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Yue S, Wang X, Wang L, Li J, Zhou Y, Chen Y, Zhou Z, Yang X, Shi X, Gao S, Wen Z, Zhu X, Wang Y, Yang S. MOTAI: A Novel Method for the Study of O-GalNAcylation and Complex O-Glycosylation in Cancer. Anal Chem 2024. [PMID: 38953491 DOI: 10.1021/acs.analchem.3c05018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
The Tn antigen, an immature truncated O-glycosylation, is a promising biomarker for cancer detection and diagnosis. However, reliable methods for analyzing O-GalNAcylation and complex O-glycosylation are lacking. Here, we develop a novel method, MOTAI, for the sequential analysis of O-glycosylation using different O-glycoproteases. MOTAI conjugates glycopeptides on a solid support and releases different types of O-glycosylation through sequential enzymatic digestion by O-glycoproteases, including OpeRATOR and IMPa. Because OpeRATOR has less activity on O-GalNAcylation, MOTAI enriches O-GalNAcylation for subsequent analysis. We demonstrate the effectiveness of MOTAI by analyzing fetuin O-glycosylation and Jurkat cell lines. We then apply MOTAI to analyze colorectal cancer and benign colorectal polyps. We identify 32 Tn/sTn-glycoproteins and 43 T/sT-glycoproteins that are significantly increased in tumor tissues. Gene Ontology analysis reveals that most of these proteins are ECM proteins involved in the adhesion process of the intercellular matrix. Additionally, the protein disulfide isomerase CRELD2 has a significant difference in Tn expression, and the abnormally glycosylated T345 and S349 O-glycosylation sites in cancer group samples may promote the secretion of CRELD2 and ultimately tumorigenesis through ECM reshaping. In summary, MOTAI provides a powerful new tool for the in-depth analysis of O-GalNAcylation and complex O-glycosylation. It also reveals the upregulation of Tn/sTn-glycoproteins in colorectal cancer, which may provide new insights into cancer biology and biomarker discovery.
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Affiliation(s)
- Shuang Yue
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Xiaotong Wang
- Department of Hepatology and Gastroenterology, The Affiliated Infectious Hospital of Soochow University, Suzhou 215004, China
| | - Lei Wang
- Protein Metrics LLC, Room 201-01, Building A, Novasiot, 58 Xiangke Road, Zhangjiang, Shanghai 201203, China
| | - Jiajia Li
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Yufeng Zhou
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Yan Chen
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Zeyang Zhou
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Xiaodong Yang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Xiaofeng Shi
- New England Biolabs, Inc., 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Song Gao
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
| | - Zhongmin Wen
- Health Management Center, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Xiaojun Zhu
- Health Management Center, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Yan Wang
- Mass Spectrometry Facility, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
- Health Management Center, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38925550 DOI: 10.1002/mas.21873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 06/28/2024]
Abstract
The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.
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Barbati C, Bromuro C, Vendetti S, Torosantucci A, Cauda R, Cassone A, Palma C. The Glycan Ectodomain of SARS-CoV-2 Spike Protein Modulates Cytokine Production and Expression of CD206 Mannose Receptor in PBMC Cultures of Pre-COVID-19 Healthy Subjects. Viruses 2024; 16:497. [PMID: 38675840 PMCID: PMC11054381 DOI: 10.3390/v16040497] [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: 01/14/2024] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The ability of recombinant, SARS-CoV-2 Spike (S) protein to modulate the production of two COVID-19 relevant, pro-inflammatory cytokines (IL-6 and IFN-γ) in PBMC cultures of healthy, pre-COVID-19 subjects was investigated. We observed that cytokine production was largely and diversely modulated by the S protein depending on antigen or mitogen stimulation, as well as on the protein source, insect (S-in) or human (S-hu) cells. While both proteins co-stimulated cytokine production by polyclonally CD3-activated T cells, PBMC activation by the mitogenic lectin Concanavalin A (Con A) was up-modulated by S-hu protein and down-modulated by S-in protein. These modulatory effects were likely mediated by the S glycans, as demonstrated by direct Con A-S binding experiments and use of yeast mannan as Con A binder. While being ineffective in modulating memory antigenic T cell responses, the S proteins and mannan were able to induce IL-6 production in unstimulated PBMC cultures and upregulate the expression of the mannose receptor (CD206), a marker of anti-inflammatory M2 macrophage. Our data point to a relevant role of N-glycans, particularly N-mannosidic chains, decorating the S protein in the immunomodulatory effects here reported. These novel biological activities of the S glycan ectodomain may add to the comprehension of COVID-19 pathology and immunity to SARS-CoV-2.
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Affiliation(s)
- Cristiana Barbati
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy; (C.B.); (C.B.); (S.V.); (A.T.)
| | - Carla Bromuro
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy; (C.B.); (C.B.); (S.V.); (A.T.)
| | - Silvia Vendetti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy; (C.B.); (C.B.); (S.V.); (A.T.)
| | - Antonella Torosantucci
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy; (C.B.); (C.B.); (S.V.); (A.T.)
| | - Roberto Cauda
- Dipartimento Salute e Bioetica, Sezione Malattie Infettive, Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli, 8, 00136 Rome, Italy;
| | - Antonio Cassone
- Polo d’Innovazione della Genomica, Genetica e Biologia, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy
| | - Carla Palma
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy; (C.B.); (C.B.); (S.V.); (A.T.)
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Tillis SB, Ossiboff RJ, Wellehan JFX. Serpentoviruses Exhibit Diverse Organization and ORF Composition with Evidence of Recombination. Viruses 2024; 16:310. [PMID: 38400085 PMCID: PMC10892116 DOI: 10.3390/v16020310] [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: 01/16/2024] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Serpentoviruses are a subfamily of positive sense RNA viruses in the order Nidovirales, family Tobaniviridae, associated with respiratory disease in multiple clades of reptiles. While the broadest viral diversity is reported from captive pythons, other reptiles, including colubrid snakes, turtles, and lizards of captive and free-ranging origin are also known hosts. To better define serpentoviral diversity, eleven novel serpentovirus genomes were sequenced with an Illumina MiSeq and, when necessary, completed with other Sanger sequencing methods. The novel serpentoviral genomes, along with 57 other previously published serpentovirus genomes, were analyzed alongside four outgroup genomes. Genomic analyses included identifying unique genome templates for each serpentovirus clade, as well as analysis of coded protein composition, potential protein function, protein glycosylation sites, differences in phylogenetic history between open-reading frames, and recombination. Serpentoviral genomes contained diverse protein compositions. In addition to the fundamental structural spike, matrix, and nucleoprotein proteins required for virion formation, serpentovirus genomes also included 20 previously uncharacterized proteins. The uncharacterized proteins were homologous to a number of previously characterized proteins, including enzymes, transcription factors, scaffolding, viral resistance, and apoptosis-related proteins. Evidence for recombination was detected in multiple instances in genomes from both captive and free-ranging snakes. These results show serpentovirus as a diverse clade of viruses with genomes that code for a wide diversity of proteins potentially enhanced by recombination events.
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Affiliation(s)
- Steven B. Tillis
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA; (R.J.O.); (J.F.X.W.J.)
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Lin Y, Du C, Ying H, Zhou Y, Kong F, Zhao H, Lan M. Multiply-mesoporous hydrophilic titanium dioxide nanohybrid for the highly-performed enrichment of N-glycopeptides from human serum. Anal Chim Acta 2024; 1287:342058. [PMID: 38182336 DOI: 10.1016/j.aca.2023.342058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 01/07/2024]
Abstract
N-glycopeptide is considered as one of significant biomarkers which provide guidance for the diagnosis and drug design of diseases. However, the direct analysis of N-glycopeptides is nearly impracticable mainly owing to their extremely low abundance and grave signal suppression from other interfering substances in the bio-samples. In this research, a multiply-mesoporous hydrophilic TiO2 nanohybrid (mM-TiO2@Cys) was synthesized by immobilizing Cys on a TiO2 substrate with hierarchical mesopores to achieve the highly-performed enrichment of N-glycopeptides. With the advantages of superior hydrophilicity and multiply-mesoporous structure, the obtained material exhibited an excellent selectivity (IgG digests and BSA digests at the molar ratio of 1/500), a high sensitivity (1 fmol μL-1 for IgG digests) and a good size-exclusion ability (IgG digests, IgG and BSA at the molar ratio of 1/500/500) in the enrichment of N-glycopeptides from IgG digests. As a result, 281 N-glycopeptides corresponded with 109 glycoproteins were identified from 2 μL serum digests of the patients with nasopharyngeal carcinoma, and 181 N-glycopeptides corresponded with 78 glycoproteins were identified from 2 μL serum digests of the healthy volunteers, revealing the potential application value of mM-TiO2@Cys in glycoproteomics.
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Affiliation(s)
- Yunfan Lin
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Chengrun Du
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Clinical Research Center for Radiation Oncology, Shanghai, 200032, China; Shanghai Key Laboratory of Radiation Oncology, Shanghai, 200032, China
| | - Hongmei Ying
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Clinical Research Center for Radiation Oncology, Shanghai, 200032, China; Shanghai Key Laboratory of Radiation Oncology, Shanghai, 200032, China.
| | - Yifan Zhou
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Fangfang Kong
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Clinical Research Center for Radiation Oncology, Shanghai, 200032, China; Shanghai Key Laboratory of Radiation Oncology, Shanghai, 200032, China
| | - Hongli Zhao
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Minbo Lan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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Stiving AQ, Foreman DJ, VanAernum ZL, Durr E, Wang S, Vlasak J, Galli J, Kafader JO, Tsukidate T, Li X, Schuessler HA, Richardson DD. Dissecting the Heterogeneous Glycan Profiles of Recombinant Coronavirus Spike Proteins with Individual Ion Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:62-73. [PMID: 38032172 DOI: 10.1021/jasms.3c00309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Surface-embedded glycoproteins, such as the spike protein trimers of coronaviruses MERS, SARS-CoV, and SARS-CoV-2, play a key role in viral function and are the target antigen for many vaccines. However, their significant glycan heterogeneity poses an analytical challenge. Here, we utilized individual ion mass spectrometry (I2MS), a multiplexed charge detection measurement with similarities to charge detection mass spectrometry (CDMS), in which a commercially available Orbitrap analyzer is used to directly produce mass profiles of these heterogeneous coronavirus spike protein trimers under native-like conditions. Analysis by I2MS shows that glycosylation contributes to the molecular mass of each protein trimer more significantly than expected by bottom-up techniques, highlighting the importance of obtaining complementary intact mass information when characterizing glycosylation of such heterogeneous proteins. Enzymatic dissection to remove sialic acid or N-linked glycans demonstrates that I2MS can be used to better understand the glycan profile from a native viewpoint. Deglycosylation of N-glycans followed by I2MS analysis indicates that the SARS-CoV-2 spike protein trimer contains glycans that are more difficult to remove than its MERS and SARS-CoV counterparts, and these differences are correlated with solvent accessibility. I2MS technology enables characterization of protein mass and intact glycan profile and is orthogonal to traditional mass analysis methods such as size exclusion chromatography-multiangle light scattering (SEC-MALS) and field flow fractionation-multiangle light scattering (FFF-MALS). An added advantage of I2MS is low sample use, requiring 100-fold less than other methodologies. This work highlights how I2MS technology can enable efficient development of vaccines and therapeutics for pharmaceutical development.
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Affiliation(s)
- Alyssa Q Stiving
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - David J Foreman
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Zachary L VanAernum
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Eberhard Durr
- Infectious Diseases and Vaccines Discovery, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Shiyi Wang
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Josef Vlasak
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Jennifer Galli
- Infectious Diseases and Vaccines Discovery, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Taku Tsukidate
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Xuanwen Li
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Hillary A Schuessler
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Douglas D Richardson
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New Jersey 07065, United States
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7
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Chatterjee S, Zaia J. Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples. MASS SPECTROMETRY REVIEWS 2024; 43:193-229. [PMID: 36177493 PMCID: PMC9538640 DOI: 10.1002/mas.21813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 05/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the on-going global pandemic of coronavirus disease 2019 (COVID-19) that continues to pose a significant threat to public health worldwide. SARS-CoV-2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin-converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high-throughput technique. Alternate strategies such as proteomics and glycoproteomics-based mass spectrometry enable a more detailed and holistic view of the viral proteins and host-pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS-CoV-2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS-CoV-2 from biological complex matrices to identify potential COVID-19 markers.
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Affiliation(s)
- Sayantani Chatterjee
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
- Bioinformatics ProgramBoston University School of MedicineBostonMassachusettsUSA
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Moy AB, Kamath A, Ternes S, Kamath J. The Challenges to Advancing Induced Pluripotent Stem Cell-Dependent Cell Replacement Therapy. MEDICAL RESEARCH ARCHIVES 2023; 11:4784. [PMID: 38188933 PMCID: PMC10768945 DOI: 10.18103/mra.v11i11.4784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Induced pluripotent stem cells (iPSC) represent a potentially exciting regenerative-medicine cell therapy for several chronic conditions such as macular degeneration, soft tissue and orthopedic conditions, cardiopulmonary disease, cancer, neurodegenerative disorders and metabolic disorders. The field of iPSC therapeutics currently exists at an early stage of development. There are several important stakeholders that include academia, industry, regulatory agencies, financial institutions and patients who are committed to advance the field. Yet, unlike more established therapeutic modalities like small and large molecules, iPSC therapies pose significant unique challenges with respect to safety, potency, genetic stability, immunogenicity, tumorgenicity, cell reproducibility, scalability and engraftment. The aim of this review article is to highlight the unique technical challenges that need to be addressed before iPSC technology can be fully realized as a cell replacement therapy. Additionally, this manuscript offers some potential solutions and identifies areas of focus that should be considered in order for the iPSC field to achieve its promise. The scope of this article covers the following areas: (1) the impact of different iPSC reprogramming methods on immunogenicity and tumorigenicity; (2) the effect of genetic instability on cell reproducibility and differentiation; (3) the role of growth factors and post-translational modification on differentiation and cell scalability; (4) the potential use of gene editing in improving iPSC differentiation; (5) the advantages and disadvantages between autologous and allogeneic cell therapy; (6) the regulatory considerations in developing a viable and reproducible cell product; and (7) the impact of local tissue inflammation on cell engraftment and cell viability.
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Affiliation(s)
- Alan B. Moy
- Cellular Engineering Technologies, Inc. Coralville, IA, 52241
- John Paul II Medical Research Institute, Coralville, IA 52241
| | - Anant Kamath
- Cellular Engineering Technologies, Inc. Coralville, IA, 52241
| | - Sara Ternes
- Cellular Engineering Technologies, Inc. Coralville, IA, 52241
| | - Jay Kamath
- John Paul II Medical Research Institute, Coralville, IA 52241
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Ballard CJ, Paserba MR, Paul Daniel EJ, Hurtado-Guerrero R, Gerken TA. Polypeptide N-acetylgalactosaminyltransferase (GalNAc-T) isozyme surface charge governs charge substrate preferences to modulate mucin type O-glycosylation. Glycobiology 2023; 33:817-836. [PMID: 37555669 PMCID: PMC10629720 DOI: 10.1093/glycob/cwad066] [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: 05/31/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023] Open
Abstract
A large family of polypeptide N-acetylgalactosaminyltransferases (GalNAc-Ts) initiate mucin type O-glycosylation transferring α-GalNAc from a UDP-GalNAc donor to the hydroxyl groups of Ser and Thr residues of peptides and proteins, thereby defining sites of O-glycosylation. Mutations and differential expression of several GalNAc-Ts are associated with many disease states including cancers. The mechanisms by which these isozymes choose their targets and their roles in disease are not fully understood. We previously showed that the GalNAc-Ts possess common and unique specificities for acceptor type, peptide sequence and prior neighboring, and/or remote substrate GalNAc glycosylation. In the present study, the role of flanking charged residues was investigated using a library of charged peptide substrates containing the central -YAVTPGP- acceptor sequence. Eleven human and one bird GalNAc-T were initially characterized revealing a range of preferences for net positive, net negative, or unique combinations of flanking N- and/or C-terminal charge, correlating to each isozyme's different electrostatic surface potential. It was further found that isoforms with high sequence identity (>70%) within a subfamily can possess vastly different charge specificities. Enzyme kinetics, activities obtained at elevated ionic strength, and molecular dynamics simulations confirm that the GalNAc-Ts differently recognize substrate charge outside the common +/-3 residue binding site. These electrostatic interactions impact how charged peptide substrates bind/orient on the transferase surface, thus modulating their activities. In summary, we show the GalNAc-Ts utilize more extended surfaces than initially thought for binding substrates based on electrostatic, and likely other hydrophobic/hydrophilic interactions, furthering our understanding of how these transferases select their target.
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Affiliation(s)
- Collin J Ballard
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Miya R Paserba
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Ramón Hurtado-Guerrero
- Department of Biomedical Engineering, The Institute for 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, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
- Fundación ARAID, Zaragoza 50018, Spain
| | - Thomas A Gerken
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
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Onigbinde S, Reyes CDG, Fowowe M, Daramola O, Atashi M, Bennett AI, Mechref Y. Variations in O-Glycosylation Patterns Influence Viral Pathogenicity, Infectivity, and Transmissibility in SARS-CoV-2 Variants. Biomolecules 2023; 13:1467. [PMID: 37892149 PMCID: PMC10604390 DOI: 10.3390/biom13101467] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023] Open
Abstract
The highly glycosylated S protein plays a vital role in host cell invasion, making it the principal target for vaccine development. Differences in mutations observed on the spike (S) protein of SARS-CoV-2 variants may result in distinct glycosylation patterns, thus influencing immunological evasion, infectivity, and transmissibility. The glycans can mask key epitopes on the S1 protein and alter its structural conformation, allowing the virus to escape the immune system. Therefore, we comprehensively characterize O-glycosylation in eleven variants of SARS-CoV-2 S1 subunits to understand the differences observed in the biology of the variants. In-depth characterization was performed with a double digestion strategy and an efficient LC-MS/MS approach. We observed that O-glycosylation is highly conserved across all variants in the region between the NTD and RBD, whereas other domains and regions exhibit variation in O-glycosylation. Notably, omicron has the highest number of O-glycosylation sites on the S1 subunit. Also, omicron has the highest level of sialylation in the RBD and RBM functional motifs. Our findings may shed light on how differences in O-glycosylation impact viral pathogenicity in variants of SARS-CoV-2 and facilitate the development of a robust vaccine with high protective efficacy against the variants of concern.
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Affiliation(s)
| | | | | | | | | | | | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (S.O.); (C.D.G.R.); (M.F.); (O.D.); (M.A.); (A.I.B.)
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11
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Reyes CDG, Onigbinde S, Sanni A, Bennett AI, Jiang P, Daramola O, Ahmadi P, Fowowe M, Atashi M, Sandilya V, Hakim MA, Mechref Y. N-Glycome Profile of the Spike Protein S1: Systemic and Comparative Analysis from Eleven Variants of SARS-CoV-2. Biomolecules 2023; 13:1421. [PMID: 37759821 PMCID: PMC10526240 DOI: 10.3390/biom13091421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/01/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
The SARS-CoV-2 virus rapidly spread worldwide, threatening public health. Since it emerged, the scientific community has been engaged in the development of effective therapeutics and vaccines. The subunit S1 in the spike protein of SARS-CoV-2 mediates the viral entry into the host and is therefore one of the major research targets. The S1 protein is extensively glycosylated, and there is compelling evidence that glycans protect the virus' active site from the human defense system. Therefore, investigation of the S1 protein glycome alterations in the different virus variants will provide a view of the glycan evolution and its relationship with the virus pathogenesis. In this study, we explored the N-glycosylation expression of the S1 protein for eleven SARS-CoV-2 variants: five variants of concern (VOC), including alpha, beta, gamma, delta, and omicron, and six variants of interest (VOI), including epsilon, eta, iota, lambda, kappa, and mu. The results showed significant differences in the N-glycome abundance of all variants. The N-glycome of the VOC showed a large increase in the abundance of sialofucosylated glycans, with the greatest abundance in the omicron variant. In contrast, the results showed a large abundance of fucosylated glycans for most of the VOI. Two glycan compositions, GlcNAc4,Hex5,Fuc,NeuAc (4-5-1-1) and GlcNAc6,Hex8,Fuc,NeuAc (6-8-1-1), were the most abundant structures across all variants. We believe that our data will contribute to understanding the S1 protein's structural differences between SARS-CoV-2 mutations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (C.D.G.R.); (S.O.); (A.S.); (A.I.B.); (P.J.); (O.D.); (P.A.); (M.F.); (M.A.); (V.S.); (M.A.H.)
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12
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Khalid K, Poh CL. The development of DNA vaccines against SARS-CoV-2. Adv Med Sci 2023; 68:213-226. [PMID: 37364379 PMCID: PMC10290423 DOI: 10.1016/j.advms.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/07/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND The COVID-19 pandemic exerted significant impacts on public health and global economy. Research efforts to develop vaccines at warp speed against SARS-CoV-2 led to novel mRNA, viral vectored, and inactivated vaccines being administered. The current COVID-19 vaccines incorporate the full S protein of the SARS-CoV-2 Wuhan strain but rapidly emerging variants of concern (VOCs) have led to significant reductions in protective efficacies. There is an urgent need to develop next-generation vaccines which could effectively prevent COVID-19. METHODS PubMed and Google Scholar were systematically reviewed for peer-reviewed papers up to January 2023. RESULTS A promising solution to the problem of emerging variants is a DNA vaccine platform since it can be easily modified. Besides expressing whole protein antigens, DNA vaccines can also be constructed to include specific nucleotide genes encoding highly conserved and immunogenic epitopes from the S protein as well as from other structural/non-structural proteins to develop effective vaccines against VOCs. DNA vaccines are associated with low transfection efficiencies which could be enhanced by chemical, genetic, and molecular adjuvants as well as delivery systems. CONCLUSIONS The DNA vaccine platform offers a promising solution to the design of effective vaccines. The challenge of limited immunogenicity in humans might be solved through the use of genetic modifications such as the addition of nuclear localization signal (NLS) peptide gene, strong promoters, MARs, introns, TLR agonists, CD40L, and the development of appropriate delivery systems utilizing nanoparticles to increase uptake by APCs in enhancing the induction of potent immune responses.
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Affiliation(s)
- Kanwal Khalid
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia.
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13
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A urine-based ELISA with recombinant non-glycosylated SARS-CoV-2 spike protein for detecting anti-SARS-CoV-2 spike antibodies. Sci Rep 2023; 13:4345. [PMID: 36927952 PMCID: PMC10018619 DOI: 10.1038/s41598-023-31382-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Serological assays have been widely used to detect anti-SARS-CoV-2 antibodies, which are generated from previous exposure to the virus or after vaccination. The presence of anti-SARS-CoV-2 Nucleocapsid antibodies was recently reported in patients´ urine using an in-house urine-based ELISA-platform, allowing a non-invasive way to collect clinical samples and assess immune conversion. In the current study, we evaluated and validated another in-house urine-based ELISA for the detection of anti-SARS-CoV-2 Spike antibodies. Three partial recombinant SARS-CoV-2 Spike proteins comprising the Receptor Binding Domain, expressed in eukaryotic or prokaryotic systems, were tested in an ELISA platform against a panel of over 140 urine and paired serum samples collected from 106 patients confirmed positive for SARS-CoV-2 by qRT-PCR. The key findings from our study were that anti-SARS-CoV-2 Spike antibodies could be detected in urine samples and that the prokaryotic expression of the rSARS-CoV-2 Spike protein was not a barrier to obtain relatively high serology efficiency for the urine-based assay. Thus, use of a urine-based ELISA assay with partial rSARS-CoV-2 Spike proteins, expressed in a prokaryotic system, could be considered as a convenient tool for screening for the presence of anti-SARS-CoV-2 Spike antibodies, and overcome the difficulties arising from sample collection and the need for recombinant proteins produced with eukaryotic expression systems.
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14
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Miller RM, Perkins GL, Bush D, Tartiere A, DeGraan‐Weber N. Glycopeptide characterization of Sf9-derived SARS-CoV-2 spike protein recombinant vaccine candidates expedited by the use of glycopeptide libraries. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9452. [PMID: 36478308 PMCID: PMC9877958 DOI: 10.1002/rcm.9452] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
RATIONALE We report the N-glycosylation pattern of Sf9 insect cell-derived recombinant spike proteins being developed as candidate vaccine antigens for SARS-CoV-2 (COVID-19) (Sanofi). The method has been optimised to produce peptides with single, isolated glycosylation sites using multiple protease digests. The development and use of glycopeptide libraries from previous developmental phases allowed for faster analysis than processing datasets from individual batches from first principles. METHODS Purified spike proteins were reduced, alkylated, and digested with proteolytic enzymes. Three different protease digests were utilised to generate peptides with isolated glycosylation sites. The glycopeptides were then analysed using a Waters Q-TOF while using a data-dependent acquisition mass spectrometry experiment. Glycopeptide mapping data processing and glycan classification were performed using Genedata Expressionist via a specialised workflow that used libraries of previously detected glycopeptides to greatly reduce processing time. RESULTS Two different spike proteins from six manufacturers were analysed. There was a strong similarity at each site across batches and manufacturers. The majority of the glycans present were of the truncated class, although at sites N61, N234, and N717/714 high mannose structures were dominant and at N1173/1170 aglycosylation was dominant for both variant proteins. A comparison was performed on a commercially available spike protein and our results were found to be similar to those of earlier reports. CONCLUSIONS Our data clearly show that the overall glycosylation pattern of both spike protein variants was highly similar from batch to batch, and between materials produced at different manufacturing facilities. The use of our glycopeptide libraries greatly expedited the generation of site-specific glycan occupancy data for a large glycoprotein. We compared our method with previously obtained data from a commercially available insect cell-derived spike protein and the results were comparable to published findings.
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15
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Huang J, Hou S, An J, Zhou C. In-depth characterization of protein N-glycosylation for a COVID-19 variant-design vaccine spike protein. Anal Bioanal Chem 2023; 415:1455-1464. [PMID: 36698045 PMCID: PMC9878482 DOI: 10.1007/s00216-023-04533-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/25/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023]
Abstract
COVID-19 is caused by SARS-CoV-2 infection and remains one of the biggest pandemics around the world since 2019. Vaccination has proved to be an effective way of preventing SARS-CoV-2 infection and alleviating the hospitalization burden. Among different forms of COVID-19 vaccine design, the spike protein of SARS-CoV-2 virus is widely used as a candidate vaccine antigen. As a surface protein on the virus envelop, the spike was reported to be heavily N-glycosylated and glycosylation had a great impact on its immunogenicity and efficacy. Besides, N-glycosylation might vary greatly on different expression systems and sequence variant designs. Therefore, comprehensive analysis of spike N-glycosylation is of great significance for better vaccine understanding and quality control. In this study, full characterization of N-glycosylation was performed for a Chinese Hamster Ovary (CHO) cell expressed variant-designed spike protein. The spike protein featured the latest six-proline substitution design together with the incorporation of a combination of mutation sites. Trypsin and Glu-C digestion coupled with PNGase F strategies were adopted, and effective LC-MS/MS methods were applied to analyze samples. As a result, a total of 19 N-glycosites were identified in the recombinant pike protein at intact N-glycopeptide level. Quantitative analysis of released glycan by LC-MS/MS was also performed, and 31 high-abundance N-glycans were identified. Sequencing analysis of glycan was further provided to assist glycan structure confirmation. Moreover, all of the analyses were performed on three consecutive manufactured batches and the glycosylation results on both glycosite and glycans showed good batch-to-batch consistency. Thus, the reported analytical strategy and N-glycosylation information may well facilitate studies on SARS-CoV-2 spike protein analysis and quality studies.
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Affiliation(s)
| | - Shouzeng Hou
- Shanghai Zerun Biotech Co., Ltd, Shanghai, China
| | - Jiao An
- Shanghai Zerun Biotech Co., Ltd, Shanghai, China
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16
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Liu Z, Xu M, Zhang W, Miao X, Wang PG, Li S, Yang S. Recent development in hydrophilic interaction liquid chromatography stationary materials for glycopeptide analysis. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:4437-4448. [PMID: 36300821 DOI: 10.1039/d2ay01369j] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein glycosylation is one of the most important post-translational modifications, and aberrant glycosylation is associated with the occurrence and development of diseases. Deciphering abnormal glycosylation changes can identify disease-specific signatures to facilitate the discovery of potential disease biomarkers. However, glycosylation analysis is challenging due to the diversity of glycans, heterogeneity of glycosites, and poor electrospray ionization of mass spectrometry. To overcome these obstacles, glycosylation is often elucidated using enriched glycopeptides by removing highly abundant non-glycopeptides. Hydrophilic interaction liquid chromatography (HILIC) is widely used for glycopeptide enrichment due to its excellent selectivity and specificity to hydrophilic glycans and compatibility with mass spectrometry. However, the development of HILIC has lagged far behind hydrophobic interaction chromatography, so efforts to further improve the performance of HILIC are beneficial for glycosylation analysis. This review discusses recent developments in HILIC materials and their advanced applications. Based on the physiochemical properties of glycopeptides, the use of amino acids or peptides as stationary phases showed improved enrichment and separation of glycopeptides. We can envision that the use of glycopeptides as stationary phases would definitely further improve the selectivity and specificity of HILIC for glycosylation analysis.
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Affiliation(s)
- Zhaoliang Liu
- 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.
| | - Wenqi Zhang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China.
- Nanjing Apollomics Biotech, Inc., Nanjing, Jiangsu 210033, China.
| | - Xinyu Miao
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China.
- Nanjing Apollomics Biotech, Inc., Nanjing, Jiangsu 210033, China.
| | - Perry G Wang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA
| | - Shuwei Li
- Nanjing Apollomics Biotech, Inc., Nanjing, Jiangsu 210033, China.
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China.
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17
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Dong X, Li X, Chen C, Zhang X, Liang X. Systematic analysis and comparison of O-glycosylation of five recombinant spike proteins in β-coronaviruses. Anal Chim Acta 2022; 1230:340394. [PMID: 36192065 PMCID: PMC9478876 DOI: 10.1016/j.aca.2022.340394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/27/2022] [Accepted: 09/11/2022] [Indexed: 12/01/2022]
Abstract
β-coronaviruses (β-CoVs), representative with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), depend on their highly glycosylated spike proteins to mediate cell entry and membrane fusion. Compared with the extensively identified N-glycosylation, less is known about O-glycosylation of β-CoVs S proteins, let alone its biological functions. Herein we comprehensively characterized O-glycosylation of five recombinant β-CoVs S1 subunits and revealed the macro- and micro-heterogeneity nature of site-specific O-glycosylation. We also uncovered the O-glycosylation differences between SARS-CoV-2 and its natural D614G mutant on functional domains. This work describes the systematic O-glycosylation analysis of β-CoVs S1 proteins and will help to guide the related vaccines and antiviral drugs development.
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Affiliation(s)
- Xuefang Dong
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China; Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, PR China.
| | - Cheng Chen
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Xiaofei Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China; Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, PR China.
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18
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Zhu B, Chen Z, Shen J, Xu Y, Lan R, Sun S. Structural- and Site-Specific N-Glycosylation Characterization of COVID-19 Virus Spike with StrucGP. Anal Chem 2022; 94:12274-12279. [PMID: 36036581 PMCID: PMC9454267 DOI: 10.1021/acs.analchem.2c02265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/23/2022] [Indexed: 11/28/2022]
Abstract
The spike (S) protein plays a key role in COVID-19 (SARS-CoV-2) infection and host-cell entry. Previous studies have systematically analyzed site-specific glycan compositions as well as many important structural motifs of the S protein. Here, we further provide structural-clear N-glycosylation of the S protein at a site-specific level by using our recently developed structural- and site-specific N-glycoproteomics sequencing algorithm, StrucGP. In addition to the common N-glycans as detected in previous studies, many uncommon glycosylation structures such as LacdiNAc structures, Lewis structures, Mannose 6-phosphate (M6P) residues, and bisected core structures were unambiguously mapped at a total of 20 glycosites in the S protein trimer and protomer. These data further support the glycosylation structural-functional investigations of the COVID-19 virus spike.
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Affiliation(s)
- Bojing Zhu
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province 710069, China
| | - Zexuan Chen
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province 710069, China
| | - Jiechen Shen
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province 710069, China
| | - Yintai Xu
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province 710069, China
| | - Rongxia Lan
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province 710069, China
| | - Shisheng Sun
- College of Life Sciences, Northwest University, Xi’an, Shaanxi Province 710069, China
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19
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Tripathi N, Goel B, Bhardwaj N, Vishwakarma RA, Jain SK. Exploring the Potential of Chemical Inhibitors for Targeting Post-translational Glycosylation of Coronavirus (SARS-CoV-2). ACS OMEGA 2022; 7:27038-27051. [PMID: 35937682 PMCID: PMC9344791 DOI: 10.1021/acsomega.2c02345] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/08/2022] [Indexed: 06/09/2023]
Abstract
The Spike (S) protein of SARS-CoV-2 expressed on the viral cell surface is of particular importance as it facilitates viral entry into the host cells. The S protein is heavily glycosylated with 22 N-glycosylation sites and a few N-glycosylation sites. During the viral surface protein synthesis via the host ribosomal machinery, glycosylation is an essential step in post-translational modifications (PTMs) and consequently vital for its life cycle, structure, immune evasion, and cell infection. Interestingly, the S protein of SARS-CoV-2 and the host receptor protein, ACE2, are also extensively glycosylated and these surface glycans are critical for the viral-host cell interaction for viral entry. The glycosylation pathway of both virus (hijacked from the host biosynthetic machinery) and target cells crucially affect SARS-CoV-2 infection at different levels. For example, the glycosaminoglycans (GAGs) of host cells serve as a cofactor as they interact with the receptor-binding domain (RBD) of S-glycoprotein and play a protective role in host immune evasion via masking the viral peptide epitopes. Hence, the post-translational glycan biosynthesis, processing, and transport events could be potential targets for developing therapeutic drugs and vaccines. Especially, inhibition of the N-glycan biosynthesis pathway amplifies S protein proteolysis and, thus, blocks viral entry. The chemical inhibitors of SARS-CoV-2 glycosylation could be evaluated for Covid-19. In this review, we discuss the current status of the chemical inhibitors (both natural and synthetically designed inhibitors) of viral glycosylation for Covid-19 and provide a future perspective. It could be an important strategy in targeting the various emerging SARS-CoV-2 variants of concern (VOCs), as these inhibitors are postulated to aid in reducing the viral load as well as infectivity.
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Affiliation(s)
- Nancy Tripathi
- Department
of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, Uttar Pradesh, India
| | - Bharat Goel
- Department
of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, Uttar Pradesh, India
| | - Nivedita Bhardwaj
- Department
of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, Uttar Pradesh, India
| | - Ram A. Vishwakarma
- Council
of Scientific and Industrial Research, Anusandhan
Bhavan, Rafi Marg, New Delhi 110001, India
| | - Shreyans K. Jain
- Department
of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, Uttar Pradesh, India
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20
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Azali MA, Mohamed S, Harun A, Hussain FA, Shamsuddin S, Johan MF. Application of Baculovirus Expression Vector system (BEV) for COVID-19 diagnostics and therapeutics: a review. J Genet Eng Biotechnol 2022; 20:98. [PMID: 35792966 PMCID: PMC9259773 DOI: 10.1186/s43141-022-00368-7] [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: 02/24/2022] [Accepted: 05/20/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND The baculovirus expression vector system has been developed for expressing a wide range of proteins, including enzymes, glycoproteins, recombinant viruses, and vaccines. The availability of the SARS-CoV-2 genome sequence has enabled the synthesis of SARS-CoV2 proteins in a baculovirus-insect cell platform for various applications. The most cloned SARS-CoV-2 protein is the spike protein, which plays a critical role in SARS-CoV-2 infection. It is available in its whole length or as subunits like S1 or the receptor-binding domain (RBD). Non-structural proteins (Nsps), another recombinant SARS-CoV-2 protein generated by the baculovirus expression vector system (BEV), are used in the identification of new medications or the repurposing of existing therapies for the treatment of COVID-19. Non-SARS-CoV-2 proteins generated by BEV for SARS-CoV-2 diagnosis or treatment include moloney murine leukemia virus reverse transcriptase (MMLVRT), angiotensin converting enzyme 2 (ACE2), therapeutic proteins, and recombinant antibodies. The recombinant proteins were modified to boost the yield or to stabilize the protein. CONCLUSION This review covers the wide application of the recombinant protein produced using the baculovirus expression technology for COVID-19 research. A lot of improvements have been made to produce functional proteins with high yields. However, there is still room for improvement and there are parts of this field of research that have not been investigated yet.
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Affiliation(s)
- Muhammad Azharuddin Azali
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.,School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, 22200, Besut, Terengganu, Malaysia
| | - Salmah Mohamed
- School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, 22200, Besut, Terengganu, Malaysia
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Faezahtul Arbaeyah Hussain
- Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Shaharum Shamsuddin
- School of Health Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Muhammad Farid Johan
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
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21
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Gao Z, Wu Z, Han Y, Zhang X, Hao P, Xu M, Huang S, Li S, Xia J, Jiang J, Yang S. Aberrant Fucosylation of Saliva Glycoprotein Defining Lung Adenocarcinomas Malignancy. ACS OMEGA 2022; 7:17894-17906. [PMID: 35664632 PMCID: PMC9161393 DOI: 10.1021/acsomega.2c01193] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Aberrant glycosylation is a hallmark of cancer found during tumorigenesis and tumor progression. Lung cancer (LC) induced by oncogene mutations has been detected in the patient's saliva, and saliva glycosylation has been altered. Saliva contains highly glycosylated glycoproteins, the characteristics of which may be related to various diseases. Therefore, elucidating cancer-specific glycosylation in the saliva of healthy, non-cancer, and cancer patients can reveal whether tumor glycosylation has unique characteristics for early diagnosis. In this work, we used a solid-phase chemoenzymatic method to study the glycosylation of saliva glycoproteins in clinical specimens. The results showed that the α1,6-core fucosylation of glycoproteins was increased in cancer patients, whereas α1,2 or α1,3 fucosylation was significantly increased. We further analyzed the expression of fucosyltransferases responsible for α1,2, α1,3, and α1,6 fucosylation. The fucosylation of the saliva of cancer patients is drastically different from that of non-cancer or health controls. These results indicate that the glycoform of saliva fucosylation distinguishes LC from other diseases, and this feature has the potential to diagnose lung adenocarcinoma.
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Affiliation(s)
- Ziyuan Gao
- Center
for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
- Department
of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Pinghai Road No. 899, Suzhou 215000, China
| | - Zhen Wu
- State
Key Laboratory of Genetic Engineering, Department of Biochemistry,
School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ying Han
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
| | - Xumin Zhang
- State
Key Laboratory of Genetic Engineering, Department of Biochemistry,
School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Piliang Hao
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
| | - Mingming Xu
- Center
for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Shan Huang
- Center
for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Shuwei Li
- Nanjing
Apollomics Biotech, Inc., Nanjing, Jiangsu 210033, China
| | - Jun Xia
- Department
of Clinical Laboratory Center, Zhejiang Provincial People’s
Hospital, People’s Hospital of Hangzhou
Medical College, Hangzhou, Zhejiang 310014, China
| | - Junhong Jiang
- Department
of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Pinghai Road No. 899, Suzhou 215000, China
- Department
of Pulmonary and Critical Care Medicine, Dushu Lake Hospital, Affiliated to Soochow University, Chongwen Road No. 9, Suzhou 215000, China
| | - Shuang Yang
- Center
for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
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22
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Ruocco V, Strasser R. Transient Expression of Glycosylated SARS-CoV-2 Antigens in Nicotiana benthamiana. PLANTS (BASEL, SWITZERLAND) 2022; 11:1093. [PMID: 35448821 PMCID: PMC9033091 DOI: 10.3390/plants11081093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 12/14/2022]
Abstract
The current COVID-19 pandemic very dramatically shows that the world lacks preparedness for novel viral diseases. In addition to newly emerging viruses, many known pathogenic viruses such as influenza are constantly evolving, leading to frequent outbreaks with severe diseases and deaths. Hence, infectious viruses are a recurrent burden to our daily life, and powerful strategies to stop the spread of human pathogens and disease progression are of utmost importance. Transient plant-based protein expression is a technology that allows fast and highly flexible manufacturing of recombinant viral proteins and, thus, can contribute to infectious disease detection and prevention. This review highlights recent progress in the transient production of viral glycoproteins in N. benthamiana with a focus on SARS-CoV-2-derived viral antigens.
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Affiliation(s)
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria;
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23
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Stagnoli S, Peccati F, Connell SR, Martinez-Castillo A, Charro D, Millet O, Bruzzone C, Palazon A, Ardá A, Jiménez-Barbero J, Ereño-Orbea J, Abrescia NGA, Jiménez-Osés G. Assessing the Mobility of Severe Acute Respiratory Syndrome Coronavirus-2 Spike Protein Glycans by Structural and Computational Methods. Front Microbiol 2022; 13:870938. [PMID: 35495643 PMCID: PMC9053831 DOI: 10.3389/fmicb.2022.870938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Two years after its emergence, the coronavirus disease-2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) remains difficult to control despite the availability of several vaccines. The extensively glycosylated SARS-CoV-2 spike (S) protein, which mediates host cell entry by binding to the angiotensin converting enzyme 2 (ACE2) through its receptor binding domain (RBD), is the major target of neutralizing antibodies. Like to many other viral fusion proteins, the SARS-CoV-2 spike protein utilizes a glycan shield to thwart the host immune response. To grasp the influence of chemical signatures on carbohydrate mobility and reconcile the cryo-EM density of specific glycans we combined our cryo-EM map of the S ectodomain to 4.1 Å resolution, reconstructed from a limited number of particles, and all-atom molecular dynamics simulations. Chemical modifications modeled on representative glycans (defucosylation, sialylation and addition of terminal LacNAc units) show no significant influence on either protein shielding or glycan flexibility. By estimating at selected sites the local correlation between the full density map and atomic model-based maps derived from molecular dynamics simulations, we provide insight into the geometries of the α-Man-(1→3)-[α-Man-(1→6)-]-β-Man-(1→4)-β-GlcNAc(1→4)-β-GlcNAc core common to all N-glycosylation sites.
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Affiliation(s)
- Soledad Stagnoli
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Francesca Peccati
- Computational Chemistry Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Sean R. Connell
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Structural Biology Unit, BioCruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Ane Martinez-Castillo
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Diego Charro
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Oscar Millet
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Chiara Bruzzone
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Asis Palazon
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Cancer Immunology and Immunotherapy Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Ana Ardá
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Chemical Glycobiology Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Jesús Jiménez-Barbero
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Chemical Glycobiology Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - June Ereño-Orbea
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Chemical Glycobiology Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Nicola G. A. Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Nicola G. A. Abrescia,
| | - Gonzalo Jiménez-Osés
- Computational Chemistry Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Gonzalo Jiménez-Osés,
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24
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Escobar EE, Wang S, Goswami R, Lanzillotti MB, Li L, McLellan JS, Brodbelt JS. Analysis of Viral Spike Protein N-Glycosylation Using Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2022; 94:5776-5784. [PMID: 35388686 PMCID: PMC9272412 DOI: 10.1021/acs.analchem.1c04874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Characterization of protein glycosylation by tandem mass spectrometry remains challenging owing to the vast diversity of oligosaccharides bound to proteins, the variation in monosaccharide linkage patterns, and the lability of the linkage between the glycan and protein. Here, we have adapted an HCD-triggered-ultraviolet photodissociation (UVPD) approach for the simultaneous localization of glycosites and full characterization of both glycan compositions and intersaccharide linkages, the latter provided by extensive cross-ring cleavages enabled by UVPD. The method is applied to study glycan compositions based on analysis of glycopeptides from proteolytic digestion of recombinant human coronaviruse spike proteins from SARS-CoV-2 and HKU1. UVPD reveals unique intersaccharide linkage information and is leveraged to localize N-linked glycoforms with confidence.
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Affiliation(s)
- Edwin E Escobar
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Shuaishuai Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | | | - Michael B Lanzillotti
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Lei Li
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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25
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Fang P, Ji Y, Oellerich T, Urlaub H, Pan KT. Strategies for Proteome-Wide Quantification of Glycosylation Macro- and Micro-Heterogeneity. Int J Mol Sci 2022; 23:ijms23031609. [PMID: 35163546 PMCID: PMC8835892 DOI: 10.3390/ijms23031609] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/03/2022] Open
Abstract
Protein glycosylation governs key physiological and pathological processes in human cells. Aberrant glycosylation is thus closely associated with disease progression. Mass spectrometry (MS)-based glycoproteomics has emerged as an indispensable tool for investigating glycosylation changes in biological samples with high sensitivity. Following rapid improvements in methodologies for reliable intact glycopeptide identification, site-specific quantification of glycopeptide macro- and micro-heterogeneity at the proteome scale has become an urgent need for exploring glycosylation regulations. Here, we summarize recent advances in N- and O-linked glycoproteomic quantification strategies and discuss their limitations. We further describe a strategy to propagate MS data for multilayered glycopeptide quantification, enabling a more comprehensive examination of global and site-specific glycosylation changes. Altogether, we show how quantitative glycoproteomics methods explore glycosylation regulation in human diseases and promote the discovery of biomarkers and therapeutic targets.
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Affiliation(s)
- Pan Fang
- Department of Biochemistry and Molecular Biology, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China;
| | - Yanlong Ji
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany;
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, Johann Wolfgang Goethe University, 60596 Frankfurt am Main, Germany
| | - Thomas Oellerich
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, Johann Wolfgang Goethe University, 60596 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany;
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
- Correspondence: (H.U.); (K.-T.P.)
| | - Kuan-Ting Pan
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, Johann Wolfgang Goethe University, 60596 Frankfurt am Main, Germany
- Correspondence: (H.U.); (K.-T.P.)
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26
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Gao Z, Xu M, Yue S, Shan H, Xia J, Jiang J, Yang S. Abnormal sialylation and fucosylation of saliva glycoproteins: Characteristics of lung cancer-specific biomarkers. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2021; 3:100079. [PMID: 35005612 PMCID: PMC8718573 DOI: 10.1016/j.crphar.2021.100079] [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: 10/25/2021] [Revised: 10/31/2021] [Accepted: 12/15/2021] [Indexed: 12/23/2022] Open
Abstract
Dysregulated surface glycoproteins play an important role in tumor cell proliferation and progression. Abnormal glycosylation of these glycoproteins may activate tumor signal transduction and lead to tumor development. The tumor microenvironment alters its molecular composition, some of which regulate protein glycosylation biosynthesis. The glycosylation of saliva proteins in lung cancer patients is different from healthy controls, in which the glycans of cancer patients are highly sialylated and hyperfucosylated. Most studies have shown that O-glycans from cancer are truncated O-glycans, while N-glycans contain fucoses and sialic acids. Because glycosylation analysis is challenging, there are few reports on how glycosylation of saliva proteins is related to the occurrence or progression of lung cancer. In this review, we discussed glycoenzymes involved in protein glycosylation, their changes in tumor microenvironment, potential tumor biomarkers present in body fluids, and abnormal glycosylation of saliva or lung glycoproteins. We further explored the effect of glycosylation changes on tumor signal transduction, and emphasized the role of receptor tyrosine kinases in tumorigenesis and metastasis.
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Affiliation(s)
- Ziyuan Gao
- Center for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
- Department of Respiratory and Critical Care Medicine, Dushu Lake Hospital to Soochow University, Suzhou, Jiangsu, 215125, China
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Soochow University; Suzhou Jiangsu, 215006, China
| | - Mingming Xu
- Center for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Shuang Yue
- Center for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Huang Shan
- Center for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Jun Xia
- Department of Clinical Laboratory Center, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Junhong Jiang
- Department of Respiratory and Critical Care Medicine, Dushu Lake Hospital to Soochow University, Suzhou, Jiangsu, 215125, China
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Soochow University; Suzhou Jiangsu, 215006, China
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
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27
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Gong Y, Qin S, Dai L, Tian Z. The glycosylation in SARS-CoV-2 and its receptor ACE2. Signal Transduct Target Ther 2021; 6:396. [PMID: 34782609 PMCID: PMC8591162 DOI: 10.1038/s41392-021-00809-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/10/2021] [Accepted: 10/24/2021] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis. Here we reviewed the detections, substrates, biological functions of the glycosylation in SARS-CoV-2 proteins as well as the human receptor ACE2, and also summarized the approved and undergoing SARS-CoV-2 therapeutics associated with glycosylation. This review may not only broad the understanding of viral glycobiology, but also provide key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.
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Affiliation(s)
- Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China
| | - Suideng Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China.
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28
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Wang Q, Wang Y, Yang S, Lin C, Aliyu L, Chen Y, Parsons L, Tian Y, Jia H, Pekosz A, Betenbaugh MJ, Cipollo JF. A Linkage-specific Sialic Acid Labeling Strategy Reveals Different Site-specific Glycosylation Patterns in SARS-CoV-2 Spike Protein Produced in CHO and HEK Cell Substrates. Front Chem 2021; 9:735558. [PMID: 34631661 PMCID: PMC8497748 DOI: 10.3389/fchem.2021.735558] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/02/2021] [Indexed: 12/11/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus utilizes the extensively glycosylated spike (S) protein protruding from the viral envelope to bind to angiotensin-converting enzyme-related carboxypeptidase (ACE2) as its primary receptor to mediate host-cell entry. Currently, the main recombinant S protein production hosts are Chinese hamster ovary (CHO) and human embryonic kidney (HEK) cells. In this study, a recombinant S protein truncated at the transmembrane domain and engineered to express a C-terminal trimerization motif was transiently produced in CHO and HEK cell suspensions. To further evaluate the sialic acid linkages presenting on S protein, a two-step amidation process, employing dimethylamine and ammonium hydroxide reactions in a solid support system, was developed to differentially modify the sialic acid linkages on the glycans and glycopeptides from the S protein. The process also adds a charge to Asp and Glu which aids in ionization. We used MALDI-TOF and LC-MS/MS with electron-transfer/higher-energy collision dissociation (EThcD) fragmentation to determine global and site-specific N-linked glycosylation patterns. We identified 21 and 19 out of the 22 predicted N-glycosites of the SARS-CoV-2 S proteins produced in CHO and HEK, respectively. It was found that the N-glycosite at 1,158 position (N1158) and at 122, 282 and 1,158 positions (N122, N282 and N1158) were absent on S from CHO and HEK cells, respectively. The structural mapping of glycans of recombinant human S proteins reveals that CHO-Spike exhibits more complex and higher sialylation (α2,3-linked) content while HEK-Spike exhibits more high-mannose and a small amount of α2,3- and α2,6-linked sialic acids. The N74 site represents the most abundant glycosite on both spike proteins. The relatively higher amount of high-mannose abundant sites (N17, N234, N343, N616, N709, N717, N801, and N1134) on HEK-Spike suggests that glycan-shielding may differ among the two constructs. HEK-Spike can also provide different host immune system interaction profiles based on known immune system active lectins. Collectively, these data underscore the importance of characterizing the site-specific glycosylation of recombinant human spike proteins from HEK and CHO cells in order to better understand the impact of the production host on this complex and important protein used in research, diagnostics and vaccines.
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Affiliation(s)
- Qiong Wang
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Baltimore, MD, United States
| | - Yan Wang
- Mass Spectrometry Facility, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, United States
| | - Shuang Yang
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Baltimore, MD, United States.,Center for Clinical Mass Spectrometry, School of Pharmaceutical Sciences, Soochow University, Jiangsu, China
| | - Changyi Lin
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Lateef Aliyu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Yiqun Chen
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Lisa Parsons
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Baltimore, MD, United States
| | - Yuan Tian
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Baltimore, MD, United States
| | - Hongpeng Jia
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - John F Cipollo
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Baltimore, MD, United States
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29
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Zhang Y, Zhao W, Mao Y, Chen Y, Zheng S, Cao W, Zhu J, Hu L, Gong M, Cheng J, Yang H. O-Glycosylation Landscapes of SARS-CoV-2 Spike Proteins. Front Chem 2021; 9:689521. [PMID: 34552909 PMCID: PMC8450404 DOI: 10.3389/fchem.2021.689521] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/24/2021] [Indexed: 02/05/2023] Open
Abstract
The densely glycosylated spike (S) proteins that are highly exposed on the surface of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) facilitate viral attachment, entry, and membrane fusion. We have previously reported all the 22 N-glycosites and site-specific N-glycans in the S protein protomer. Herein, we report the O-glycosylation landscapes of SARS-CoV-2 S proteins, which were characterized through high-resolution mass spectrometry. Following digestion with trypsin and trypsin/Glu-C, and de-N-glycosylation using PNGase F, we determined the GalNAc-type O-glycosylation pattern of S proteins, including O-glycosites and the six most common O-glycans occupying them, via Byonic identification and manual validation. Finally, 255 intact O-glycopeptides composed of 50 peptides sequences and 43 O-glycosites were discovered by higher energy collision-induced dissociation (HCD), and three O-glycosites were confidently identified by electron transfer/higher energy collision-induced dissociation (EThcD) in the insect cell-expressed S protein. Most glycosites were modified by non-sialylated O-glycans such as HexNAc(1) and HexNAc(1)Hex (1). In contrast, in the human cell-expressed S protein S1 subunit, 407 intact O-glycopeptides composed of 34 peptides sequences and 30 O-glycosites were discovered by HCD, and 11 O-glycosites were unambiguously assigned by EThcD. However, the measurement of O-glycosylation occupancy hasn’t been made. Most glycosites were modified by sialylated O-glycans such as HexNAc(1)Hex (1)NeuAc (1) and HexNAc(1)Hex (1)NeuAc (2). Our results reveal that the SARS-CoV-2 S protein is an O-glycoprotein; the O-glycosites and O-glycan compositions vary with the host cell type. These comprehensive O-glycosylation landscapes of the S protein are expected to provide novel insights into the viral binding mechanism and present a strategy for the development of vaccines and targeted drugs.
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Affiliation(s)
- Yong Zhang
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjun Zhao
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yonghong Mao
- Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Yaohui Chen
- Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Shanshan Zheng
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Cao
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiang Zhu
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Liqiang Hu
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Meng Gong
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiu Cheng
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Yang
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
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