3 abundantly expressed by liver and gall bladder, respectively, showed in vitro a capacity to transfer GalNAc (Tn) to multiple RCL sites suggesting their involvement in RCL O-glycosylation. Recombinant CBG was then used to determine roles of RCL O-glycosylation through longitudinal NE-centric proteolysis experiments, which demonstrated that both sialoglycans (disialyl T) and asialoglycans (T) decorating Thr345 inhibit NE proteolysis. Synthetic RCL O-glycopeptides expanded on these findings by showing that Thr345-Tn and Thr342-Tn confer strong and moderate protection against NE cleavage, respectively. Molecular dynamics substantiated that short Thr345-linked O-glycans abrogate NE interactions. In conclusion, we report on biologically relevant CBG RCL glycosylation events, which improve our understanding of mechanisms governing cortisol delivery to inflamed tissues.
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Affiliation(s)
- Anastasia Chernykh
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Jodie L Abrahams
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Lucas Kambanis
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Zeynep Sumer-Bayraktar
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Glycometabolic Biochemistry Team, Cluster of Pioneering Research, RIKEN, Wako, Saitama, Japan
| | - Julian Ugonotti
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Rebeca Kawahara
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| | - Leo Corcilius
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan.
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4
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Chien YC, Wang YS, Sridharan D, Kuo CW, Chien CT, Uchihashi T, Kato K, Angata T, Meng TC, Hsu STD, Khoo KH. High Density of N- and O-Glycosylation Shields and Defines the Structural Dynamics of the Intrinsically Disordered Ectodomain of Receptor-type Protein Tyrosine Phosphatase Alpha. JACS AU 2023; 3:1864-1875. [PMID: 37502146 PMCID: PMC10369406 DOI: 10.1021/jacsau.3c00124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 07/29/2023]
Abstract
The intracellular phosphatase domain of the receptor-type protein tyrosine phosphatase alpha (PTPRA) is known to regulate various signaling pathways related to cell adhesion through c-Src kinase activation. In contrast, the functional significance of its relatively short, intrinsically disordered, and heavily glycosylated ectodomain remains unclear. Through detailed mass spectrometry analyses of a combination of protease and glycosidase digests, we now provide the first experimental evidence for its site-specific glycosylation pattern. This includes the occurrence of O-glycan at the N-glycosylation sequon among the more than 30 O-glycosylation sites confidently identified beside the 7 N-glycosylation sites. The closely spaced N- and O-glycans appear to have mutually limited the extent of further galactosylation and sialylation. An immature smaller form of full-length PTPRA was found to be deficient in O-glycosylation, most likely due to failure to transit the Golgi. N-glycosylation, on the other hand, is dispensable for cell surface expression and contributes less than the extensive O-glycosylation to the overall solution structure of the ectodomain. The glycosylation information is combined with the overall structural features of the ectodomain derived from small-angle X-ray scattering and high-speed atomic force microscopy monitoring to establish a dynamic structural model of the densely glycosylated PTPRA ectodomain. The observed high structural flexibility, as manifested by continuous transitioning from fully to partially extended and fold-back conformations, suggests that the receptor-type phosphatase is anchored to the membrane and kept mostly at a monomeric state through an ectodomain shaped and fully shielded by glycosylation.
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Affiliation(s)
- Yu-Chun Chien
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Yong-Sheng Wang
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Deepa Sridharan
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chu-Wei Kuo
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Ta Chien
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Takayuki Uchihashi
- Department
of Physics, Nagoya University, Nagoya 464-8602, Japan
- Exploratory
Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Koichi Kato
- Exploratory
Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
- Institute
for Molecular Science, National Institutes
of Natural Sciences, Okazaki 444-8787, Japan
- Graduate
School of Pharmaceutical Sciences, Nagoya
City University, Nagoya 467-8603, Japan
| | - Takashi Angata
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Tzu-Ching Meng
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Shang-Te Danny Hsu
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
- International
Institute for Sustainability with Knotted Chiral Meta Matter, Hiroshima University, Higashihiroshima 739-8527, Japan
| | - Kay-Hooi Khoo
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
- Exploratory
Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
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5
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Gonzalez-Rodriguez E, Zol-Hanlon M, Bineva-Todd G, Marchesi A, Skehel M, Mahoney KE, Roustan C, Borg A, Di Vagno L, Kjær S, Wrobel AG, Benton DJ, Nawrath P, Flitsch SL, Joshi D, González-Ramírez A, Wilkinson KA, Wilkinson RJ, Wall EC, Hurtado-Guerrero R, Malaker SA, Schumann B. O-Linked Sialoglycans Modulate the Proteolysis of SARS-CoV-2 Spike and Likely Contribute to the Mutational Trajectory in Variants of Concern. ACS CENTRAL SCIENCE 2023; 9:393-404. [PMID: 36968546 PMCID: PMC10037455 DOI: 10.1021/acscentsci.2c01349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Indexed: 06/18/2023]
Abstract
The emergence of a polybasic cleavage motif for the protease furin in SARS-CoV-2 spike has been established as a major factor for human viral transmission. The region N-terminal to that motif is extensively mutated in variants of concern (VOCs). Besides furin, spikes from these variants appear to rely on other proteases for maturation, including TMPRSS2. Glycans near the cleavage site have raised questions about proteolytic processing and the consequences of variant-borne mutations. Here, we identify that sialic acid-containing O-linked glycans on Thr678 of SARS-CoV-2 spike influence furin and TMPRSS2 cleavage and posit O-linked glycosylation as a likely driving force for the emergence of VOC mutations. We provide direct evidence that the glycosyltransferase GalNAc-T1 primes glycosylation at Thr678 in the living cell, an event that is suppressed by mutations in the VOCs Alpha, Delta, and Omicron. We found that the sole incorporation of N-acetylgalactosamine did not impact furin activity in synthetic O-glycopeptides, but the presence of sialic acid reduced the furin rate by up to 65%. Similarly, O-glycosylation with a sialylated trisaccharide had a negative impact on TMPRSS2 cleavage. With a chemistry-centered approach, we substantiate O-glycosylation as a major determinant of spike maturation and propose disruption of O-glycosylation as a substantial driving force for VOC evolution.
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Affiliation(s)
- Edgar Gonzalez-Rodriguez
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Department
of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Mia Zol-Hanlon
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Signalling
and Structural Biology Lab, The Francis
Crick Institute, NW1 1AT London, United Kingdom
| | - Ganka Bineva-Todd
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
| | - Andrea Marchesi
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Department
of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Mark Skehel
- Proteomics
Science Technology Platform, The Francis
Crick Institute, NW1 1AT London, United Kingdom
| | - Keira E. Mahoney
- Department
of Chemistry, Yale University, 275 Prospect Street, 06511 New Haven, Connecticut, United States
| | - Chloë Roustan
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Annabel Borg
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Lucia Di Vagno
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Proteomics
Science Technology Platform, The Francis
Crick Institute, NW1 1AT London, United Kingdom
| | - Svend Kjær
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Antoni G. Wrobel
- Structural
Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Donald J. Benton
- Structural
Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Philipp Nawrath
- Structural
Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Sabine L. Flitsch
- Manchester
Institute of Biotechnology, University of
Manchester, 131 Princess Street, M1 7DN Manchester, United Kingdom
| | - Dhira Joshi
- Chemical
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Katalin A. Wilkinson
- Tuberculosis
Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Wellcome
Centre for Infectious Diseases Research in Africa, University of Cape Town, 7925 Observatory, Cape Town, South Africa
| | - Robert J. Wilkinson
- Tuberculosis
Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Wellcome
Centre for Infectious Diseases Research in Africa, University of Cape Town, 7925 Observatory, Cape Town, South Africa
- Department
of Infectious Diseases, Imperial College
London, W12 0NN London, United Kingdom
- Institute
of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, 7925 Observatory, Cape Town, South Africa
| | - Emma C. Wall
- The Francis
Crick Institute, NW1 1AT London, United Kingdom
- University
College London Hospitals (UCLH) Biomedical Research Centre, W1T 7DN London, United Kingdom
| | - Ramón Hurtado-Guerrero
- Institute
of Biocomputation and Physics of Complex Systems, University of Zaragoza, 50018 Zaragoza, Spain
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
- Fundación
ARAID, 50018 Zaragoza, Spain
| | - Stacy A. Malaker
- Department
of Chemistry, Yale University, 275 Prospect Street, 06511 New Haven, Connecticut, United States
| | - Benjamin Schumann
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Department
of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
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6
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Riley NM, Bertozzi CR. Deciphering O-glycoprotease substrate preferences with O-Pair Search. Mol Omics 2022; 18:908-922. [PMID: 36373229 PMCID: PMC10010678 DOI: 10.1039/d2mo00244b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
O-Glycoproteases are an emerging class of enzymes that selectively digest glycoproteins at positions decorated with specific O-linked glycans. O-Glycoprotease substrates range from any O-glycoprotein (albeit with specific O-glycan modifications) to only glycoproteins harboring specific O-glycosylated sequence motifs, such as those found in mucin domains. Their utility for multiple glycoproteomic applications is driving the search to both discover new O-glycoproteases and to understand how structural features of characterized O-glycoproteases influence their substrate specificities. One challenge of defining O-glycoprotease specificity restraints is the need to characterize O-glycopeptides with site-specific analysis of O-glycosites. Here, we demonstrate how O-Pair Search, a recently developed O-glycopeptide-centric identification platform that enables rapid searches and confident O-glycosite localization, can be used to determine substrate specificities of various O-glycoproteases de novo from LC-MS/MS data of O-glycopeptides. Using secreted protease of C1 esterase inhibitor (StcE) from enterohemorrhagic Escherichia coli and O-endoprotease OgpA from Akkermansia mucinophila, we explore numerous settings that effect O-glycopeptide identification and show how non-specific and semi-tryptic searches of O-glycopeptide data can produce candidate cleavage motifs. These putative motifs can be further used to define new protease cleavage settings that lower search times and improve O-glycopeptide identifications. We use this platform to generate a consensus motif for the recently characterized immunomodulating metalloprotease (IMPa) from Pseudomonas aeruginosa and show that IMPa is a favorable O-glycoprotease for characterizing densely O-glycosylated mucin-domain glycoproteins.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Sarafan ChEM-H, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Sarafan ChEM-H, Stanford University, Stanford, California, USA. .,Howard Hughes Medical Institute, Stanford, California, USA
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7
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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] [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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8
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Riley NM, Wen RM, Bertozzi CR, Brooks JD, Pitteri SJ. Measuring the multifaceted roles of mucin-domain glycoproteins in cancer. Adv Cancer Res 2022; 157:83-121. [PMID: 36725114 PMCID: PMC10582998 DOI: 10.1016/bs.acr.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Mucin-domain glycoproteins are highly O-glycosylated cell surface and secreted proteins that serve as both biochemical and biophysical modulators. Aberrant expression and glycosylation of mucins are known hallmarks in numerous malignancies, yet mucin-domain glycoproteins remain enigmatic in the broad landscape of cancer glycobiology. Here we review the multifaceted roles of mucins in cancer through the lens of the analytical and biochemical methods used to study them. We also describe a collection of emerging tools that are specifically equipped to characterize mucin-domain glycoproteins in complex biological backgrounds. These approaches are poised to further elucidate how mucin biology can be understood and subsequently targeted for the next generation of cancer therapeutics.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States.
| | - Ru M Wen
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States; Howard Hughes Medical Institute, Stanford, CA, United States
| | - James D Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States; Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States.
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9
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Recent applications of ionic liquid-based tags in glycoscience. Carbohydr Res 2022; 520:108643. [PMID: 35977445 DOI: 10.1016/j.carres.2022.108643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/22/2022]
Abstract
The functionalization of glycosides with ionic compounds such as ionic liquids provides enhanced polarity for the labelled glycans thanks to the presence of a permanent positive charge. The chemical derivatisation of glycans with ionic liquids constitutes an emerging strategy to boost the detection sensitivity in MS applications. This allows the straightforward monitoring and detection of the presence of labelled glycans in complex matrices and in those cases where very limited amounts of material were available such as in biological samples and chemoenzymatic reactions. The use of ionic liquid based derivatisation agents can be further exploited for the labelling of live cells via metabolic oligosaccharide engineering for the detection of cancer biomarkers and for the tuning of live cells-surface properties with implications in cancer prognosis and progression. In this mini-review we summarise the latest development of the ionic liquid based derivatisation agents in glycoscience focussing on their use for sensitive MS applications.
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10
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Zhou S, Liu D, Chen J, Xiang C, Xiang J, Yang M. Electrochemical Quantitation of the Glycosylation Level of Serum Neurofilament Light Chain for the Diagnosis of Neurodegeneration: An Interface-Solution Dual-Path Amplification Strategy. Anal Chem 2022; 94:11433-11440. [PMID: 35913270 DOI: 10.1021/acs.analchem.2c02753] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Serum neurofilament light chain (NFL), a potential general biomarker for neurodegenerative diseases, is not specific enough to differentiate neurodegenerative diseases from other brain diseases such as cerebral thrombosis (CT). According to the importance of glycosylation in neurodegenerative pathogenesis, the NFL glycosylation level (oNFL/tNFL), defined as the ratio of glycosylated NFL (oNFL) to total NFL (tNFL), may be a more effective index. The major challenge in serum oNFL/tNFL detection is the ultra-low abundance of both NFL forms. In this paper, we achieved a convenient one-step electrochemical quantitation of oNFL/tNFL based on an interface-solution dual-path amplification strategy. Two amplified electrochemical signals─the reduction of Cu2+ from adsorbed porous nanoparticles on the sensor interface and the reduction of O2 from horseradish peroxidase-catalyzed H2O2 disproportionation in solution─were adopted to quantify tNFL and oNFL, respectively. The electrochemical sensor displayed good sensitivity, selectivity, and reproducibility. The dynamic range is 1-25 pg mL-1 for tNFL and 0.25-25 pg mL-1 for oNFL, respectively. By analyzing the clinic serum samples, for the first time, our work provided the abundance of oNFL in human serum and revealed that the oNFL/tNFL is effective not only in differentiating three kinds of brain damage patients from healthy people but also in differentiating neurodegeneration from non-neurodegeneration CT patients. As a general biomarker, the oNFL/tNFL is more specific than NFL, which is hoped to be a new and valid indicator for the diagnosis, progression, prediction, and treatment evaluation of neurodegenerative diseases.
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Affiliation(s)
- Siqiuyue Zhou
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China.,National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha 410083, P. R. China
| | - Dan Liu
- Eye Center of Xiangya Hospital, Central South University, Changsha 410083, P. R. China
| | - Jia Chen
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Chao Xiang
- Wuhan Red Cross Hospital, Wuhan 430015, P. R. China
| | - Juan Xiang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China.,National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha 410083, P. R. China
| | - Minghui Yang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
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11
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Li J, Zhang J, Xu M, Yang Z, Yue S, Zhou W, Gui C, Zhang H, Li S, Wang PG, Yang S. Advances in glycopeptide enrichment methods for the analysis of protein glycosylation over the past decade. J Sep Sci 2022; 45:3169-3186. [PMID: 35816156 DOI: 10.1002/jssc.202200292] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/16/2022] [Accepted: 07/01/2022] [Indexed: 11/12/2022]
Abstract
Advances in bioanalytical technology have accelerated the analysis of complex protein glycosylation, which is beneficial to understanding glycosylation in drug discovery and disease diagnosis. Due to its biological uniqueness in the course of disease occurrence and development, disease-specific glycosylation requires quantitative characterization of protein glycosylation. We provide a comprehensive review of recent advances in glycosylation analysis, including workflows for glycoprotein digestion, glycopeptide separation and enrichment, and mass-spectrometry sequencing. We specifically focus on different strategies for glycopeptide enrichment through physical interaction, chemical oxidation, or metabolic labeling of intact glycopeptides. The recent advances and challenges of O-glycosylation analysis are presented, and the development of improved enrichment methods combining different proteases to analyze O-glycosylation is also proposed. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jiajia Li
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Jie Zhang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Mingming Xu
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Zeren Yang
- AstraZeneca, Medimmune Ct, Frederick, MD, 21703, USA
| | - Shuang Yue
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Wanlong Zhou
- U.S. Food and Drug Administration, Forensic Chemistry Center, Cincinnati, OH, 45237, USA
| | - Chunshan Gui
- Department of Pharmaceutical Analysis, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Haiyang Zhang
- Department of Pharmaceutical Analysis, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Shuwei Li
- Nanjing Apollomics Biotech, Inc., Nanjing, Jiangsu, 210033, China
| | - Perry G Wang
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, 20740, USA
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China.,Department of Pharmaceutical Analysis, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
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12
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Dworkin LA, Clausen H, Joshi HJ. Applying transcriptomics to studyglycosylation at the cell type level. iScience 2022; 25:104419. [PMID: 35663018 PMCID: PMC9156939 DOI: 10.1016/j.isci.2022.104419] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/30/2022] [Accepted: 05/12/2022] [Indexed: 11/22/2022] Open
Abstract
The complex multi-step process of glycosylation occurs in a single cell, yet current analytics generally cannot measure the output (the glycome) of a single cell. Here, we addressed this discordance by investigating how single cell RNA-seq data can be used to characterize the state of the glycosylation machinery and metabolic network in a single cell. The metabolic network involves 214 glycosylation and modification enzymes outlined in our previously built atlas of cellular glycosylation pathways. We studied differential mRNA regulation of enzymes at the organ and single cell level, finding that most of the general protein and lipid oligosaccharide scaffolds are produced by enzymes exhibiting limited transcriptional regulation among cells. We predict key enzymes within different glycosylation pathways to be highly transcriptionally regulated as regulatable hotspots of the cellular glycome. We designed the Glycopacity software that enables investigators to extract and interpret glycosylation information from transcriptome data and define hotspots of regulation. RNA-seq can provide information on the glycosylation metabolic network state It is possible to readout glycosylation capacity from single cell RNA-seq data Genes regulating the biosynthesis of common glycan scaffolds show little regulation Key enzymes in the glycosylation network are predicted to be regulatable hotspots
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Affiliation(s)
- Leo Alexander Dworkin
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Hiren Jitendra Joshi
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
- Corresponding author
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13
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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] [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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14
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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] [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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15
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Abstract
Mucin-domain glycoproteins comprise a class of proteins whose densely O-glycosylated mucin domains adopt a secondary structure with unique biophysical and biochemical properties. The canonical family of mucins is well-known to be involved in various diseases, especially cancer. Despite this, very little is known about the site-specific molecular structures and biological activities of mucins, in part because they are extremely challenging to study by mass spectrometry (MS). Here, we summarize recent advancements toward this goal, with a particular focus on mucin-domain glycoproteins as opposed to general O-glycoproteins. We summarize proteolytic digestion techniques, enrichment strategies, MS fragmentation, and intact analysis, as well as new bioinformatic platforms. In particular, we highlight mucin directed technologies such as mucin-selective proteases, tunable mucin platforms, and a mucinomics strategy to enrich mucin-domain glycoproteins from complex samples. Finally, we provide examples of targeted mucin-domain glycoproteomics that combine these techniques in comprehensive site-specific analyses of proteins. Overall, this Review summarizes the methods, challenges, and new opportunities associated with studying enigmatic mucin domains.
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Affiliation(s)
- Valentina Rangel-Angarita
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States
| | - Stacy A. Malaker
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States
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16
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Calle B, Bineva-Todd G, Marchesi A, Flynn H, Ghirardello M, Tastan OY, Roustan C, Choi J, Galan MC, Schumann B, Malaker SA. Benefits of Chemical Sugar Modifications Introduced by Click Chemistry for Glycoproteomic Analyses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2366-2375. [PMID: 33871988 PMCID: PMC7611619 DOI: 10.1021/jasms.1c00084] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Mucin-type O-glycosylation is among the most complex post-translational modifications. Despite mediating many physiological processes, O-glycosylation remains understudied compared to other modifications, simply because the right analytical tools are lacking. In particular, analysis of intact O-glycopeptides by mass spectrometry is challenging for several reasons; O-glycosylation lacks a consensus motif, glycopeptides have low charge density which impairs ETD fragmentation, and the glycan structures modifying the peptides are unpredictable. Recently, we introduced chemically modified monosaccharide analogues that allowed selective tracking and characterization of mucin-type O-glycans after bioorthogonal derivatization with biotin-based enrichment handles. In doing so, we realized that the chemical modifications used in these studies have additional benefits that allow for improved analysis by tandem mass spectrometry. In this work, we built on this discovery by generating a series of new GalNAc analogue glycopeptides. We characterized the mass spectrometric signatures of these modified glycopeptides and their signature residues left by bioorthogonal reporter reagents. Our data indicate that chemical methods for glycopeptide profiling offer opportunities to optimize attributes such as increased charge state, higher charge density, and predictable fragmentation behavior.
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Affiliation(s)
- Beatriz Calle
- Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
- Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ, London, United Kingdom
| | - Ganka Bineva-Todd
- Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
| | - Andrea Marchesi
- Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
- Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ, London, United Kingdom
| | - Helen Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Mattia Ghirardello
- School of Chemistry, Cantock’s Close, University of Bristol, BS8 1TS, United Kingdom
| | - Omur Y. Tastan
- Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
| | - Chloe Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Junwon Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - M. Carmen Galan
- School of Chemistry, Cantock’s Close, University of Bristol, BS8 1TS, United Kingdom
| | - Benjamin Schumann
- Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
- Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ, London, United Kingdom
| | - Stacy A. Malaker
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, CT 06511, United States
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17
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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] [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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18
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Wandall HH, Nielsen MAI, King-Smith S, de Haan N, Bagdonaite I. Global functions of O-glycosylation: promises and challenges in O-glycobiology. FEBS J 2021; 288:7183-7212. [PMID: 34346177 DOI: 10.1111/febs.16148] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/23/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022]
Abstract
Mucin type O-glycosylation is one of the most diverse types of glycosylation, playing essential roles in tissue development and homeostasis. In complex organisms, O-GalNAc glycans comprise a substantial proportion of the glycocalyx, with defined functions in hemostatic, gastrointestinal, and respiratory systems. Furthermore, O-GalNAc glycans are important players in host-microbe interactions, and changes in O-glycan composition are associated with certain diseases and metabolic conditions, which in some instances can be used for diagnosis or therapeutic intervention. Breakthroughs in O-glycobiology have gone hand in hand with the development of new technologies, such as advancements in mass spectrometry, as well as facilitation of genetic engineering in mammalian cell lines. High-throughput O-glycoproteomics have enabled us to draw a comprehensive map of O-glycosylation, and mining this information has supported the definition and confirmation of functions related to site-specific O-glycans. This includes protection from proteolytic cleavage, as well as modulation of binding affinity or receptor function. Yet, there is still much to discover, and among the important next challenges will be to define the context-dependent functions of O-glycans in different stages of cellular differentiation, cellular metabolism, host-microbiome interactions, and in disease. In this review, we present the achievements and the promises in O-GalNAc glycobiology driven by technological advances in analytical methods, genetic engineering, and systems biology.
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Affiliation(s)
- Hans H Wandall
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Mathias A I Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Sarah King-Smith
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Noortje de Haan
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Ieva Bagdonaite
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
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19
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Čaval T, Buettner A, Haberger M, Reusch D, Heck AJ. Discrepancies between High-Resolution Native and Glycopeptide-Centric Mass Spectrometric Approaches: A Case Study into the Glycosylation of Erythropoietin Variants. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2099-2104. [PMID: 33856811 PMCID: PMC8343523 DOI: 10.1021/jasms.1c00060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Glycosylation represents a critical quality attribute modulating a myriad of physiochemical properties and effector functions of biotherapeutics. Furthermore, a rising landscape of glycosylated biotherapeutics including biosimilars, biobetters, and fusion proteins harboring complicated and dynamic glycosylation profiles requires tailored analytical approaches capable of characterizing their heterogeneous nature. In this work, we perform in-depth evaluation of the glycosylation profiles of three glycoengineered variants of the widely used biotherapeutic erythropoietin. We analyzed these samples in parallel using a glycopeptide-centric liquid chromatography/mass spectrometry approach and high-resolution native mass spectrometry. Although for all of the studied variants the glycopeptide and native mass spectrometry data were in good qualitative agreement, we observed substantial quantitative differences arising from ionization deficiencies and unwanted neutral losses, in particular, for sialylated glycopeptides in the glycoproteomics approach. However, the latter provides direct information about glycosite localization. We conclude that the combined parallel use of native mass spectrometry and bottom-up glycoproteomics offers superior characterization of glycosylated biotherapeutics and thus provides a valuable attribute in the characterization of glycoengineered proteins and other complex biotherapeutics.
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Affiliation(s)
- Tomislav Čaval
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, Utrecht 3584 CH, The Netherlands
| | - Alexander Buettner
- Pharma
Technical Development, Roche Diagnostics
GmbH, Penzberg 82377, Germany
| | - Markus Haberger
- Pharma
Technical Development, Roche Diagnostics
GmbH, Penzberg 82377, Germany
| | - Dietmar Reusch
- Pharma
Technical Development, Roche Diagnostics
GmbH, Penzberg 82377, Germany
| | - Albert J.R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, Utrecht 3584 CH, The Netherlands
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Habermann FA, Kaltner H, Higuero AM, García Caballero G, Ludwig AK, C. Manning J, Abad-Rodríguez J, Gabius HJ. What Cyto- and Histochemistry Can Do to Crack the Sugar Code. Acta Histochem Cytochem 2021; 54:31-48. [PMID: 34012175 PMCID: PMC8116616 DOI: 10.1267/ahc.21-00017] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/18/2021] [Indexed: 12/13/2022] Open
Abstract
As letters form the vocabulary of a language, biochemical 'symbols' (the building blocks of oligo- and polymers) make writing molecular messages possible. Compared to nucleotides and amino acids, sugars have chemical properties that facilitate to reach an unsurpassed level of oligomer diversity. These glycans are a part of the ubiquitous cellular glycoconjugates. Cyto- and histochemically, the glycans' structural complexity is mapped by glycophenotyping of cells and tissues using receptors ('readers', thus called lectins), hereby revealing its dynamic spatiotemporal regulation: these data support the concept of a sugar code. When proceeding from work with plant (haem)agglutinins as such tools to the discovery of endogenous (tissue) lectins, it became clear that a broad panel of biological meanings can indeed be derived from the sugar-based vocabulary (the natural glycome incl. post-synthetic modifications) by glycan-lectin recognition in situ. As consequence, the immunocyto- and histochemical analysis of lectin expression is building a solid basis for the steps toward tracking down functional correlations, for example in processes leading to cell adhesion, apoptosis, autophagy or growth regulation as well as targeted delivery of glycoproteins. Introduction of labeled tissue lectins to glycan profiling assists this endeavor by detecting counterreceptor(s) in situ. Combining these tools and their applications strategically will help to take the trip toward the following long-range aim: to compile a dictionary for the glycan vocabulary that translates each message (oligosaccharide) into its bioresponse(s), that is to crack the sugar code.
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Affiliation(s)
- Felix A. Habermann
- Institute of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Herbert Kaltner
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Alonso M. Higuero
- Membrane and Axonal Repair Laboratory, National Hospital for Paraplegics (SESCAM), Finca La Peraleda s/n, 45071 Toledo, Spain
| | - Gabriel García Caballero
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Anna-Kristin Ludwig
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Joachim C. Manning
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - José Abad-Rodríguez
- Membrane and Axonal Repair Laboratory, National Hospital for Paraplegics (SESCAM), Finca La Peraleda s/n, 45071 Toledo, Spain
| | - Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany
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