1
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Wang H, Liu D, Meng X, Sun W, Li C, Lu H, Zheng D, Wu L, Sun S, Wang Y. Bidirectional Two-Sample Mendelian Randomization Study of Immunoglobulin G N-Glycosylation and Senescence-Associated Secretory Phenotype. Int J Mol Sci 2024; 25:6337. [PMID: 38928043 PMCID: PMC11203829 DOI: 10.3390/ijms25126337] [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: 05/22/2024] [Revised: 06/01/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Observational studies revealed changes in Immunoglobulin G (IgG) N-glycosylation during the aging process. However, it lacks causal insights and remains unclear in which direction causal relationships exist. The two-sample bidirectional Mendelian randomization (MR) design was adopted to explore causal associations between IgG N-glycans and the senescence-associated secretory phenotype (SASP). Inverse variance weighted (IVW) and Wald ratio methods were used as the main analyses, supplemented by sensitivity analyses. Forward MR analyses revealed causal associations between the glycan peak (GP) and SASP, including GP6 (odds ratio [OR] = 0.428, 95% confidence interval [CI] = 0.189-0.969) and GP17 (OR = 0.709, 95%CI = 0.504-0.995) with growth/differentiation factor 15 (GDF15), GP19 with an advanced glycosylation end-product-specific receptor (RAGE) (OR = 2.142, 95% CI = 1.384-3.316), and GP15 with matrix metalloproteinase 2 (MMP2) (OR = 1.136, 95% CI =1.008-1.282). The reverse MR indicated that genetic liability to RAGE was associated with increased levels of GP17 (OR = 1.125, 95% CI = 1.003-1.261) and GP24 (OR = 1.222, 95% CI = 1.046-1.428), while pulmonary and activation-regulated chemokines (PARC) exhibited causal associations with GP10 (OR = 1.269, 95% CI = 1.048-1.537) and GP15 (OR = 1.297, 95% CI = 1.072-1.570). The findings provided suggested evidence on the bidirectional causality between IgG N-glycans and SASP, which might reveal potential regulatory mechanisms.
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Affiliation(s)
- Haotian Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Di Liu
- Centre for Biomedical Information Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiaoni Meng
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Wenxin Sun
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Cancan Li
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Huimin Lu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Deqiang Zheng
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Lijuan Wu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Shengzhi Sun
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Youxin Wang
- School of Public Health, North China University of Science and Technology, Tangshan 063210, China
- Centre for Precision Medicine, Edith Cowan University, Perth 6027, Australia
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2
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Liu L, Liu L, Wang Y, Fang Z, Bian Y, Zhang W, Wang Z, Gao X, Zhao C, Tian M, Liu X, Qin H, Guo Z, Liang X, Dong M, Nie Y, Ye M. Robust Glycoproteomics Platform Reveals a Tetra-Antennary Site-Specific Glycan Capping with Sialyl-Lewis Antigen for Early Detection of Gastric Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306955. [PMID: 38084450 PMCID: PMC10916543 DOI: 10.1002/advs.202306955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/16/2023] [Indexed: 03/07/2024]
Abstract
The lack of efficient biomarkers for the early detection of gastric cancer (GC) contributes to its high mortality rate, so it is crucial to discover novel diagnostic targets for GC. Recent studies have implicated the potential of site-specific glycans in cancer diagnosis, yet it is challenging to perform highly reproducible and sensitive glycoproteomics analysis on large cohorts of samples. Here, a highly robust N-glycoproteomics (HRN) platform comprising an automated enrichment method, a stable microflow LC-MS/MS system, and a sensitive glycopeptide-spectra-deciphering tool is developed for large-scale quantitative N-glycoproteome analysis. The HRN platform is applied to analyze serum N-glycoproteomes of 278 subjects from three cohorts to investigate glycosylation changes of GC. It identifies over 20 000 unique site-specific glycans from discovery and validation cohorts, and determines four site-specific glycans as biomarker candidates. One candidate has branched tetra-antennary structure capping with sialyl-Lewis antigen, and it significantly outperforms serum CEA with AUC values > 0.89 compared against < 0.67 for diagnosing early-stage GC. The four-marker panel can provide improved diagnostic performances. Besides, discrimination powers of four candidates are also testified with a verification cohort using PRM strategy. This findings highlight the value of this strong tool in analyzing aberrant site-specific glycans for cancer detection.
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Affiliation(s)
- Luyao Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian116023China
- University of Chinese Academy of SciencesBeijing101408China
| | - Lei Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian116023China
- University of Chinese Academy of SciencesBeijing101408China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian116023China
| | - Zheng Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian116023China
| | - Yangyang Bian
- The College of Life SciencesNorthwest UniversityXi'an710127China
| | - Wenyao Zhang
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive DiseasesFourth Military Medical UniversityXi'an710068China
| | - Zhongyu Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian116023China
| | - Xianchun Gao
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive DiseasesFourth Military Medical UniversityXi'an710068China
| | - Changrui Zhao
- MOE Key Laboratory of Bio‐Intelligent Manufacturing, School of BioengineeringDalian University of TechnologyDalian116024China
| | - Miaomiao Tian
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive DiseasesFourth Military Medical UniversityXi'an710068China
| | - Xiaoyan Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian116023China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian116023China
| | - Zhimou Guo
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian116023China
| | - Xinmiao Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian116023China
| | - Mingming Dong
- MOE Key Laboratory of Bio‐Intelligent Manufacturing, School of BioengineeringDalian University of TechnologyDalian116024China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive DiseasesFourth Military Medical UniversityXi'an710068China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian116023China
- University of Chinese Academy of SciencesBeijing101408China
- State Key Laboratory of Medical ProteomicsBeijing102206China
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3
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Zhao Y, Raidas S, Mao Y, Li N. High-Throughput Glycan Profiling of Human Serum IgG Subclasses Using Parallel Reaction Monitoring Peptide Bond Fragmentation of Glycopeptides and Microflow LC-MS. J Proteome Res 2024; 23:585-595. [PMID: 38231888 DOI: 10.1021/acs.jproteome.3c00311] [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] [Indexed: 01/19/2024]
Abstract
LC-MS-based N-glycosylation profiling in four human serum IgG subclasses (IgG1, IgG2, IgG3, and IgG4) often requires additional affinity-based enrichment of specific IgG subclasses, owing to the high amino acid sequence similarity of Fc glycopeptides among subclasses. Notably, for IgG4 and the major allotype of IgG3, the glycopeptide precursors share identical retention time and mass and therefore cannot be distinguished based on precursor or glycan fragmentation. Here, we developed a parallel reaction monitoring (PRM)-based method for quantifying Fc glycopeptides through combined transitions generated from both glycosidic and peptide bond fragmentation. The latter enables the subpopulation of IgG3 and IgG4 to be directly distinguished according to mass differences without requiring further enrichment of specific IgG subclasses. In addition, a multinozzle electrospray emitter coupled to a capillary flow liquid chromatograph was used to increase the robustness and detection sensitivity of the method for low-yield peptide backbone fragment ions. The gradient was optimized to decrease the overall run time and make the method compatible with high-throughput analysis. We demonstrated that this method can be used to effectively monitor the relative levels of 13 representative glycoforms, with a good limit of detection for individual IgG subclasses.
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Affiliation(s)
- Yunlong Zhao
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591, United States
| | - Shivkumar Raidas
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591, United States
| | - Yuan Mao
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591, United States
| | - Ning Li
- Analytical Chemistry, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591, United States
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4
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Springer V, Zhou Y, Aguilera ÁY, Emmer Å. User-friendly platform for analysis of high mass intact proteins and glycopeptides by laser desorption/ionization-mass spectrometry based on copper oxide particles. Anal Bioanal Chem 2024; 416:861-872. [PMID: 38062198 PMCID: PMC10800303 DOI: 10.1007/s00216-023-05072-0] [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: 10/04/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 01/23/2024]
Abstract
Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) based on micro/nanostructured materials with different natures has received increasing attention for the analysis of a wide variety of analytes. However, up to now, only a few studies have shown the application of simple platforms in MALDI-MS for the identification of intact proteins. The present work reports on the application of copper oxide particles (Cu2O PS), obtained by a greener route, in combination with low amounts of 2,5-dihydroxybenzoic acid (DHB) as a novel hybrid platform. The combined Cu2O PS@DHB matrix, containing only 2.5 mg mL-1 of particles and 10 mg mL-1 of DHB, was easily applicable in MALDI-MS without surface modification of target plates. Under optimal conditions, the analysis of intact proteins up to 150,000 Da was possible, including immunoglobulin G, bovine serum albumin, and cytochrome C with adequate spot-to-spot signal reproducibility (RSD < 10%). In addition, the analysis of glycopeptides from IgG digests was carried out to prove the multipurpose application of the Cu2O PS@DHB platform in the low m/z range (2500-3000 Da). From the obtained results, it can be concluded that the optical and surface properties of as-synthesized Cu2O PS are likely to be responsible for the superior performance of Cu2O PS@DHB in comparison with conventional matrices. In this sense, the proposed user-friendly methodology opens up the prospect for possible implementation in bioanalysis and diagnostic research.
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Affiliation(s)
- Valeria Springer
- INQUISUR - Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, B8000CPB, Bahía Blanca, Buenos Aires, Argentina
| | - Yuye Zhou
- Department of Chemistry, Analytical Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden
| | - Ángela Y Aguilera
- INQUISUR - Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, B8000CPB, Bahía Blanca, Buenos Aires, Argentina
| | - Åsa Emmer
- Department of Chemistry, Analytical Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden.
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5
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Ding JH, Xiao Y, Yang F, Song XQ, Xu Y, Ding XH, Ding R, Shao ZM, Di GH, Jiang YZ. Guanosine diphosphate-mannose suppresses homologous recombination repair and potentiates antitumor immunity in triple-negative breast cancer. Sci Transl Med 2024; 16:eadg7740. [PMID: 38170790 DOI: 10.1126/scitranslmed.adg7740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer with poor prognosis. TNBCs with high homologous recombination deficiency (HRD) scores benefit from DNA-damaging agents, including platinum drugs and poly(ADP-ribose) polymerase (PARP) inhibitors, whereas those with low HRD scores still lack therapeutic options. Therefore, we sought to exploit metabolic alterations to induce HRD and sensitize DNA-damaging agents in TNBCs with low HRD scores. We systematically analyzed TNBC metabolomics and identified a metabolite, guanosine diphosphate (GDP)-mannose (GDP-M), that impeded homologous recombination repair (HRR). Mechanistically, the low expression of the upstream enzyme GDP-mannose-pyrophosphorylase-A (GMPPA) led to the endogenous up-regulation of GDP-M in TNBC. The accumulation of GDP-M in tumor cells further reduced the interaction between breast cancer susceptibility gene 2 (BRCA2) and ubiquitin-specific peptidase 21 (USP21), which promoted the ubiquitin-mediated degradation of BRCA2 to inhibit HRR. Therapeutically, we illustrated that the supplementation of GDP-M sensitized DNA-damaging agents to impair tumor growth in both in vitro (cancer cell line and patient-derived organoid) and in vivo (xenograft in immunodeficient mouse) models. Moreover, the combination of GDP-M with DNA-damaging agents activated STING-dependent antitumor immunity in immunocompetent syngeneic mouse models. Therefore, GDP-M supplementation combined with PARP inhibition augmented the efficacy of anti-PD-1 antibodies. Together, these findings suggest that GDP-M is a crucial HRD-related metabolite and propose a promising therapeutic strategy for TNBCs with low HRD scores using the combination of GDP-M, PARP inhibitors, and anti-PD-1 immunotherapy.
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Affiliation(s)
- Jia-Han Ding
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 201203, P. R. China
| | - Yi Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Fan Yang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Xiao-Qing Song
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Ying Xu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Xiao-Hong Ding
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Rui Ding
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Gen-Hong Di
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
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6
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Sun W, Zhang Q, Zhang X, Tran NH, Ziaur Rahman M, Chen Z, Peng C, Ma J, Li M, Xin L, Shan B. Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics. Nat Commun 2023; 14:4046. [PMID: 37422459 PMCID: PMC10329677 DOI: 10.1038/s41467-023-39699-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 06/19/2023] [Indexed: 07/10/2023] Open
Abstract
Here we present GlycanFinder, a database search and de novo sequencing tool for the analysis of intact glycopeptides from mass spectrometry data. GlycanFinder integrates peptide-based and glycan-based search strategies to address the challenge of complex fragmentation of glycopeptides. A deep learning model is designed to capture glycan tree structures and their fragment ions for de novo sequencing of glycans that do not exist in the database. We performed extensive analyses to validate the false discovery rates (FDRs) at both peptide and glycan levels and to evaluate GlycanFinder based on comprehensive benchmarks from previous community-based studies. Our results show that GlycanFinder achieved comparable performance to other leading glycoproteomics softwares in terms of both FDR control and the number of identifications. Moreover, GlycanFinder was also able to identify glycopeptides not found in existing databases. Finally, we conducted a mass spectrometry experiment for antibody N-linked glycosylation profiling that could distinguish isomeric peptides and glycans in four immunoglobulin G subclasses, which had been a challenging problem to previous studies.
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Affiliation(s)
- Weiping Sun
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada
| | - Qianqiu Zhang
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada
| | - Xiyue Zhang
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada
| | - Ngoc Hieu Tran
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada
| | - M Ziaur Rahman
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada
| | - Zheng Chen
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada
| | - Chao Peng
- BaizhenBio Inc., Wuhan, China
- Wuhan BioBank, Wuhan, China
| | - Jun Ma
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada
| | - Ming Li
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada.
- Henan Academy of Sciences, Zhengzhou, Henan, China.
| | - Lei Xin
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada.
| | - Baozhen Shan
- Bioinformatics Solutions Inc., Waterloo, Ontario, Canada.
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7
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Feng X, BaiMaYangJin, Mo X, Zhang F, Hu W, Feng Z, Zhang T, Wei L, Lu H. IgG glycomic profiling identifies potential biomarkers for diagnosis of echinococcosis. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1227:123838. [PMID: 37540936 DOI: 10.1016/j.jchromb.2023.123838] [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: 02/01/2023] [Revised: 06/25/2023] [Accepted: 07/18/2023] [Indexed: 08/06/2023]
Abstract
Echinococcosis caused by larval stage of the genus Echinococcus, is a serious and potentially fatal parasitic zoonosis distributed globally. The two types of the disease in human are cystic echinococcosis (CE) and alveolar echinococcosis (AE). As the biological and encysting characteristics of the parasite, early diagnosis remains to address. In the present study, we demonstrate the value of Immunoglobulin G (IgG) glycome as a potential diagnostic biomarker for echinococcosis. Serum IgG glycome profiles were analyzed by ultra-performance liquid chromatography in a cohort comprised of 127 echinococcosis patients, of them 98 were diagnosed as CE and 29 as AE. IgG N-glycome analysis in pretreatment serum of echinococcosis patients presents 25 glycans and 64 derived traits. Compared with IgG glycans of healthy control group, neutral glycans, fucosylation and agalactosylated N-glycans increased while sialylation and galactosylation decreased in echinococcosis patients. Combined with a machine-learning-based approach, we built three biomarker combinations to distinguish CE, AE and healthy controls. Meanwhile, galactosylation, sialylation and A2BG2S1 in IgG glycan profiles were evidently associated with different types of CE (from CE1 to CE5). Our findings suggest that the alterations in IgG N-glycome may be of value in CE and AE diagnosis and follow-up CE disease progress. The role of IgG N-glycans as diagnostic biomarker remains to be verified in future study.
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Affiliation(s)
- Xiaoxiao Feng
- The Fifth People's Hospital of Shanghai, Institutes of Biomedical Sciences, Shanghai Cancer Center, Department of Chemistry & NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, People's Republic of China
| | - BaiMaYangJin
- National Health Commission Key Laboratory of Echinococcosis Prevention and Control, Xizang Center for Disease Control and Prevention, Lhasa 850000, Tibet Autonomous Region, People's Republic of China
| | - Xiaojin Mo
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, People's Republic of China
| | - Fangyan Zhang
- Waters Technologies, Pudong New District, Shanghai 201203, People's Republic of China
| | - Wei Hu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, People's Republic of China
| | - Zheng Feng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, People's Republic of China
| | - Ting Zhang
- National Health Commission Key Laboratory of Echinococcosis Prevention and Control, Xizang Center for Disease Control and Prevention, Lhasa 850000, Tibet Autonomous Region, People's Republic of China; National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, People's Republic of China.
| | - Liming Wei
- The Fifth People's Hospital of Shanghai, Institutes of Biomedical Sciences, Shanghai Cancer Center, Department of Chemistry & NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, People's Republic of China.
| | - Haojie Lu
- The Fifth People's Hospital of Shanghai, Institutes of Biomedical Sciences, Shanghai Cancer Center, Department of Chemistry & NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, People's Republic of China.
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8
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Li M, Feng Y, Ma M, Kapur A, Patankar M, Li L. High-Throughput Quantitative Glycomics Enabled by 12-plex Isobaric Multiplex Labeling Reagents for Carbonyl-Containing Compound (SUGAR) Tags. J Proteome Res 2023; 22:1557-1563. [PMID: 36700627 PMCID: PMC10164053 DOI: 10.1021/acs.jproteome.2c00773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Glycans, which are widely distributed on most proteins and cell surfaces, are a class of important biomolecules playing crucial roles in various biological processes such as immune response and cellular communication. Modern mass spectrometry (MS) coupled with novel chemical probes greatly facilitates routine analysis of glycans. However, the requirement of high-throughput analysis still calls for advanced tools to be developed. Recently, we devised isobaric multiplex reagents for carbonyl-containing compound (SUGAR) tags for 4-plex N-glycan analysis. To further improve the throughput, we utilized the subtle mass differences among different isotopologues and expanded the multiplexing capacity to 12 channels, a 3-fold throughput improvement for the original SUGAR tag design and achieved high-throughput N-glycan analysis in a single LC-MS/MS injection. We then applied 12-plex SUGAR tags to profile the N-glycans in four subtypes of human Immunoglobulin G (IgG) and to investigate the N-glycan changes in the endometrial cancer cells (ECC1) treated with Atovaquone, a quinone antimicrobial medication, and a dihydroorotate dehydrogenase (DHODH) inhibitor. Data are available via ProteomeXchange with the identifier PXD038501.
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9
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Sun Z, Fu B, Wang G, Zhang L, Xu R, Zhang Y, Lu H. High-throughput site-specific N-glycoproteomics reveals glyco-signatures for liver disease diagnosis. Natl Sci Rev 2023; 10:nwac059. [PMID: 36879659 PMCID: PMC9985154 DOI: 10.1093/nsr/nwac059] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 03/15/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
The glycoproteome has emerged as a prominent target for screening biomarkers, as altered glycosylation is a hallmark of cancer cells. In this work, we incorporated tandem mass tag labeling into quantitative glycoproteomics by developing a chemical labeling-assisted complementary dissociation method for the multiplexed analysis of intact N-glycopeptides. Benefiting from the complementary nature of two different mass spectrometry dissociation methods for identification and multiplex labeling for quantification of intact N-glycopeptides, we conducted the most comprehensive site-specific and subclass-specific N-glycosylation profiling of human serum immunoglobulin G (IgG) to date. By analysing the serum of 90 human patients with varying severities of liver diseases, as well as healthy controls, we identified that the combination of IgG1-H3N5F1 and IgG4-H4N3 can be used for distinguishing between different stages of liver diseases. Finally, we used targeted parallel reaction monitoring to successfully validate the expression changes of glycosylation in liver diseases in a different sample cohort that included 45 serum samples.
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Affiliation(s)
- Zhenyu Sun
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Bin Fu
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Guoli Wang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Lei Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Ruofan Xu
- Eleanor Roosevelt College, University of California San Diego, La Jolla, CA92093, USA
| | - Ying Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Haojie Lu
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
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10
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. MASS SPECTROMETRY REVIEWS 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
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11
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Li M, Zhong X, Feng Y, Li L. Novel Isobaric Tagging Reagent Enabled Multiplex Quantitative Glycoproteomics via Electron-Transfer/Higher-Energy Collisional Dissociation (EThcD) Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1874-1882. [PMID: 36095095 PMCID: PMC10160164 DOI: 10.1021/jasms.2c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Protein glycosylation, covalent attachment of carbohydrates to polypeptide chains, is a highly important post-translational modification involved in many essential physiological processes. Comprehensive site-specific and quantitative analysis is crucial for revealing the diverse functions and dynamics of glycosylation. To characterize intact glycopeptides, mass spectrometry (MS)-based glycoproteomics employs versatile fragmentation methods, among which electron-transfer/higher-energy collision dissociation (EThcD) has gained great popularity. However, the inherent limitation of EThcD in fragmenting low-charge ions has prevented its widespread applications. Furthermore, there is a need to develop a high-throughput strategy for comparative glycoproteomics with a large cohort of samples. Herein, we developed isobaric N,N-dimethyl leucine-derivatized ethylenediamine (DiLeuEN) tags to increase the charge states of glycopeptides, thereby improving the fragmentation efficiency and allowing for in-depth intact glycopeptide analysis, especially for sialoglycopeptides. Moreover, the unique reporter ions of DiLeuEN-labeled glycopeptides generated in tandem MS spectra enable relative quantification of up to four samples in a single analysis, which represents a new high-throughput method for quantitative glycoproteomics.
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12
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Ren W, Bian Q, Cai Y. Mass spectrometry-based N-glycosylation analysis in kidney disease. Front Mol Biosci 2022; 9:976298. [PMID: 36072428 PMCID: PMC9442644 DOI: 10.3389/fmolb.2022.976298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/18/2022] [Indexed: 11/14/2022] Open
Abstract
Kidney disease is a global health concern with an enormous expense. It is estimated that more than 10% of the population worldwide is affected by kidney disease and millions of patients would progress to death prematurely and unnecessarily. Although creatinine detection and renal biopsy are well-established tools for kidney disease diagnosis, they are limited by several inevitable defects. Therefore, diagnostic tools need to be upgraded, especially for the early stage of the disease and possible progression. As one of the most common post-translational modifications of proteins, N-glycosylation plays a vital role in renal structure and function. Deepening research on N-glycosylation in kidney disease provides new insights into the pathophysiology and paves the way for clinical application. In this study, we reviewed recent N-glycosylation studies on several kidney diseases. We also summarized the development of mass spectrometric methods in the field of N-glycoproteomics and N-glycomics.
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Affiliation(s)
- Weifu Ren
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Nephrology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Qi Bian
- Department of Nephrology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yan Cai
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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13
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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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14
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Gyebrovszki B, Ács A, Szabó D, Auer F, Novozánszki S, Rojkovich B, Magyar A, Hudecz F, Vékey K, Drahos L, Sármay G. The Role of IgG Fc Region N-Glycosylation in the Pathomechanism of Rheumatoid Arthritis. Int J Mol Sci 2022; 23:ijms23105828. [PMID: 35628640 PMCID: PMC9146365 DOI: 10.3390/ijms23105828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 11/30/2022] Open
Abstract
Anti-citrullinated protein antibodies (ACPAs) are involved in the pathogenesis of rheumatoid arthritis. N-glycosylation pattern of ACPA-IgG and healthy IgG Fc differs. The aim of this study is to determine the relative sialylation and galactosylation level of ACPAs and control IgG to assess their capability of inducing TNFα production, and furthermore, to analyze the correlations between the composition of Fc glycans and inflammatory markers in RA. We isolated IgG from sera of healthy volunteers and RA patients, and purified ACPAs on a citrulline-peptide column. Immunocomplexes (IC) were formed by adding an F(ab)2 fragment of anti-human IgG. U937 cells were used to monitor the binding of IC to FcγR and to trigger TNFα release determined by ELISA. To analyze glycan profiles, control IgG and ACPA-IgG were digested with trypsin and the glycosylation patterns of glycopeptides were analyzed by determining site-specific N-glycosylation using nano-UHPLC-MS/MS. We found that both sialylation and galactosylation levels of ACPA-IgG negatively correlate with inflammation-related parameters such as CRP, ESR, and RF. Functional assays show that dimerized ACPA-IgG significantly enhances TNFα release in an FcγRI-dependent manner, whereas healthy IgG does not. TNFα production inversely correlates with the relative intensities of the G0 glycoform, which lacks galactose and terminal sialic acid moieties.
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Affiliation(s)
- Balázs Gyebrovszki
- Department of Immunology, Eötvös Loránd University, 1117 Budapest, Hungary; (B.G.); (F.A.); (S.N.)
| | - András Ács
- MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary; (A.Á.); (D.S.); (K.V.); (L.D.)
| | - Dániel Szabó
- MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary; (A.Á.); (D.S.); (K.V.); (L.D.)
- Hevesy György PhD School of Chemistry, Faculty of Science, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Felícia Auer
- Department of Immunology, Eötvös Loránd University, 1117 Budapest, Hungary; (B.G.); (F.A.); (S.N.)
- Translational Glycomics Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 8200 Veszprém, Hungary
| | - Soma Novozánszki
- Department of Immunology, Eötvös Loránd University, 1117 Budapest, Hungary; (B.G.); (F.A.); (S.N.)
- Central Laboratory-Microbiology Profile, Molecular Department, National Institute of Hematology and Infectious Diseases, Central Hospital of Southern Pest, 1097 Budapest, Hungary
| | - Bernadette Rojkovich
- Rheumatology Department III, Polyclinic of the Hospitaller Brothers of St. John of God, 1027 Budapest, Hungary;
| | - Anna Magyar
- ELKH-ELTE Research Group of Peptide Chemistry, 1117 Budapest, Hungary; (A.M.); (F.H.)
| | - Ferenc Hudecz
- ELKH-ELTE Research Group of Peptide Chemistry, 1117 Budapest, Hungary; (A.M.); (F.H.)
| | - Károly Vékey
- MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary; (A.Á.); (D.S.); (K.V.); (L.D.)
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary; (A.Á.); (D.S.); (K.V.); (L.D.)
| | - Gabriella Sármay
- Department of Immunology, Eötvös Loránd University, 1117 Budapest, Hungary; (B.G.); (F.A.); (S.N.)
- Correspondence:
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15
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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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16
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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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17
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Gutierrez-Reyes CD, Jiang P, Atashi M, Bennett A, Yu A, Peng W, Zhong J, Mechref Y. Advances in mass spectrometry-based glycoproteomics: An update covering the period 2017-2021. Electrophoresis 2021; 43:370-387. [PMID: 34614238 DOI: 10.1002/elps.202100188] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/30/2021] [Accepted: 09/25/2021] [Indexed: 12/23/2022]
Abstract
Protein glycosylation is one of the most common posttranslational modifications, and plays an essential role in a wide range of biological processes such as immune response, intercellular signaling, inflammation, host-pathogen interaction, and protein stability. Glycoproteomics is a proteomics subfield dedicated to identifying and characterizing the glycans and glycoproteins in a given cell or tissue. Aberrant glycosylation has been associated with various diseases such as Alzheimer's disease, viral infections, inflammation, immune deficiencies, congenital disorders, and cancers. However, glycoproteomic analysis remains challenging because of the low abundance, site-specific heterogeneity, and poor ionization efficiency of glycopeptides during LC-MS analyses. Therefore, the development of sensitive and accurate approaches to efficiently characterize protein glycosylation is crucial. Methods such as metabolic labeling, enrichment, and derivatization of glycopeptides, coupled with different mass spectrometry techniques and bioinformatics tools, have been developed to achieve sophisticated levels of quantitative and qualitative analyses of glycoproteins. This review attempts to update the recent developments in the field of glycoproteomics reported between 2017 and 2021.
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Affiliation(s)
| | - Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Andrew Bennett
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Jieqiang Zhong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
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18
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Cui Y, Dong X, Zhang X, Chen C, Fu D, Li X, Liang X. Deciphering the O-Glycosylation of HKU1 Spike Protein With the Dual-Functional Hydrophilic Interaction Chromatography Materials. Front Chem 2021; 9:707235. [PMID: 34485242 PMCID: PMC8414140 DOI: 10.3389/fchem.2021.707235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/13/2021] [Indexed: 01/21/2023] Open
Abstract
HKU1 is a human beta coronavirus and infects host cells via highly glycosylated spike protein (S). The N-glycosylation of HKU1 S has been reported. However, little is known about its O-glycosylation, which hinders the in-depth understanding of its biological functions. Herein, a comprehensive study of O-glycosylation of HKU1 S was carried out based on dual-functional histidine-bonded silica (HBS) materials. The enrichment method for O-glycopeptides with HBS was developed and validated using standard proteins. The application of the developed method to the HKU1 S1 subunit resulted in 46 novel O-glycosylation sites, among which 55.6% were predicted to be exposed on the outer protein surface. Moreover, the O-linked glycans and their abundance on each HKU1 S1 site were analyzed. The obtained O-glycosylation dataset will provide valuable insights into the structure of HKU1 S.
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Affiliation(s)
- Yun Cui
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Xuefang Dong
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xiaofei Zhang
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Cheng Chen
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Dongmei Fu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Xiuling Li
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xinmiao Liang
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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19
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Calle B, Bineva-Todd G, Marchesi A, Flynn H, Ghirardello M, Tastan OY, Roustan C, Choi J, Galan MC, Schumann B, Malaker SA. Benefits of Chemical Sugar Modifications Introduced by Click Chemistry for Glycoproteomic Analyses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2366-2375. [PMID: 33871988 PMCID: PMC7611619 DOI: 10.1021/jasms.1c00084] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Mucin-type O-glycosylation is among the most complex post-translational modifications. Despite mediating many physiological processes, O-glycosylation remains understudied compared to other modifications, simply because the right analytical tools are lacking. In particular, analysis of intact O-glycopeptides by mass spectrometry is challenging for several reasons; O-glycosylation lacks a consensus motif, glycopeptides have low charge density which impairs ETD fragmentation, and the glycan structures modifying the peptides are unpredictable. Recently, we introduced chemically modified monosaccharide analogues that allowed selective tracking and characterization of mucin-type O-glycans after bioorthogonal derivatization with biotin-based enrichment handles. In doing so, we realized that the chemical modifications used in these studies have additional benefits that allow for improved analysis by tandem mass spectrometry. In this work, we built on this discovery by generating a series of new GalNAc analogue glycopeptides. We characterized the mass spectrometric signatures of these modified glycopeptides and their signature residues left by bioorthogonal reporter reagents. Our data indicate that chemical methods for glycopeptide profiling offer opportunities to optimize attributes such as increased charge state, higher charge density, and predictable fragmentation behavior.
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Affiliation(s)
- Beatriz Calle
- Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
- Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ, London, United Kingdom
| | - Ganka Bineva-Todd
- Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
| | - Andrea Marchesi
- Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
- Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ, London, United Kingdom
| | - Helen Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Mattia Ghirardello
- School of Chemistry, Cantock’s Close, University of Bristol, BS8 1TS, United Kingdom
| | - Omur Y. Tastan
- Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
| | - Chloe Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Junwon Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - M. Carmen Galan
- School of Chemistry, Cantock’s Close, University of Bristol, BS8 1TS, United Kingdom
| | - Benjamin Schumann
- Chemical Glycobiology Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
- Department of Chemistry, Imperial College London, 80 Wood Lane, W12 0BZ, London, United Kingdom
| | - Stacy A. Malaker
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, CT 06511, United States
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20
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Nmagu D, Singh SK, Lee KH. Creation of monoclonal antibody expressing CHO cell lines grown with sodium butyrate and characterization of resulting antibody glycosylation. Methods Enzymol 2021; 660:267-295. [PMID: 34742393 DOI: 10.1016/bs.mie.2021.06.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Chinese hamster ovary (CHO) cells are the primary mammalian cell lines utilized to produce monoclonal antibodies (mAbs). The upsurge in biosimilar development and the proven health benefits of mAb treatments reinforces the need for innovative methods to generate robust CHO clones and enhance production, while maintaining desired product quality attributes. Among various product titer-enhancing approaches, the use of histone deacetylase inhibitors (HDACis) such as sodium butyrate (NaBu) has yielded promising results. The titer-enhancing effect of HDACi treatment has generally been observed in lower producer cell lines but those studies are typically done on individual clones. Here, we describe a cell line development (CLD) platform approach for creating clones with varying productivities. We then describe a method for selecting an optimal NaBu concentration to evaluate potential titer-enhancing capabilities in a fed-batch study. Finally, a method for purifying the mAb using protein A chromatography, followed by glycosylation analysis using mass spectrometry, is described. The proposed workflow can be applied for a robust CLD process optimization to generate robust clones, enhance product expression, and improve product quality attributes.
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Affiliation(s)
- Douglas Nmagu
- Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States
| | - Sumit K Singh
- Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States
| | - Kelvin H Lee
- Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States.
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21
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Dong X, Chen C, Yan J, Zhang X, Li X, Liang X. Comprehensive O-Glycosylation Analysis of the SARS-CoV-2 Spike Protein with Biomimetic Trp-Arg Materials. Anal Chem 2021; 93:10444-10452. [PMID: 34284575 DOI: 10.1021/acs.analchem.0c04634] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a serious public health threat. Most vaccines against SARS-CoV-2 target the highly glycosylated spike protein (S). A good knowledge of the glycosylation profile of this protein is key to successful vaccine development. Unlike the 22 confirmed N-glycosylation sites on SARS-CoV-2 S, only a few O-glycosylation sites on this protein have been reported. This difference is mainly ascribed to the extremely low stoichiometry of O-glycosylation. Herein, we designed the biomimetic materials, Trp-Arg (WR) monomer-grafted silica microspheres (designated as WR-SiO2), and these biomimetic materials can enrich N- and O-linked glycopeptides with high selectivity. And WR-SiO2 can resist the nonglycopeptides' interference with the 100 molar fold of BSA during O-linked glycopeptide enrichment. We utilized WR-SiO2 to comprehensively analyze the O-glycosylation profile of recombinant SARS-CoV-2 S. Twenty-seven O-glycosylation sites including 18 unambiguous sites are identified on SARS-CoV-2 S. Our study demonstrates that the biomimetic polymer can offer specific selectivity for O-linked glycopeptides and pave the way for O-glycosylation research in biological fields. The O-glycosylation profile of SARS-CoV-2 S might supplement the comprehensive glycosylation in addition to N-glycosylation of SARS-CoV-2 S.
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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, P. R. China
| | - Cheng Chen
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Jingyu Yan
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xiaofei Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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22
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Sun Z, Ji G, Wang G, Wei L, Zhang Y, Lu H. One step carboxyl group isotopic labeling for quantitative analysis of intact N-glycopeptides by mass spectrometry. Chem Commun (Camb) 2021; 57:4154-4157. [PMID: 33908447 DOI: 10.1039/d1cc00197c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Here, we have developed an approach termed methylamine stable isotope labeling (MeSIL) to relatively quantify N-glycopeptides through one step labeling. It is the first time that this approach is applied to measure N-glycopeptide changes in huh7 cells after Zika virus infection and it has been revealed that differentially expressed N-glycopeptides played important roles in virus infection at the glycosylation site-specific level.
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Affiliation(s)
- Zhenyu Sun
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai 200032, China.
| | - Guanghui Ji
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Guoli Wang
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai 200032, China.
| | - Lei Wei
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Ying Zhang
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai 200032, China. and Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Haojie Lu
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai 200032, China. and Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
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23
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Cheng M, Shu H, Peng Y, Feng X, Yan G, Zhang L, Yao J, Bao H, Lu H. Specific Analysis of α-2,3-Sialylated N-Glycan Linkage Isomers by Microchip Capillary Electrophoresis-Mass Spectrometry. Anal Chem 2021; 93:5537-5546. [PMID: 33752328 DOI: 10.1021/acs.analchem.1c00064] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Sialylated N-glycan isomers with α-2,3 and α-2,6 linkages play crucial and distinctive roles in diverse physiological and pathological processes. Changes of α-2,3-linked sialic acids in sialylated N-glycans are especially important in monitoring the initiation and progression of diseases. However, the specific analysis of α-2,3-sialylated N-glycan linkage isomers remains challenging due to their extremely low abundance and technical limitations in separation and detection. Herein, we designed an integrated strategy that combines linkage-specific derivatization and a charge-sensitive separation method based on microfluidic chip capillary electrophoresis-mass spectrometry (microchip CE-MS) for specific analysis of α-2,3-sialylated N-glycan linkage isomers for the first time. The α-2,6- and α-2,3-sialic acids were selectively labeled with methylamine (MA) and N,N-dimethylethylenediamine (DMEN), respectively, which selectively makes α-2,3-sialylated N-glycans positively charged and realizes online purification, concentration, and discrimination of α-2,3-sialylated N-glycans from other N-glycans in microchip CE-MS. This new approach was demonstrated with standard multisialylated N-glycans, and it was found that only the α-2,3-sialylated N-glycans migrated and were detected in order according to the number of α-2,3-sialic acids. Finally, this strategy was successfully applied in highly sensitive profiling and reproducible quantitation of the serum α-2,3-sialylated N-glycome from ovarian cancer (OC) patients, where 7 of 33 detected α-2,3-sialylated N-glycans significantly changed in the OC group compared with healthy controls.
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Affiliation(s)
- Mengxia Cheng
- Department of Chemistry and Shanghai Cancer Center, Fudan University, Shanghai 200032, People's Republic of China.,Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, People's Republic of China
| | - Hong Shu
- Department of Clinical Laboratory, Affiliated Tumor Hospital of Guangxi Medical University, Nanning 530021, People's Republic of China
| | - Ye Peng
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, People's Republic of China
| | - Xiaoxiao Feng
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, People's Republic of China
| | - Guoquan Yan
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, People's Republic of China
| | - Lei Zhang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, People's Republic of China
| | - Jun Yao
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, People's Republic of China
| | - Huimin Bao
- Department of Chemistry and Shanghai Cancer Center, Fudan University, Shanghai 200032, People's Republic of China
| | - Haojie Lu
- Department of Chemistry and Shanghai Cancer Center, Fudan University, Shanghai 200032, People's Republic of China.,Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, People's Republic of China
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24
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Zhang Y, Fang C, Bao H, Yuan W, Lu H. Discover the
Post‐Translational
Modification Proteome Using Mass Spectrometry. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202000515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ying Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University Shanghai 200032 China
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University Shanghai 200032 China
| | - Caiyun Fang
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University Shanghai 200032 China
| | - Huimin Bao
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University Shanghai 200032 China
| | - Wenjuan Yuan
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University Shanghai 200032 China
| | - Haojie Lu
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University Shanghai 200032 China
- Department of Chemistry and NHC Key Laboratory of Glycoconjugates Research, Fudan University Shanghai 200032 China
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25
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Cao W, Liu M, Kong S, Wu M, Zhang Y, Yang P. Recent Advances in Software Tools for More Generic and Precise Intact Glycopeptide Analysis. Mol Cell Proteomics 2021; 20:100060. [PMID: 33556625 PMCID: PMC8724820 DOI: 10.1074/mcp.r120.002090] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Intact glycopeptide identification has long been known as a key and challenging barrier to the comprehensive and accurate understanding the role of glycosylation in an organism. Intact glycopeptide analysis is a blossoming field that has received increasing attention in recent years. MS-based strategies and relative software tools are major drivers that have greatly facilitated the analysis of intact glycopeptides, particularly intact N-glycopeptides. This article provides a systematic review of the intact glycopeptide-identification process using MS data generated in shotgun proteomic experiments, which typically focus on N-glycopeptide analysis. Particular attention is paid to the software tools that have been recently developed in the last decade for the interpretation and quality control of glycopeptide spectra acquired using different MS strategies. The review also provides information about the characteristics and applications of these software tools, discusses their advantages and disadvantages, and concludes with a discussion of outstanding tools.
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Affiliation(s)
- Weiqian Cao
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China; NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China; The Shanghai Key Laboratory of Medical Epigenetics and the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai, China.
| | - Mingqi Liu
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Siyuan Kong
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Mengxi Wu
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China; Department of Chemistry, Fudan University, Shanghai, China
| | - Yang Zhang
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China; The Shanghai Key Laboratory of Medical Epigenetics and the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai, China
| | - Pengyuan Yang
- The Fifth People's Hospital of Fudan University and Institutes of Biomedical Sciences, Fudan University, Shanghai, China; NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China; The Shanghai Key Laboratory of Medical Epigenetics and the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai, China; Department of Chemistry, Fudan University, Shanghai, China.
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26
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Wang D, Baudys J, Bundy JL, Solano M, Keppel T, Barr JR. Comprehensive Analysis of the Glycan Complement of SARS-CoV-2 Spike Proteins Using Signature Ions-Triggered Electron-Transfer/Higher-Energy Collisional Dissociation (EThcD) Mass Spectrometry. Anal Chem 2020; 92:14730-14739. [PMID: 33064451 PMCID: PMC7586457 DOI: 10.1021/acs.analchem.0c03301] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/06/2020] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a global pandemic of coronavirus disease 2019 (COVID-19). The spike protein expressed on the surface of this virus is highly glycosylated and plays an essential role during the process of infection. We conducted a comprehensive mass spectrometric analysis of the N-glycosylation profiles of the SARS-CoV-2 spike proteins using signature ions-triggered electron-transfer/higher-energy collision dissociation (EThcD) mass spectrometry. The patterns of N-glycosylation within the recombinant ectodomain and S1 subunit of the SARS-CoV-2 spike protein were characterized using this approach. Significant variations were observed in the distribution of glycan types as well as the specific individual glycans on the modification sites of the ectodomain and subunit proteins. The relative abundance of sialylated glycans in the S1 subunit compared to the full-length protein could indicate differences in the global structure and function of these two species. In addition, we compared N-glycan profiles of the recombinant spike proteins produced from different expression systems, including human embryonic kidney (HEK 293) cells and Spodoptera frugiperda (SF9) insect cells. These results provide useful information for the study of the interactions of SARS-CoV-2 viral proteins and for the development of effective vaccines and therapeutics.
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Affiliation(s)
- Dongxia Wang
- Division of Laboratory
Sciences,
National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Northeast, Atlanta, Georgia 30341, United States
| | - Jakub Baudys
- Division of Laboratory
Sciences,
National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Northeast, Atlanta, Georgia 30341, United States
| | - Jonathan L. Bundy
- Division of Laboratory
Sciences,
National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Northeast, Atlanta, Georgia 30341, United States
| | - Maria Solano
- Division of Laboratory
Sciences,
National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Northeast, Atlanta, Georgia 30341, United States
| | - Theodore Keppel
- Division of Laboratory
Sciences,
National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Northeast, Atlanta, Georgia 30341, United States
| | - John R. Barr
- Division of Laboratory
Sciences,
National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Northeast, Atlanta, Georgia 30341, United States
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27
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Fernandes E, Sores J, Cotton S, Peixoto A, Ferreira D, Freitas R, Reis CA, Santos LL, Ferreira JA. Esophageal, gastric and colorectal cancers: Looking beyond classical serological biomarkers towards glycoproteomics-assisted precision oncology. Am J Cancer Res 2020; 10:4903-4928. [PMID: 32308758 PMCID: PMC7163443 DOI: 10.7150/thno.42480] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/16/2020] [Indexed: 12/24/2022] Open
Abstract
Esophageal (OC), gastric (GC) and colorectal (CRC) cancers are amongst the digestive track tumors with higher incidence and mortality due to significant molecular heterogeneity. This constitutes a major challenge for patients' management at different levels, including non-invasive detection of the disease, prognostication, therapy selection, patient's follow-up and the introduction of improved and safer therapeutics. Nevertheless, important milestones have been accomplished pursuing the goal of molecular-based precision oncology. Over the past five years, high-throughput technologies have been used to interrogate tumors of distinct clinicopathological natures, generating large-scale biological datasets (e.g. genomics, transcriptomics, and proteomics). As a result, GC and CRC molecular subtypes have been established to assist patient stratification in the clinical settings. However, such molecular panels still require refinement and are yet to provide targetable biomarkers. In parallel, outstanding advances have been made regarding targeted therapeutics and immunotherapy, paving the way for improved patient care; nevertheless, important milestones towards treatment personalization and reduced off-target effects are also to be accomplished. Exploiting the cancer glycoproteome for unique molecular fingerprints generated by dramatic alterations in protein glycosylation may provide the necessary molecular rationale towards this end. Therefore, this review presents functional and clinical evidences supporting a reinvestigation of classical serological glycan biomarkers such as sialyl-Tn (STn) and sialyl-Lewis A (SLeA) antigens from a tumor glycoproteomics perspective. We anticipate that these glycobiomarkers that have so far been employed in non-invasive cancer prognostication may hold unexplored value for patients' management in precision oncology settings.
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28
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Cao WQ, Liu MQ, Kong SY, Wu MX, Huang ZZ, Yang PY. Novel methods in glycomics: a 2019 update. Expert Rev Proteomics 2020; 17:11-25. [PMID: 31914820 DOI: 10.1080/14789450.2020.1708199] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Introduction: Glycomics, which aims to define the glycome of a biological system to better assess the biological attributes of the glycans, has attracted increasing interest. However, the complexity and diversity of glycans present challenging barriers to glycome definition. Technological advances are major drivers in glycomics.Areas covered: This review summarizes the main methods and emphasizes the most recent advances in mass spectrometry-based methods regarding glycomics following the general workflow in glycomic analysis.Expert opinion: Recent mass spectrometry-based technological advances have significantly lowered the barriers in glycomics. The field of glycomics is moving toward both generic and precise analysis.
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Affiliation(s)
- Wei-Qian Cao
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Ming-Qi Liu
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Si-Yuan Kong
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Meng-Xi Wu
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
| | - Zheng-Ze Huang
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Peng-Yuan Yang
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
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