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Zhang H, Liu S, Wang Y, Huang H, Sun L, Yuan Y, Cheng L, Liu X, Ning K. Deep learning enhanced the diagnostic merit of serum glycome for multiple cancers. iScience 2024; 27:108715. [PMID: 38226168 PMCID: PMC10788220 DOI: 10.1016/j.isci.2023.108715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/24/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024] Open
Abstract
Protein glycosylation is associated with the pathogenesis of various cancers. The utilization of certain glycans in cancer diagnosis models holds promise, yet their accuracy is not always guaranteed. Here, we investigated the utility of deep learning techniques, specifically random forests combined with transfer learning, in enhancing serum glycome's discriminative power for cancer diagnosis (including ovarian cancer, non-small cell lung cancer, gastric cancer, and esophageal cancer). We started with ovarian cancer and demonstrated that transfer learning can achieve superior performance in data-disadvantaged cohorts (AUROC >0.9), outperforming the approach of PLS-DA. We identified a serum glycan-biomarker panel including 18 serum N-glycans and 4 glycan derived traits, most of which were featured with sialylation. Furthermore, we validated advantage of the transfer learning scheme across other cancer groups. These findings highlighted the superiority of transfer learning in improving the performance of glycans-based cancer diagnosis model and identifying cancer biomarkers, providing a new high-fidelity cancer diagnosis venue.
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Affiliation(s)
- Haobo Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Si Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, Fujian, China
| | - Yi Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hanhui Huang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lukang Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Youyuan Yuan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xin Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
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2
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Yin H, Zhu J. Methods for quantification of glycopeptides by liquid separation and mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:887-917. [PMID: 35099083 PMCID: PMC9339036 DOI: 10.1002/mas.21771] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/14/2021] [Accepted: 01/13/2022] [Indexed: 05/05/2023]
Abstract
Recent advances in analytical techniques provide the opportunity to quantify even low-abundance glycopeptides derived from complex biological mixtures, allowing for the identification of glycosylation differences between healthy samples and those derived from disease states. Herein, we discuss the sample preparation procedures and the mass spectrometry (MS) strategies that have facilitated glycopeptide quantification, as well as the standards used for glycopeptide quantification. For sample preparation, various glycopeptide enrichment methods are summarized including the columns used for glycopeptide separation in liquid chromatography separation. For MS analysis strategies, MS1 level-based quantification and MS2 level-based quantification are described, either with or without labeling, where we have covered isotope labeling, TMT/iTRAQ labeling, data dependent acquisition, data independent acquisition, multiple reaction monitoring, and parallel reaction monitoring. The strengths and weaknesses of these methods are compared, particularly those associated with the figures of merit that are important for clinical biomarker studies and the pathological and functional studies of glycoproteins in various diseases. Possible future developments for glycopeptide quantification are discussed.
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Affiliation(s)
- Haidi Yin
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
| | - Jianhui Zhu
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
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Liang Y, Fu B, Zhang Y, Lu H. Progress of proteomics-driven precision medicine: From a glycosylation view. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9288. [PMID: 35261114 DOI: 10.1002/rcm.9288] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 05/08/2023]
Abstract
Currently, cancer is one of the leading causes of death worldwide, partially owing to the lack of early diagnosis methods and effective therapies. With the rapid development of various omics, the precision medicine strategy becomes a promising way to increase the survival rates by considering individual differences. Glycosylation is one of the most essential protein post-translational modifications and plays important roles in a variety of biological processes. Therefore, it is highly possible to acquire understanding of the molecular mechanisms as well as discover novel potential markers for diagnosis and prognosis based on glycoproteomics research. This review summarizes the recent glycoproteomics studies about N-glycosylation of several cancer types, mainly in the past 5 years. We also highlight corresponding mass spectrometry-based analytical methods to give a brief overview on the main techniques applied in glycoproteomics.
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Affiliation(s)
- Yuying Liang
- Shanghai Cancer Center and Department of Chemistry, Fudan University, Shanghai, People's Republic of China
| | - Bin Fu
- Shanghai Cancer Center and Department of Chemistry, Fudan University, Shanghai, People's Republic of China
| | - Ying Zhang
- Shanghai Cancer Center and Department of Chemistry, Fudan University, Shanghai, People's Republic of China
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, People's Republic of China
| | - Haojie Lu
- Shanghai Cancer Center and Department of Chemistry, Fudan University, Shanghai, People's Republic of China
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, People's Republic of China
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4
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Zeng W, Zheng S, Su T, Cheng J, Mao Y, Zhong Y, Liu Y, Chen J, Zhao W, Lin T, Liu F, Li G, Yang H, Zhang Y. Comparative N-Glycoproteomics Analysis of Clinical Samples Via Different Mass Spectrometry Dissociation Methods. Front Chem 2022; 10:839470. [PMID: 35281567 PMCID: PMC8907888 DOI: 10.3389/fchem.2022.839470] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Site-specific N-glycosylation characterization requires intact N-glycopeptide analysis based on suitable tandem mass spectrometry (MS/MS) method. Electron-transfer/higher-energy collisional dissociation (EThcD), stepped collision energy/higher-energy collisional dissociation (sceHCD), higher-energy collisional dissociation-product-dependent electron-transfer dissociation (HCD-pd-ETD), and a hybrid mass spectrometry fragmentation method EThcD-sceHCD have emerged as valuable approaches for glycoprotein analysis. However, each of them incurs some compromise, necessitating the systematic performance comparisons when applied to the analysis of complex clinical samples (e.g., plasma, urine, cells, and tissues). Herein, we compared the performance of EThcD-sceHCD with those previous approaches (EThcD, sceHCD, HCD-pd-ETD, and sceHCD-pd-ETD) in the intact N-glycopeptide analysis, and determined its applicability for clinical N-glycoproteomic study. The intact N-glycopeptides of distinct samples, namely, plasma from prostate cancer (PCa) patients, urine from immunoglobulin A nephropathy (IgAN) patients, human hepatocarcinoma cell line (HepG2), and thyroid tissues from thyroid cancer (TC) patients were analyzed by these methods. We found that EThcD-sceHCD outperformed other methods in the balance of depth and accuracy of intact N-glycopeptide identification, and sceHCD and EThcD-sceHCD have good complementarity. EThcD-sceHCD holds great potential for biomarker discovery from clinical samples.
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Affiliation(s)
- Wenjuan Zeng
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Shanshan Zheng
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Su
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiahan Cheng
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Yonghong Mao
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Zhong
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Yueqiu Liu
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Jianhai Chen
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjun Zhao
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Tianhai Lin
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Fang Liu
- Division of Nephrology, West China Hospital, Sichuan University, Chengdu, China
| | - Guisen Li
- Renal Department and Institute of Nephrology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu, China
| | - Hao Yang
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Hao Yang, ; Yong Zhang,
| | - Yong Zhang
- Institutes for Systems Genetics, National Health Commission (NHC) Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Hao Yang, ; Yong Zhang,
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Abstract
Glycosylation, one of the most common post-translational modifications in mammalian cells, impacts many biological processes such as cell adhesion, proliferation and differentiation. As the most abundant glycoprotein in human serum, immunoglobulin G (IgG) plays a vital role in immune response and protection. There is a growing body of evidence suggests that IgG structure and function are modulated by attached glycans, especially N-glycans, and aberrant glycosylation is associated with disease states. In this chapter, we review IgG glycan repertoire and function, strategies for profiling IgG N-glycome and recent studies. Mass spectrometry (MS) based techniques are the most powerful tools for profiling IgG glycome. IgG glycans can be divided into high-mannose, biantennary complex and hybrid types, modified with mannosylation, core-fucosylation, galactosylation, bisecting GlcNAcylation, or sialylation. Glycosylation of IgG affects antibody half-life and their affinity and avidity for antigens, regulates crystallizable fragment (Fc) structure and Fcγ receptor signaling, as well as antibody effector function. Because of their critical roles, IgG N-glycans appear to be promising biomarkers for various disease states. Specific IgG glycosylation can convert a pro-inflammatory response to an anti-inflammatory activity. Accordingly, IgG glycoengineering provides a powerful approach to potentially develop effective drugs and treat disease. Based on the understanding of the functional role of IgG glycans, the development of vaccines with enhanced capacity and long-term protection are possible in the near future.
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Zhang Y, Zheng S, Mao Y, Cao W, Zhao L, Wu C, Cheng J, Liu F, Li G, Yang H. Systems analysis of plasma IgG intact N-glycopeptides from patients with chronic kidney diseases via EThcD-sceHCD-MS/MS. Analyst 2021; 146:7274-7283. [PMID: 34747425 DOI: 10.1039/d1an01657a] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Immunoglobulin G (IgG) molecules modulate an immune response. However, site-specific N-glycosylation signatures of plasma IgG in patients with chronic kidney disease (CKD) remain unclear. This study aimed to propose a novel method to explore the N-glycosylation pattern of IgG and to compare it with reported methods. We separated human plasma IgG from 58 healthy controls (HC) and 111 patients with CKD. Purified IgG molecules were digested by trypsin. Tryptic peptides without enrichment of intact N-glycopeptides were analyzed using a combination of electron-transfer/higher-energy collisional dissociation (EThcD) and stepped collision energy/higher-energy collisional dissociation (sceHCD) mass spectrometry (EThcD-sceHCD-MS/MS). This resulted in higher spectral quality, more informative fragment ions, higher Byonic score, and nearly twice the depth of intact N-glycopeptide identification than sceHCD or EThcD alone. Site-specific N-glycosylation mapping revealed that intact N-glycopeptides were differentially expressed in HC and CKD patients; thus, it can be a diagnostic tool. This study provides a method for the determination of glycosylation patterns in CKD and a framework for understanding the role of IgG in the pathophysiology of CKD. Data are available via ProteomeXchange with identifier PXD027174.
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Affiliation(s)
- Yong Zhang
- NHC Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics; National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China. .,Sichuan Provincial Engineering Laboratory of Pathology in Clinical Application, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Shanshan Zheng
- NHC Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics; National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Yonghong Mao
- Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wei Cao
- NHC Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics; National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Lijun Zhao
- Division of Nephrology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Changwei Wu
- Renal Department and Institute of Nephrology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 611731, China.
| | - Jingqiu Cheng
- NHC Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics; National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Fang Liu
- Division of Nephrology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Guisen Li
- Renal Department and Institute of Nephrology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 611731, China.
| | - Hao Yang
- NHC Key Laboratory of Transplant Engineering and Immunology, Institutes for Systems Genetics; National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China. .,Sichuan Provincial Engineering Laboratory of Pathology in Clinical Application, West China Hospital, Sichuan University, Chengdu 610041, China
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Zhang Y, Zhao W, Mao Y, Chen Y, Wang S, Zhong Y, Su T, Gong M, Du D, Lu X, Cheng J, Yang H. Site-specific N-glycosylation Characterization of Recombinant SARS-CoV-2 Spike Proteins. Mol Cell Proteomics 2021; 20:100058. [PMID: 33077685 DOI: 10.1101/2020.03.28.013276] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
The glycoprotein spike (S) on the surface of severe acute respiratory syndrome coronavirus (SARS-CoV-2) is a determinant for viral invasion and host immune response. Herein, we characterized the site-specific N-glycosylation of S protein at the level of intact glycopeptides. All 22 potential N-glycosites were identified in the S-protein protomer and were found to be preserved among the 753 SARS-CoV-2 genome sequences. The glycosites exhibited glycoform heterogeneity as expected for a human cell-expressed protein subunit. We identified masses that correspond to 157 N-glycans, primarily of the complex type. In contrast, the insect cell-expressed S protein contained 38 N-glycans, completely of the high-mannose type. Our results revealed that the glycan types were highly determined by the differential processing of N-glycans among human and insect cells, regardless of the glycosites' location. Moreover, the N-glycan compositions were conserved among different sizes of subunits. Our study indicates that the S protein N-glycosylation occurs regularly at each site, albeit the occupied N-glycans were diverse and heterogenous. This N-glycosylation landscape and the differential N-glycan patterns among distinct host cells are expected to shed light on the infection mechanism and present a positive view for the development of vaccines and targeted drugs.
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Affiliation(s)
- Yong Zhang
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjun Zhao
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yonghong Mao
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yaohui Chen
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Shisheng Wang
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Zhong
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Su
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Meng Gong
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Dan Du
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaofeng Lu
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiu Cheng
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China.
| | - Hao Yang
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China.
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Zhang Y, Zhao W, Mao Y, Chen Y, Wang S, Zhong Y, Su T, Gong M, Du D, Lu X, Cheng J, Yang H. Site-specific N-glycosylation Characterization of Recombinant SARS-CoV-2 Spike Proteins. Mol Cell Proteomics 2021; 20:100058. [PMID: 33077685 PMCID: PMC7876485 DOI: 10.1074/mcp.ra120.002295] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The glycoprotein spike (S) on the surface of severe acute respiratory syndrome coronavirus (SARS-CoV-2) is a determinant for viral invasion and host immune response. Herein, we characterized the site-specific N-glycosylation of S protein at the level of intact glycopeptides. All 22 potential N-glycosites were identified in the S-protein protomer and were found to be preserved among the 753 SARS-CoV-2 genome sequences. The glycosites exhibited glycoform heterogeneity as expected for a human cell-expressed protein subunit. We identified masses that correspond to 157 N-glycans, primarily of the complex type. In contrast, the insect cell-expressed S protein contained 38 N-glycans, completely of the high-mannose type. Our results revealed that the glycan types were highly determined by the differential processing of N-glycans among human and insect cells, regardless of the glycosites' location. Moreover, the N-glycan compositions were conserved among different sizes of subunits. Our study indicates that the S protein N-glycosylation occurs regularly at each site, albeit the occupied N-glycans were diverse and heterogenous. This N-glycosylation landscape and the differential N-glycan patterns among distinct host cells are expected to shed light on the infection mechanism and present a positive view for the development of vaccines and targeted drugs.
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Affiliation(s)
- Yong Zhang
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjun Zhao
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yonghong Mao
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yaohui Chen
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Shisheng Wang
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Zhong
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Su
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Meng Gong
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Dan Du
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaofeng Lu
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiu Cheng
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China.
| | - Hao Yang
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China; Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu, China.
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