1
|
Zeng J, Rong W, Meng B, Zheng L, Peng T, Zhai R, Jiang Y, Xiao T, Fang X, Zhang Y, Zhao Y, Dai X. Integrated plasma proteomics and N-glycoproteomics reveals alterations in the N-glycosylation in Chinese hepatocellular carcinoma patients. Proteomics Clin Appl 2024; 18:e202300029. [PMID: 38345243 DOI: 10.1002/prca.202300029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 01/11/2024] [Accepted: 01/26/2024] [Indexed: 07/19/2024]
Abstract
Hepatocellular carcinoma (HCC) is a life-threatening disease that presents diagnostic challenges due to the absence of reliable biomarkers. Recently, plasma proteomics and glycoproteomics have emerged as powerful tools for identifying potential diagnostic biomarkers for various diseases. In this study, we conducted a comprehensive proteomic and glycoproteomic analysis of plasma samples from 11 HCC patients and 11 healthy control (HC) individuals. We identified 20 differentially expressed (DE) proteins and 32 DE intact glycosylated peptides (IGPs) that can effectively differentiate between HCC patients and HC samples. Our findings demonstrate that IGP profiles had better predictive power than protein profiles for screening HCC. Pathways associated with DE proteins and IGPs were identified. It was reported that the protein expression level of galectin 3 binding protein (LGALS3BP) and its N-linked glycosylation at the N398 and N551 sites might serve as valuable candidates for HCC diagnosis. These results highlight the importance of N-glycoproteomics in advancing our understanding of HCC and suggest possible candidates for the future diagnosis of this disease.
Collapse
Affiliation(s)
- Jiaming Zeng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
- College of Chemical Engineering, Shenyang University of Chemical Technology, Shenyang, China
| | - Weiqi Rong
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bo Meng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Linlin Zheng
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Peng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Rui Zhai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - You Jiang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Ting Xiao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yong Zhang
- Department of Nephrology and Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Zhao
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
- College of Chemical Engineering, Shenyang University of Chemical Technology, Shenyang, China
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| |
Collapse
|
2
|
Chamrád I, Simerský R, Lenobel R, Novák O. Exploring affinity chromatography in proteomics: A comprehensive review. Anal Chim Acta 2024; 1306:342513. [PMID: 38692783 DOI: 10.1016/j.aca.2024.342513] [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: 12/12/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.
Collapse
Affiliation(s)
- Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic.
| | - Radim Simerský
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| |
Collapse
|
3
|
Goumenou A, Chendo C, Combès A, Fournier T, Pichon V, Delaunay N. Characterization of Concanavalin A-based lectin sorbents for the extraction of the human chorionic gonadotropin glycoforms prior to analysis by nano liquid chromatography-high resolution mass spectrometry. J Pharm Biomed Anal 2024; 242:116022. [PMID: 38354538 DOI: 10.1016/j.jpba.2024.116022] [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: 12/08/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Human chorionic gonadotropin (hCG) is constituted of the hCGα and hCGβ subunits and is a highly glycosylated protein. Affinity supports based on immobilized Concanavalin A (Con A) lectin were used in solid phase extraction (SPE) to fractionate the hCG glycoforms according to their glycosylation state. For the first time, the lectin SPE fractions were off-line analysed by a nano liquid chromatography - high-resolution mass spectrometry (nanoLC-HRMS) method keeping the glycoforms intact. For this, home-made Con A sorbents were prepared by immobilizing lectin on Sepharose with a mean grafting yield of 98.2% (relative standard deviation (RSD) of 3.5%, n = 15). A capacity of about 100 μg of purified urinary hCG (uhCG) per ml of sorbent, grafted with a density of 10 mg of Con A per ml, was estimated. Average extraction yields of around 60% for both hCGα and hCGβ glycoforms were obtained after optimization of the extraction protocol. Intra- and inter-assay evaluation led to average RSD values of around 10%, indicating a repeatable extraction procedure. Similar results were obtained with commercial Con A-based sorbents but only after their 3rd use or after an extensive pre-conditioning step. Finally, the Con A SPE led to the fractionation of some glycoforms of uhCG, allowing the detection of an hCGα glycoform with two tetra-antennary N-glycans that couldn't be detected by direct analysis in nanoLC-HRMS without Con A SPE. Regarding a recombinant hCG, a fractionation was also observed leading to the detection of unretained hCGα glycoforms with tri-antennary N-glycans. Therefore, the combination of lectin SPE with intact protein analysis by nanoLC-HRMS can contribute to a more detailed glycosylation characterization of the hCG protein.
Collapse
Affiliation(s)
- Anastasia Goumenou
- Laboratory of Analytical, Bioanalytical Sciences and Miniaturization, Chemistry, Biology and Innovation (CBI) UMR 8231, ESPCI Paris PSL, CNRS, PSL Research University, Paris, France
| | - Christophe Chendo
- Laboratory of Analytical, Bioanalytical Sciences and Miniaturization, Chemistry, Biology and Innovation (CBI) UMR 8231, ESPCI Paris PSL, CNRS, PSL Research University, Paris, France
| | - Audrey Combès
- Laboratory of Analytical, Bioanalytical Sciences and Miniaturization, Chemistry, Biology and Innovation (CBI) UMR 8231, ESPCI Paris PSL, CNRS, PSL Research University, Paris, France
| | - Thierry Fournier
- Université Paris Cité, INSERM, "Pathophysiology & Pharmacotoxicology of the Human Placenta, pre & postnatal Microbiota", 3PHM, F-75006 Paris, France
| | - Valérie Pichon
- Laboratory of Analytical, Bioanalytical Sciences and Miniaturization, Chemistry, Biology and Innovation (CBI) UMR 8231, ESPCI Paris PSL, CNRS, PSL Research University, Paris, France; Sorbonne Université, Paris, France
| | - Nathalie Delaunay
- Laboratory of Analytical, Bioanalytical Sciences and Miniaturization, Chemistry, Biology and Innovation (CBI) UMR 8231, ESPCI Paris PSL, CNRS, PSL Research University, Paris, France.
| |
Collapse
|
4
|
Wu D, Yan R, Song S, Swansiger AK, Li Y, Prell JS, Zhou Q, Robinson CV. The complete assembly of human LAT1-4F2hc complex provides insights into its regulation, function and localisation. Nat Commun 2024; 15:3711. [PMID: 38697966 PMCID: PMC11065870 DOI: 10.1038/s41467-024-47948-4] [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: 09/05/2023] [Accepted: 04/17/2024] [Indexed: 05/05/2024] Open
Abstract
The LAT1-4F2hc complex (SLC7A5-SLC3A2) facilitates uptake of essential amino acids, hormones and drugs. Its dysfunction is associated with many cancers and immune/neurological disorders. Here, we apply native mass spectrometry (MS)-based approaches to provide evidence of super-dimer formation (LAT1-4F2hc)2. When combined with lipidomics, and site-directed mutagenesis, we discover four endogenous phosphatidylethanolamine (PE) molecules at the interface and C-terminus of both LAT1 subunits. We find that interfacial PE binding is regulated by 4F2hc-R183 and is critical for regulation of palmitoylation on neighbouring LAT1-C187. Combining native MS with mass photometry (MP), we reveal that super-dimerization is sensitive to pH, and modulated by complex N-glycans on the 4F2hc subunit. We further validate the dynamic assemblies of LAT1-4F2hc on plasma membrane and in the lysosome. Together our results link PTM and lipid binding with regulation and localisation of the LAT1-4F2hc super-dimer.
Collapse
Affiliation(s)
- Di Wu
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK.
| | - Renhong Yan
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong Province, China
| | - Siyuan Song
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK
| | - Andrew K Swansiger
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, Oregon, 97403-1253, USA
| | - Yaning Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - James S Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, Oregon, 97403-1253, USA
| | - Qiang Zhou
- Research Center for Industries of the Future, Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang Province, China
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK.
| |
Collapse
|
5
|
Li P, Chang Q, Liu M, Lei K, Ping S, Wang J, Gu Y, Ren H, Ma Y. DNA-Encoded and Spatial Proximity Replaced Glycoprotein Analysis Reveals Glycosylation Heterogeneity of Extracellular Vesicles. Anal Chem 2023; 95:17467-17476. [PMID: 38009238 DOI: 10.1021/acs.analchem.3c01501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
Glycosylation of proteins is an essential feature of extracellular vesicles (EVs). However, while the glycosylation heterogeneity focusing on specific EV subtypes and proteins will better reveal the functions of EVs, the determination of their specific glycans remains highly challenging. Herein, we report a method of protein-specific glycan recognition using DNA-encoded affinity ligands to label proteins and glycans. Manipulating the sequences of DNA tags and employing a DNA logic gate to trigger a spatial proximity-induced DNA replacement reaction enabled the release of glycan-representative DNA strands for the quantitative detection of multiple glycoforms. After size-dependent isolation of EV subgroups and decoding of three typical glycoforms on the epithelial growth factor receptor (EGFR), we found that the different EV subgroups of the EGFR glycoprotein varied with respect to glycan types and abundance. The distinctive glycoforms of the EV subgroups could interfere with the EGFR-related EV functions. Furthermore, the sialylation of small EVs possessed the potential as a cancer biomarker. This method provides new insights into the role of protein-specific glycoforms in EV functions.
Collapse
Affiliation(s)
- Ping Li
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Qi Chang
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Mengmeng Liu
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Ke Lei
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China
| | - Shuai Ping
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China
| | - Jia Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China
| | - Yueqing Gu
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - He Ren
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China
| | - Yi Ma
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| |
Collapse
|
6
|
Townsend JA, Marty MT. What's the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry. Methods 2023; 218:1-13. [PMID: 37482149 PMCID: PMC10529358 DOI: 10.1016/j.ymeth.2023.07.004] [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: 04/21/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
Many membrane proteins form functional complexes that are either homo- or hetero-oligomeric. However, it is challenging to characterize membrane protein oligomerization in intact lipid bilayers, especially for polydisperse mixtures. Native mass spectrometry of membrane proteins and peptides inserted in lipid nanodiscs provides a unique method to study the oligomeric state distribution and lipid preferences of oligomeric assemblies. To interpret these complex spectra, we developed novel data analysis methods using macromolecular mass defect analysis. Here, we provide an overview of how mass defect analysis can be used to study oligomerization in nanodiscs, discuss potential limitations in interpretation, and explore strategies to resolve these ambiguities. Finally, we review recent work applying this technique to studying formation of antimicrobial peptide, amyloid protein, and viroporin complexes with lipid membranes.
Collapse
Affiliation(s)
- Julia A Townsend
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA.
| |
Collapse
|
7
|
Zheng H, Wang Z, Jia Q. Simultaneous Profiling of Palmitoylomics and Glycomics with Photo/pH Dual-Responsive Magnetic Nanocomposites. SMALL METHODS 2023; 7:e2300254. [PMID: 37231570 DOI: 10.1002/smtd.202300254] [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: 02/27/2023] [Revised: 04/10/2023] [Indexed: 05/27/2023]
Abstract
Following an in-depth examination of a single type of protein posttranslational modification, the synergistic analysis of two or more modification types has gradually emerged as a focal point in proteomic research. Palmitoylation and glycosylation are both critical for protein, implicated in carcinogenesis and inflammation. In this study, novel dual-responsive magnetic nanocomposites that serve as an ideal platform for the sequential or simultaneous enrichment of palmitoyl and glycopeptides are reported. The nanocomposites denoted as magDVS-VBA are constructed by modifying magnetic nanoparticles with azobenzene and divinyl sulfone (DVS), and self-assembled with 4-vinylbenzeneboronic acid (VBA)-immobilized β-cyclodextrin, which responds to light. The incorporated DVS component possesses the ability to recognize palmitoyl or glycopeptides under different pH conditions, whereas the introduction of VBA enhances the affinity of the nanocomposite for glycopeptides. Notably, magDVS-VBA exhibits flexible photo-, pH-, and magnetic-responsive capabilities, enabling the simultaneous recognition of hydrophobic palmitoyl peptides and hydrophilic glycopeptides for the first time. The developed platform demonstrates high specificity for sensitive palmitoylomics and glycomics analysis of mouse liver tissue, providing an effective method for studying of their crosstalk, and potential implications in clinical applications.
Collapse
Affiliation(s)
- Haijiao Zheng
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Zirui Wang
- College of Chemistry, Jilin University, Changchun, 130012, China
| | - Qiong Jia
- College of Chemistry, Jilin University, Changchun, 130012, China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Sciences, Jilin University, Changchun, 130012, China
| |
Collapse
|
8
|
Shen D, Lu X, Li W, Zou L, Tong Y, Wang L, Rao L, Zhang Y, Hou L, Sun G, Chen L. Identification and characterization of an α-1,3 mannosidase from Elizabethkingia meningoseptica and its potential attenuation impact on allergy associated with cross-reactive carbohydratedeterminant. Biochem Biophys Res Commun 2023; 672:17-26. [PMID: 37331167 DOI: 10.1016/j.bbrc.2023.06.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 06/10/2023] [Indexed: 06/20/2023]
Abstract
Core α-1,3 mannose is structurally near the core xylose and core fucose on core pentasaccharide from plant and insect glycoproteins. Mannosidase is a useful tool for characterization the role of core α-1,3 mannose in the composition of glycan related epitope, especially for those epitopes in which core xylose and core fucose are involved. Through functional genomic analysis, we identified a glycoprotein α-1,3 mannosidase and named it MA3. We used MA3 to treat allergen horseradish peroxidase (HRP) and phospholipase A2 (PLA2) separately. The results showed that after MA3 removed α-1,3 mannose on HRP, the reactivity of HRP with anti-core xylose polyclonal antibody almost disappeared. And the reactivity of MA3-treated PLA2 with anti-core fucose polyclonal antibody decreased partially. In addition, when PLA2 was conducted enzyme digestion by MA3, the reactivity between PLA2 and allergic patients' sera diminished. These results demonstrated that α-1,3 mannose was an critical component of glycan related epitope.
Collapse
Affiliation(s)
- Danfeng Shen
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xinrong Lu
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Wenjie Li
- Clinical Laboratory, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Lin Zou
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yongliang Tong
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Lei Wang
- Department of Research and Development, SysDiagno Biomedtech, Nanjing, 211800, Jiangsu Province, China
| | - Lin Rao
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yuxin Zhang
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China
| | - Linlin Hou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, China.
| | - Guiqin Sun
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang Province, China.
| | - Li Chen
- Dept. of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| |
Collapse
|
9
|
Nickerson JL, Baghalabadi V, Rajendran SRCK, Jakubec PJ, Said H, McMillen TS, Dang Z, Doucette AA. Recent advances in top-down proteome sample processing ahead of MS analysis. MASS SPECTROMETRY REVIEWS 2023; 42:457-495. [PMID: 34047392 DOI: 10.1002/mas.21706] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/21/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Top-down proteomics is emerging as a preferred approach to investigate biological systems, with objectives ranging from the detailed assessment of a single protein therapeutic, to the complete characterization of every possible protein including their modifications, which define the human proteoform. Given the controlling influence of protein modifications on their biological function, understanding how gene products manifest or respond to disease is most precisely achieved by characterization at the intact protein level. Top-down mass spectrometry (MS) analysis of proteins entails unique challenges associated with processing whole proteins while maintaining their integrity throughout the processes of extraction, enrichment, purification, and fractionation. Recent advances in each of these critical front-end preparation processes, including minimalistic workflows, have greatly expanded the capacity of MS for top-down proteome analysis. Acknowledging the many contributions in MS technology and sample processing, the present review aims to highlight the diverse strategies that have forged a pathway for top-down proteomics. We comprehensively discuss the evolution of front-end workflows that today facilitate optimal characterization of proteoform-driven biology, including a brief description of the clinical applications that have motivated these impactful contributions.
Collapse
Affiliation(s)
| | - Venus Baghalabadi
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Subin R C K Rajendran
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
- Verschuren Centre for Sustainability in Energy and the Environment, Sydney, Nova Scotia, Canada
| | - Philip J Jakubec
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Hammam Said
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Teresa S McMillen
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ziheng Dang
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| |
Collapse
|
10
|
Reid DJ, Thibert S, Zhou M. Dissecting the structural heterogeneity of proteins by native mass spectrometry. Protein Sci 2023; 32:e4612. [PMID: 36851867 PMCID: PMC10031758 DOI: 10.1002/pro.4612] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
A single gene yields many forms of proteins via combinations of post-transcriptional/post-translational modifications. Proteins also fold into higher-order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the "bottom-up" approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher-order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the "top-down" approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in-depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero-complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near-native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding molecular heterogeneity of proteins. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Deseree J Reid
- Chemical and Biological Signature Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Stephanie Thibert
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| |
Collapse
|
11
|
Qin R, Mahal LK, Bojar D. Deep learning explains the biology of branched glycans from single-cell sequencing data. iScience 2022; 25:105163. [PMID: 36217547 PMCID: PMC9547197 DOI: 10.1016/j.isci.2022.105163] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/06/2022] [Accepted: 09/16/2022] [Indexed: 11/03/2022] Open
Abstract
Glycosylation is ubiquitous and often dysregulated in disease. However, the regulation and functional significance of various types of glycosylation at cellular levels is hard to unravel experimentally. Multi-omics, single-cell measurements such as SUGAR-seq, which quantifies transcriptomes and cell surface glycans, facilitate addressing this issue. Using SUGAR-seq data, we pioneered a deep learning model to predict the glycan phenotypes of cells (mouse T lymphocytes) from transcripts, with the example of predicting β1,6GlcNAc-branching across T cell subtypes (test set F1 score: 0.9351). Model interpretation via SHAP (SHapley Additive exPlanations) identified highly predictive genes, in part known to impact (i) branched glycan levels and (ii) the biology of branched glycans. These genes included physiologically relevant low-abundance genes that were not captured by conventional differential expression analysis. Our work shows that interpretable deep learning models are promising for uncovering novel functions and regulatory mechanisms of glycans from integrated transcriptomic and glycomic datasets.
Collapse
Affiliation(s)
- Rui Qin
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Lara K. Mahal
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Daniel Bojar
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| |
Collapse
|
12
|
Cramer DAT, Franc V, Caval T, Heck AJR. Charting the Proteoform Landscape of Serum Proteins in Individual Donors by High-Resolution Native Mass Spectrometry. Anal Chem 2022; 94:12732-12741. [PMID: 36074704 PMCID: PMC9494300 DOI: 10.1021/acs.analchem.2c02215] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Most proteins in serum are glycosylated, with several
annotated
as biomarkers and thus diagnostically important and of interest for
their role in disease. Most methods for analyzing serum glycoproteins
employ either glycan release or glycopeptide centric mass spectrometry-based
approaches, which provide excellent tools for analyzing known glycans
but neglect previously undefined or unknown glycosylation and/or other
co-occurring modifications. High-resolution native mass spectrometry
is a relatively new technique for the analysis of intact glycoproteins,
providing a “what you see is what you get” mass profile
of a protein, allowing the qualitative and quantitative observation
of all modifications present. So far, a disadvantage of this approach
has been that it centers mostly on just one specific serum glycoprotein
at the time. To address this issue, we introduce an ion-exchange chromatography-based
fractionation method capable of isolating and analyzing, in parallel,
over 20 serum (glyco)proteins, covering a mass range between 30 and
190 kDa, from 150 μL of serum. Although generating data in parallel
for all these 20 proteins, we focus the discussion on the very complex
proteoform profiles of four selected proteins, i.e., α-1-antitrypsin,
ceruloplasmin, hemopexin, and complement protein C3. Our analyses
provide an insight into the extensive proteoform landscape of serum
proteins in individual donors, caused by the occurrence of various N- and O-glycans, protein cysteinylation,
and co-occurring genetic variants. Moreover, native mass intact mass
profiling also provided an edge over alternative approaches revealing
the presence of apo- and holo-forms of ceruloplasmin and the endogenous
proteolytic processing in plasma of among others complement protein
C3. We also applied our approach to a small cohort of serum samples
from healthy and diseased individuals. In these, we qualitatively
and quantitatively monitored the changes in proteoform profiles of
ceruloplasmin and revealed a substantial increase in fucosylation
and glycan occupancy in patients with late-stage hepatocellular carcinoma
and pancreatic cancer as compared to healthy donor samples.
Collapse
Affiliation(s)
- Dario A T Cramer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Centre, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Vojtech Franc
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Centre, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Tomislav Caval
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Centre, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Science, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Centre, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
| |
Collapse
|
13
|
Yi L, Fu M, Shao Y, Tang K, Yan Y, Ding CF. Bifunctional super-hydrophilic mesoporous nanocomposite: a novel nanoprobe for investigation of glycosylation and phosphorylation in Alzheimer's disease. J Chromatogr A 2022; 1676:463236. [PMID: 35709605 DOI: 10.1016/j.chroma.2022.463236] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 10/18/2022]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disease. Abnormal glycosylation and phosphorylation modification in AD may be closely related to its pathology. It is of substantial practical significance to simultaneously investigate the roles of phosphorylation and glycosylation in AD. In this work, a bifunctional super-hydrophilic mesoporous nanocomposite (denoted mTiO2@AuCG) was prepared, which combined hydrophilic interaction chromatography (HILIC) and metal oxide affinity chromatography (MOAC) enrichment strategies to enrich phosphopeptides and glycopeptides, respectively or simultaneously. The mTiO2@AuCG exhibited excellent performance on the high-efficiency enrichment of glycopeptides (selectivity, 5000:1 molar ratios of BSA/HRP; sensitivity, 0.1 fmol HRP; satisfactory recovery rate; loading capacity, 200 mg/g) and phosphopeptides (selectivity, 1000:1 molar ratios of BSA/β-casein; sensitivity, 0.2 fmol β-casein; satisfactory recovery rate; loading capacity, 200 mg/g). Using these advantages, after single-step enrichment of mTiO2@AuCG, a total of 209 glycopeptides related to 93 glycoproteins, and 17 phosphopeptides related to 13 phosphoproteins were detected from normal human serum. By contrast, 167 glycopeptides related to 88 glycoproteins, and 14 phosphopeptides related to 12 phosphoproteins were found in AD serum.
Collapse
Affiliation(s)
- Linhua Yi
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Mengyao Fu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yifan Shao
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Keqi Tang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| |
Collapse
|
14
|
Wu D, Robinson CV. Understanding glycoprotein structural heterogeneity and interactions: Insights from native mass spectrometry. Curr Opin Struct Biol 2022; 74:102351. [DOI: 10.1016/j.sbi.2022.102351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 11/25/2022]
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
Collapse
Affiliation(s)
- Amber D. Rolland
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene, OR, USA 97403-1253
- Materials Science Institute, 1252 University of Oregon, Eugene, OR, USA 97403-1252
| |
Collapse
|
17
|
Abstract
Native mass spectrometry (MS) involves the analysis and characterization of macromolecules, predominantly intact proteins and protein complexes, whereby as much as possible the native structural features of the analytes are retained. As such, native MS enables the study of secondary, tertiary, and even quaternary structure of proteins and other biomolecules. Native MS represents a relatively recent addition to the analytical toolbox of mass spectrometry and has over the past decade experienced immense growth, especially in enhancing sensitivity and resolving power but also in ease of use. With the advent of dedicated mass analyzers, sample preparation and separation approaches, targeted fragmentation techniques, and software solutions, the number of practitioners and novel applications has risen in both academia and industry. This review focuses on recent developments, particularly in high-resolution native MS, describing applications in the structural analysis of protein assemblies, proteoform profiling of─among others─biopharmaceuticals and plasma proteins, and quantitative and qualitative analysis of protein-ligand interactions, with the latter covering lipid, drug, and carbohydrate molecules, to name a few.
Collapse
Affiliation(s)
- Sem Tamara
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Maurits A. den Boer
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584
CH Utrecht, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
18
|
Konstantinidi A, Nason R, Čaval T, Sun L, Sørensen DM, Furukawa S, Ye Z, Vincentelli R, Narimatsu Y, Vakhrushev SY, Clausen H. Exploring the glycosylation of mucins by use of O-glycodomain reporters recombinantly expressed in glycoengineered HEK293 cells. J Biol Chem 2022; 298:101784. [PMID: 35247390 PMCID: PMC8980628 DOI: 10.1016/j.jbc.2022.101784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 12/18/2022] Open
Abstract
Mucins and glycoproteins with mucin-like regions contain densely O-glycosylated domains often found in tandem repeat (TR) sequences. These O-glycodomains have traditionally been difficult to characterize because of their resistance to proteolytic digestion, and knowledge of the precise positions of O-glycans is particularly limited for these regions. Here, we took advantage of a recently developed glycoengineered cell-based platform for the display and production of mucin TR reporters with custom-designed O-glycosylation to characterize O-glycodomains derived from mucins and mucin-like glycoproteins. We combined intact mass and bottom-up site-specific analysis for mapping O-glycosites in the mucins, MUC2, MUC20, MUC21, protein P-selectin-glycoprotein ligand 1, and proteoglycan syndecan-3. We found that all the potential Ser/Thr positions in these O-glycodomains were O-glycosylated when expressed in human embryonic kidney 293 SimpleCells (Tn-glycoform). Interestingly, we found that all potential Ser/Thr O-glycosites in TRs derived from secreted mucins and most glycosites from transmembrane mucins were almost fully occupied, whereas TRs from a subset of transmembrane mucins were less efficiently processed. We further used the mucin TR reporters to characterize cleavage sites of glycoproteases StcE (secreted protease of C1 esterase inhibitor from EHEC) and BT4244, revealing more restricted substrate specificities than previously reported. Finally, we conducted a bottom-up analysis of isolated ovine submaxillary mucin, which supported our findings that mucin TRs in general are efficiently O-glycosylated at all potential glycosites. This study provides insight into O-glycosylation of mucins and mucin-like domains, and the strategies developed open the field for wider analysis of native mucins.
Collapse
Affiliation(s)
- Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rebecca Nason
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tomislav Čaval
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lingbo Sun
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Daniel M Sørensen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sanae Furukawa
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
19
|
Zhang S, Go EP, Ding H, Anang S, Kappes JC, Desaire H, Sodroski JG. Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. J Virol 2022; 96:e0162621. [PMID: 34817202 PMCID: PMC8827021 DOI: 10.1128/jvi.01626-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/12/2021] [Indexed: 12/17/2022] Open
Abstract
The SARS-CoV-2 coronavirus, the etiologic agent of COVID-19, uses its spike (S) glycoprotein anchored in the viral membrane to enter host cells. The S glycoprotein is the major target for neutralizing antibodies elicited by natural infection and by vaccines. Approximately 35% of the SARS-CoV-2 S glycoprotein consists of carbohydrate, which can influence virus infectivity and susceptibility to antibody inhibition. We found that virus-like particles produced by coexpression of SARS-CoV-2 S, M, E, and N proteins contained spike glycoproteins that were extensively modified by complex carbohydrates. We used a fucose-selective lectin to purify the Golgi-modified fraction of a wild-type SARS-CoV-2 S glycoprotein trimer and determined its glycosylation and disulfide bond profile. Compared with soluble or solubilized S glycoproteins modified to prevent proteolytic cleavage and to retain a prefusion conformation, more of the wild-type S glycoprotein N-linked glycans are processed to complex forms. Even Asn 234, a significant percentage of which is decorated by high-mannose glycans on other characterized S trimer preparations, is predominantly modified in the Golgi compartment by processed glycans. Three incompletely occupied sites of O-linked glycosylation were detected. Viruses pseudotyped with natural variants of the serine/threonine residues implicated in O-linked glycosylation were generally infectious and exhibited sensitivity to neutralization by soluble ACE2 and convalescent antisera comparable to that of the wild-type virus. Unlike other natural cysteine variants, a Cys15Phe (C15F) mutant retained partial, but unstable, infectivity. These findings enhance our understanding of the Golgi processing of the native SARS-CoV-2 S glycoprotein carbohydrates and could assist the design of interventions. IMPORTANCE The SARS-CoV-2 coronavirus, which causes COVID-19, uses its spike glycoprotein to enter host cells. The viral spike glycoprotein is the main target of host neutralizing antibodies that help to control SARS-CoV-2 infection and are important for the protection provided by vaccines. The SARS-CoV-2 spike glycoprotein consists of a trimer of two subunits covered with a coat of carbohydrates (sugars). Here, we describe the disulfide bonds that assist the SARS-CoV-2 spike glycoprotein to assume the correct shape and the composition of the sugar moieties on the glycoprotein surface. We also evaluate the consequences of natural virus variation in O-linked sugar addition and in the cysteine residues involved in disulfide bond formation. This information can expedite the improvement of vaccines and therapies for COVID-19.
Collapse
Affiliation(s)
- Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Eden P. Go
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Saumya Anang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - John C. Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, Alabama, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Joseph G. Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| |
Collapse
|
20
|
Bai H, Zhang B, Cheng X, Liu J, Wang X, Qin W, Zhang M. Synthesis of zwitterionic polymer modified graphene oxide for hydrophilic enrichment of N-glycopeptides from urine of healthy subjects and patients with lung adenocarcinoma. Talanta 2022; 237:122938. [PMID: 34736669 DOI: 10.1016/j.talanta.2021.122938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/26/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
As one of the most common and important post-translational modifications, protein N-glycosylation plays essential roles in many biological processes and have long been considered closely correlated with the occurrence and progression of multiple diseases. Systematic characterization of these disease-related protein N-glycosylation is one of the most convenient ways for new diagnostic biomarker and therapeutic drug target discovering. However, the biological samples are extremely complex and the abundance of N-glycoproteins are especially low, which make highly efficient N-glycoprotein/glycopeptide enrichment before mass spectrometry analysis a prerequisite. In this work, a new type of hydrophilic material (GO-pDMAPS) was prepared by in situ growth of linear zwitterionic polymer chains on the surface of GO and it was successfully applied for N-glycopeptide enrichment from human urine. Due to the excellent hydrophilicity and the facilitate interactions between this GO-pDMAPS and the targets, a total of 1426 N-glycosylated sites corresponding to 766 N-glycoproteins as well as 790 N-glycosylation sites corresponding to 470 N-glycoproteins were enriched and identified from urine of healthy subjects and patients with lung adenocarcinoma, respectively. Among which, 27 N-glycoproteins were expressed exclusively and 4 N-glycoproteins were upregulated at least 3 times comparing with the healthy group, demonstrating the tremendous potential of this new hydrophilic material for large scale and in depth N-glycoproteome research.
Collapse
Affiliation(s)
- Haihong Bai
- Clinical Laboratory Medicine, Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, PR China; Phase Ⅰ Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, PR China
| | - Baoying Zhang
- Phase Ⅰ Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, PR China; State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, 102206, PR China
| | - Xiaoqiang Cheng
- Phase Ⅰ Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, PR China
| | - Ju Liu
- Phase Ⅰ Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, PR China
| | - Xinghe Wang
- Phase Ⅰ Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, PR China
| | - Weijie Qin
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing, 102206, PR China
| | - Man Zhang
- Clinical Laboratory Medicine, Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, PR China.
| |
Collapse
|
21
|
Xu Y, Gao Z, Hu R, Wang Y, Wang Y, Su Z, Zhang X, Yang J, Mei M, Ren Y, Li M, Zhou X. PD-L2 glycosylation promotes immune evasion and predicts anti-EGFR efficacy. J Immunother Cancer 2021; 9:jitc-2021-002699. [PMID: 34697216 PMCID: PMC8547513 DOI: 10.1136/jitc-2021-002699] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2021] [Indexed: 12/25/2022] Open
Abstract
Background Combination therapy has been explored for advanced head and neck squamous cell carcinoma (HNSCC) owing to the limited efficacy of anti-epidermal growth factor receptor (EGFR) therapy. Increased expression and glycosylation of immune checkpoint molecules in tumors are responsible for cetuximab therapy refractoriness. The role of programmed death ligand 2 (PD-L2), a ligand of PD-1, in the immune function is unclear. Here, we examined the regulatory mechanism of PD-L2 glycosylation and its role in antitumor immunity and cetuximab therapy. Methods Single-cell RNA sequencing and immunohistochemical staining were used to investigate PD-L2 expression in cetuximab-resistant/sensitive HNSCC tissues. The mechanism of PD-L2 glycosylation regulation was explored in vitro. The effects of PD-L2 glycosylation on immune evasion and cetuximab efficacy were verified in vitro and using mice bearing orthotopic SCC7 tumors. Results The PD-L2 levels were elevated and N-glycosylated in patients with cetuximab-resistant HNSCC. Glycosylated PD-L2 formed a complex with EGFR, which resulted in the activation of EGFR/signal transducer and activator of transcription 3 (STAT3) signaling and decreased the cetuximab binding affinity to EGFR. The N-glycosyltransferase fucosyltransferase (FUT8), a transcriptional target of STAT3, was required for PD-L2 glycosylation. Moreover, glycosylation modification stabilized PD-L2 by blocking ubiquitin-dependent lysosomal degradation, which consequently promoted its binding to PD-1 and immune evasion. Inhibition of PD-L2 glycosylation using Stattic, a specific STAT3 inhibitor, or PD-L2 mutation blocking its binding to FUT8, increased cytotoxic T lymphocyte activity and augmented response to cetuximab. Conclusions Increased expression and glycosylation of PD-L2 in tumors are an important mechanism for cetuximab therapy refractoriness. Thus, the combination of PD-L2 glycosylation inhibition and cetuximab is a potential therapeutic strategy for cancer.
Collapse
Affiliation(s)
- Yiqi Xu
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China.,Department of Maxillofacial and Otorhinolaryngology Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Zhenyue Gao
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China.,Department of Maxillofacial and Otorhinolaryngology Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Ruxin Hu
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Yuqing Wang
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Yuhong Wang
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Zheng Su
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Xiaoyue Zhang
- Department of Maxillofacial and Otorhinolaryngology Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Jingxuan Yang
- Department of Medicine, Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Mei Mei
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Yu Ren
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Min Li
- Department of Medicine, Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Xuan Zhou
- Department of Maxillofacial and Otorhinolaryngology Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| |
Collapse
|
22
|
Abstract
Mucin-domain glycoproteins comprise a class of proteins whose densely O-glycosylated mucin domains adopt a secondary structure with unique biophysical and biochemical properties. The canonical family of mucins is well-known to be involved in various diseases, especially cancer. Despite this, very little is known about the site-specific molecular structures and biological activities of mucins, in part because they are extremely challenging to study by mass spectrometry (MS). Here, we summarize recent advancements toward this goal, with a particular focus on mucin-domain glycoproteins as opposed to general O-glycoproteins. We summarize proteolytic digestion techniques, enrichment strategies, MS fragmentation, and intact analysis, as well as new bioinformatic platforms. In particular, we highlight mucin directed technologies such as mucin-selective proteases, tunable mucin platforms, and a mucinomics strategy to enrich mucin-domain glycoproteins from complex samples. Finally, we provide examples of targeted mucin-domain glycoproteomics that combine these techniques in comprehensive site-specific analyses of proteins. Overall, this Review summarizes the methods, challenges, and new opportunities associated with studying enigmatic mucin domains.
Collapse
Affiliation(s)
- Valentina Rangel-Angarita
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States
| | - Stacy A. Malaker
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States
| |
Collapse
|
23
|
[Preparation of multi-functional magnetic nanoparticles for harvesting low-molecular-weight glycoproteins]. Se Pu 2021; 39:1102-1110. [PMID: 34505432 PMCID: PMC9404145 DOI: 10.3724/sp.j.1123.2021.07019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
低分子量糖蛋白被认为是发现疾病生物标志物的宝库。特异性的萃取吸附剂对这一类化合物的萃取和富集是必不可少的。硼亲和材料在近年来取得了很大的发展,但专门用于选择性富集低分子量糖蛋白的硼亲和材料目前鲜有报道。该文提出了具有多种功能的磁性纳米颗粒(MNPs),用于低分子量糖蛋白的选择性捕获。该多功能磁性纳米颗粒是用硼酸功能化聚合物网络包裹的磁性纳米复合物。该多功能磁性纳米材料是利用磁性的纳米颗粒内核通过在其表面修饰苯硼酸功能团的聚丙烯酸高分子网络链制备得到。该材料不仅具有常规磁性材料在磁分离方面的基本优势,还能提供三重预先设计的先进功能:1)尺寸排阻效应,去除高分子量蛋白质的干扰;2)对低分子量糖蛋白的选择性萃取;3)保护捕获到的低分子量糖蛋白不被降解和污染。该材料的选择性萃取功能来自于硼酸配基与糖蛋白的顺式二醇部分的亲和性,而尺寸限制效应和保护功能则依赖于磁性纳米颗粒表面修饰的聚合物网络,允许低分子量化合物选择性通过。通过实验验证了这些预设的功能,且通过改变聚合物链长可以调节限径效应的阈值。这种多功能磁性纳米复合物可以进一步发展成有前景的纳米探针,不仅可以选择性捕获低分子量糖蛋白,还可以选择性捕获核苷和聚糖等其他具有重要生物学意义的顺式二醇分子。因此,该文报道的材料制备策略为从复杂样品中选择性萃取靶标化合物的多功能吸附剂的设计和合成提供了新思路。
Collapse
|
24
|
Yao X, Zhang S, Qian L, Du M. Dendrimer-assisted boronate affinity cellulose foams for the efficient and selective separation of glycoproteins. Carbohydr Polym 2021; 265:118082. [PMID: 33966846 DOI: 10.1016/j.carbpol.2021.118082] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 12/18/2022]
Abstract
Surfaces engineered to identify and enrich glycoproteins are of considerable interest in the diagnostic and detection fields. A boronate affinity (BA) material was proposed as a potential candidate for the isolation of glycoproteins. However, this material has the disadvantages of low efficiency and non-degradability. Herein, a novel dendrimer-amplified BA cellulose foam (PEI-PBA-CF) was fabricated via a mild two-step approach. The as-prepared PEI-PBA-CF exhibited a rapid adsorption equilibrium rate (within 60 min) and outstanding adsorption capacity for horseradish peroxidase (537.4 mg g-1) and ovalbumin (495.5 mg g-1). Furthermore, competitive adsorption experiments demonstrated that PEI-PBA-CF could achieve selective separation and purification of glycoproteins from complex biological samples due to the synergistic effect of the improved BA capacity by the dendrimer and the well-interconnected porous structure of the biomass matrix. Consequently, these cellulose foams might present new application opportunities in analytical and biomedical fields.
Collapse
Affiliation(s)
- Xue Yao
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, National Demonstration Center for Experimental Light Chemistry Engineering Education, Key Laboratory of Paper Based Functional Materials of China National Light Industry, Shaanxi University of Science and Technology, Xian, 710021, China
| | - Sufeng Zhang
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, National Demonstration Center for Experimental Light Chemistry Engineering Education, Key Laboratory of Paper Based Functional Materials of China National Light Industry, Shaanxi University of Science and Technology, Xian, 710021, China.
| | - Liwei Qian
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, National Demonstration Center for Experimental Light Chemistry Engineering Education, Key Laboratory of Paper Based Functional Materials of China National Light Industry, Shaanxi University of Science and Technology, Xian, 710021, China.
| | - Min Du
- Shaanxi Provincial Key Laboratory of Papermaking Technology and Specialty Paper Development, National Demonstration Center for Experimental Light Chemistry Engineering Education, Key Laboratory of Paper Based Functional Materials of China National Light Industry, Shaanxi University of Science and Technology, Xian, 710021, China
| |
Collapse
|
25
|
[Synthesis of zwitterionic dual-functional metal-organic framework nanocomposite with ultra-hydrophilicity for selective enrichment of glycopeptides]. Se Pu 2021; 39:205-210. [PMID: 34227302 PMCID: PMC9403811 DOI: 10.3724/sp.j.1123.2020.11006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
蛋白糖基化是生物体中普遍发生且重要的生物学过程,其参与多种分子生物学的功能和途径,是临床诊断重要的生物标志物。但是,糖肽因其丰度低、离子化效率低、糖链异质性等难点,使糖蛋白分析一直面临巨大的挑战。因此,研究合成了一种新型的两性离子双功能化纳米金(AuGC)修饰的超亲水性沸石咪唑骨架(ZIF-8)纳米复合材料(AuGC/ZIF-8),并建立了亲水相互作用色谱(HILIC)和基质辅助激光解吸电离-飞行时间质谱(MALDI-TOF MS)联用选择性富集糖肽的分析方法。谷胱甘肽和半胱氨酸双功能化的协同作用,使MOF具有超亲水性和低空间位阻,为糖肽选择性富集提供了更多的亲和位点。研究以辣根过氧化物酶(HRP)为模式糖蛋白,通过AuGC/ZIF-8富集后,MALDI-TOF MS分析。结果表明,AuGC/ZIF-8对HRP糖肽的富集能力高达250 μg/mg,且在与牛血清白蛋白(BSA)混合溶液中(HRP-BSA (1∶200,质量比))显示出对HRP糖肽的高选择性,以及极低含量下(0.3 ng/μL)的高灵敏度。因此,在复杂生物样品糖蛋白的富集分离中具有很大的应用潜力。
Collapse
|
26
|
Chen S, Wu D, Robinson CV, Struwe WB. Native Mass Spectrometry Meets Glycomics: Resolving Structural Detail and Occupancy of Glycans on Intact Glycoproteins. Anal Chem 2021; 93:10435-10443. [PMID: 34279906 DOI: 10.1021/acs.analchem.1c01460] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Glycoproteins are inherently heterogeneous and therefore resolving structures in their entirety remains a major challenge in structural biology. Native mass spectrometry has transformed our ability to study glycoproteins, and despite advances in high-resolution instrumentation, there are comparatively a few studies demonstrating its potential with data largely limited to an overall measure of monosaccharide composition for all glycans across glycosylation sites for a given protein. Clearly, these readouts lack glycan topology information, namely, monosaccharide linkage and glycan branching. To address this deficiency, we developed a new approach that joins native mass spectrometry with glycan exoglycosidase sequencing, the combination of which provides remarkable glycoprotein structural details. We show how N-glycan branching, terminal fucosylation, LacNAc extensions, and N- and O-glycan occupancy (i.e., total number of glycans) can be directly characterized on intact glycoproteins with minimal sample preparation. Taken together, native exoglycosidase sequencing mass spectrometry (NES-MS) notably improves our ability to characterize protein glycosylation, addressing a significant need in structural biology that will enable new routes to understand glycoprotein function.
Collapse
Affiliation(s)
- Siyun Chen
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
| | - Di Wu
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
| | - Carol V Robinson
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
| | - Weston B Struwe
- Physical and Theoretical Chemistry, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, U.K
| |
Collapse
|
27
|
Wu D, Robinson CV. Connecting ‘multi-omics’ approaches to endogenous protein complexes. TRENDS IN CHEMISTRY 2021. [DOI: 10.1016/j.trechm.2021.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
28
|
Kong S, Zhang Q, Yang L, Huang Y, Liu M, Yan G, Zhao H, Wu M, Zhang X, Yang P, Cao W. Effective Enrichment Strategy Using Boronic Acid-Functionalized Mesoporous Graphene-Silica Composites for Intact N- and O-Linked Glycopeptide Analysis in Human Serum. Anal Chem 2021; 93:6682-6691. [PMID: 33877808 DOI: 10.1021/acs.analchem.0c05482] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The heterogeneity and low abundance of protein glycosylation present challenging barriers to the analysis of intact glycopeptides, which is key to comprehensively understanding the role of glycosylation in an organism. Efficient and specific enrichment of intact glycopeptides could help greatly with this problem. Here, we propose a new enrichment strategy using a boronic acid (BA)-functionalized mesoporous graphene-silica composite (denoted as GO@mSiO2-GLYMO-APB) for isolating intact glycopeptides from complex biological samples. The merits of this composite, including high surface area and synergistic effect from size exclusion functionality of mesoporous material, hydrophilic interaction of silica, and the reversible covalent binding with BA, enable the effective and specific enrichment of both intact N- and O-glycopeptides. The results from the enrichment performance of the strategy evaluated by standard glycoproteins and the application to global N- and O-glycosylation analyses in human serum indicate the robustness and potential of the strategy for intact glycopeptide analysis.
Collapse
Affiliation(s)
- Siyuan Kong
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Quanqing Zhang
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Lujie Yang
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yuanyu Huang
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Mingqi Liu
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Guoquan Yan
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Huanhuan Zhao
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Mengxi Wu
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Xiangmin Zhang
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China.,Department of Chemistry, Fudan University, Shanghai 200043, China
| | - Pengyuan Yang
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China.,Department of Chemistry, Fudan University, Shanghai 200043, China
| | - Weiqian Cao
- The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| |
Collapse
|
29
|
Zhang S, Go EP, Ding H, Anang S, Kappes JC, Desaire H, Sodroski J. Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33821278 PMCID: PMC8020978 DOI: 10.1101/2021.04.01.438120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The SARS-CoV-2 coronavirus, the etiologic agent of COVID-19, uses its spike (S) glycoprotein anchored in the viral membrane to enter host cells. The S glycoprotein is the major target for neutralizing antibodies elicited by natural infection and by vaccines. Approximately 35% of the SARS-CoV-2 S glycoprotein consists of carbohydrate, which can influence virus infectivity and susceptibility to antibody inhibition. We found that virus-like particles produced by coexpression of SARS-CoV-2 S, M, E and N proteins contained spike glycoproteins that were extensively modified by complex carbohydrates. We used a fucose-selective lectin to enrich the Golgi-resident fraction of a wild-type SARS-CoV-2 S glycoprotein trimer, and determined its glycosylation and disulfide bond profile. Compared with soluble or solubilized S glycoproteins modified to prevent proteolytic cleavage and to retain a prefusion conformation, more of the wild-type S glycoprotein N-linked glycans are processed to complex forms. Even Asn 234, a significant percentage of which is decorated by high-mannose glycans on soluble and virion S trimers, is predominantly modified in the Golgi by processed glycans. Three incompletely occupied sites of O-linked glycosylation were detected. Viruses pseudotyped with natural variants of the serine/threonine residues implicated in O-linked glycosylation were generally infectious and exhibited sensitivity to neutralization by soluble ACE2 and convalescent antisera comparable to that of the wild-type virus. Unlike other natural cysteine variants, a Cys15Phe (C15F) mutant retained partial, but unstable, infectivity. These findings enhance our understanding of the Golgi processing of the native SARS-CoV-2 S glycoprotein carbohydrates and could assist the design of interventions.
Collapse
|
30
|
Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
Collapse
Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
| |
Collapse
|
31
|
Čaval T, Heck AJR, Reiding KR. Meta-heterogeneity: Evaluating and Describing the Diversity in Glycosylation Between Sites on the Same Glycoprotein. Mol Cell Proteomics 2020; 20:100010. [PMID: 33561609 PMCID: PMC8724623 DOI: 10.1074/mcp.r120.002093] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/14/2020] [Accepted: 07/31/2020] [Indexed: 12/26/2022] Open
Abstract
Mass spectrometry-based glycoproteomics has gone through some incredible developments over the last few years. Technological advances in glycopeptide enrichment, fragmentation methods, and data analysis workflows have enabled the transition of glycoproteomics from a niche application, mainly focused on the characterization of isolated glycoproteins, to a mature technology capable of profiling thousands of intact glycopeptides at once. In addition to numerous biological discoveries catalyzed by the technology, we are also observing an increase in studies focusing on global protein glycosylation and the relationship between multiple glycosylation sites on the same protein. It has become apparent that just describing protein glycosylation in terms of micro- and macro-heterogeneity, respectively, the variation and occupancy of glycans at a given site, is not sufficient to describe the observed interactions between sites. In this perspective we propose a new term, meta-heterogeneity, to describe a higher level of glycan regulation: the variation in glycosylation across multiple sites of a given protein. We provide literature examples of extensive meta-heterogeneity on relevant proteins such as antibodies, erythropoietin, myeloperoxidase, and a number of serum and plasma proteins. Furthermore, we postulate on the possible biological reasons and causes behind the intriguing meta-heterogeneity observed in glycoproteins.
Collapse
Affiliation(s)
- Tomislav Čaval
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands; Netherlands Proteomics Center, Utrecht, the Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands; Netherlands Proteomics Center, Utrecht, the Netherlands.
| | - Karli R Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands; Netherlands Proteomics Center, Utrecht, the Netherlands.
| |
Collapse
|
32
|
Barth M, Schmidt C. Native mass spectrometry-A valuable tool in structural biology. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4578. [PMID: 32662584 DOI: 10.1002/jms.4578] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 05/16/2023]
Abstract
Proteins and the complexes they form with their ligands are the players of cellular action. Their function is directly linked with their structure making the structural analysis of protein-ligand complexes essential. Classical techniques of structural biology include X-ray crystallography, nuclear magnetic resonance spectroscopy and recently distinguished cryo-electron microscopy. However, protein-ligand complexes are often dynamic and heterogeneous and consequently challenging for these techniques. Alternative approaches are therefore needed and gained importance during the last decades. One alternative is native mass spectrometry, which is the analysis of intact protein complexes in the gas phase. To achieve this, sample preparation and instrument conditions have to be optimised. Native mass spectrometry then reveals stoichiometry, protein interactions and topology of protein assemblies. Advanced techniques such as ion mobility and high-resolution mass spectrometry further add to the range of applications and deliver information on shape and microheterogeneity of the complexes. In this tutorial, we explain the basics of native mass spectrometry including sample requirements, instrument modifications and interpretation of native mass spectra. We further discuss the developments of native mass spectrometry and provide example spectra and applications.
Collapse
Affiliation(s)
- Marie Barth
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| |
Collapse
|
33
|
Measurement of macro- and micro-heterogeneity of glycosylation in biopharmaceuticals: a pharmacopeia perspective. FUTURE DRUG DISCOVERY 2020. [DOI: 10.4155/fdd-2020-0021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
|
34
|
Ugonotti J, Chatterjee S, Thaysen-Andersen M. Structural and functional diversity of neutrophil glycosylation in innate immunity and related disorders. Mol Aspects Med 2020; 79:100882. [PMID: 32847678 DOI: 10.1016/j.mam.2020.100882] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022]
Abstract
The granulated neutrophils are abundant innate immune cells that utilize bioactive glycoproteins packed in cytosolic granules to fight pathogenic infections, but the neutrophil glycobiology remains poorly understood. Facilitated by technological advances in glycoimmunology, systems glycobiology and glycoanalytics, a considerable body of literature reporting on novel aspects of neutrophil glycosylation has accumulated. Herein, we summarize the building knowledge of the structural and functional diversity displayed by N- and O-linked glycoproteins spatiotemporally expressed and sequentially brought-into-action across the diverse neutrophil life stages during bone marrow maturation, movements to, from and within the blood circulation and microbicidal processes at the inflammatory sites in peripheral tissues. It transpires that neutrophils abundantly decorate their granule glycoproteins including neutrophil elastase, myeloperoxidase and cathepsin G with peculiar glyco-signatures not commonly reported in other areas of human glycobiology such as hyper-truncated chitobiose core- and paucimannosidic-type N-glycans and monoantennary complex-type N-glycans. Sialyl Lewisx, Lewisx, poly-N-acetyllactosamine extensions and core 1-/2-type O-glycans are also common neutrophil glyco-signatures. Granule-specific glycosylation is another fascinating yet not fully understood feature of neutrophils. Recent literature suggests that unconventional biosynthetic pathways and functions underpin these prominent neutrophil-associated glyco-phenotypes. The impact of glycosylation on key neutrophil effector functions including extravasation, degranulation, phagocytosis and formation of neutrophil extracellular traps during normal physiological conditions and in innate immune-related diseases is discussed. We also highlight new technologies that are expected to further advance neutrophil glycobiology and briefly discuss the untapped diagnostic and therapeutic potential of neutrophil glycosylation that could open avenues to combat the increasingly prevalent innate immune disorders.
Collapse
Affiliation(s)
- Julian Ugonotti
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| | - Sayantani Chatterjee
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, 2109, Australia.
| |
Collapse
|
35
|
Xie Y, Sheng Y, Li Q, Ju S, Reyes J, Lebrilla CB. Determination of the glycoprotein specificity of lectins on cell membranes through oxidative proteomics. Chem Sci 2020; 11:9501-9512. [PMID: 34094216 PMCID: PMC8162070 DOI: 10.1039/d0sc04199h] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/13/2020] [Indexed: 12/25/2022] Open
Abstract
The cell membrane is composed of a network of glycoconjugates including glycoproteins and glycolipids that presents a dense matrix of carbohydrates playing critical roles in many biological processes. Lectin-based technology has been widely used to characterize glycoconjugates in tissues and cell lines. However, their specificity toward their putative glycan ligand and sensitivity in situ have been technologically difficult to study. Additionally, because they recognize primarily glycans, the underlying glycoprotein targets are generally not known. In this study, we employed lectin proximity oxidative labeling (Lectin PROXL) to identify cell surface glycoproteins that contain glycans that are recognized by lectins. Commonly used lectins were modified with a probe to produce hydroxide radicals in the proximity of the labeled lectins. The underlying polypeptides of the glycoproteins recognized by the lectins are oxidized and identified by the standard proteomic workflow. As a result, approximately 70% of identified glycoproteins were oxidized in situ by all the lectin probes, while only 5% of the total proteins were oxidized. The correlation between the glycosites and oxidation sites demonstrated the effectiveness of the lectin probes. The specificity and sensitivity of each lectin were determined using site-specific glycan information obtained through glycomic and glycoproteomic analyses. Notably, the sialic acid-binding lectins and the fucose-binding lectins had higher specificity and sensitivity compared to other lectins, while those that were specific to high mannose glycans have poor sensitivity and specificity. This method offers an unprecedented view of the interactions of lectins with specific glycoproteins as well as protein networks that are mediated by specific glycan types on cell membranes.
Collapse
Affiliation(s)
- Yixuan Xie
- Department of Chemistry, University of California Davis Davis California USA
| | - Ying Sheng
- Department of Chemistry, Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California Davis Davis California USA
| | - Qiongyu Li
- Department of Chemistry, University of California Davis Davis California USA
| | - Seunghye Ju
- Department of Chemistry, University of California Davis Davis California USA
| | - Joe Reyes
- Marine Science Institute, University of the Philippines Diliman Quezon City Philippines
| | - Carlito B Lebrilla
- Department of Chemistry, University of California Davis Davis California USA
- Department of Biochemistry, University of California Davis Davis California USA
| |
Collapse
|
36
|
Tamara S, Franc V, Heck AJR. A wealth of genotype-specific proteoforms fine-tunes hemoglobin scavenging by haptoglobin. Proc Natl Acad Sci U S A 2020; 117:15554-15564. [PMID: 32561649 PMCID: PMC7355005 DOI: 10.1073/pnas.2002483117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The serum haptoglobin protein (Hp) scavenges toxic hemoglobin (Hb) leaked into the bloodstream from erythrocytes. In humans, there are two frequently occurring allelic forms of Hp, resulting in three genotypes: Homozygous Hp 1-1 and Hp 2-2, and heterozygous Hp 2-1. The Hp genetic polymorphism has an intriguing effect on the quaternary structure of Hp. The simplest form, Hp 1-1, forms dimers consisting of two α1β units, connected by disulfide bridges. Hp 2-1 forms mixtures of linear (α1)2(α2)n-2(β)n oligomers (n > 1) while Hp 2-2 occurs in cyclic (α2)n(β)n oligomers (n > 2). Different Hp genotypes bind Hb with different affinities, with Hp 2-2 being the weakest binder. This behavior has a significant influence on Hp's antioxidant capacity, with potentially distinctive personalized clinical consequences. Although Hp has been studied extensively in the past, the finest molecular details of the observed differences in interactions between Hp and Hb are not yet fully understood. Here, we determined the full proteoform profiles and proteoform assemblies of all three most common genetic Hp variants. We combined several state-of-the-art analytical methods, including various forms of chromatography, mass photometry, and different tiers of mass spectrometry, to reveal how the tens to hundreds distinct proteoforms and their assemblies influence Hp's capacity for Hb binding. We extend the current knowledge by showing that Hb binding does not just depend on the donor's genotype, but is also affected by variations in Hp oligomerization, glycosylation, and proteolytic processing of the Hp α-chain.
Collapse
Affiliation(s)
- Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands
| | - Vojtech Franc
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands
- Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands;
- Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
37
|
Chen Q, Tan Z, Guan F, Ren Y. The Essential Functions and Detection of Bisecting GlcNAc in Cell Biology. Front Chem 2020; 8:511. [PMID: 32719771 PMCID: PMC7350706 DOI: 10.3389/fchem.2020.00511] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/18/2020] [Indexed: 12/11/2022] Open
Abstract
The N-glycans of mammalian glycoproteins vary greatly in structure, and the biological importance of these variations is mostly unknown. It is widely acknowledged that the bisecting N-acetylglucosamine (GlcNAc) structure, a β1,4-linked GlcNAc attached to the core β-mannose residue, represents a special type of N-glycosylated modification, and it has been reported to be involved in various biological processes, such as cell adhesion, fertilization and fetal development, neuritogenesis, and tumor development. In particular, the occurrence of N-glycans with a bisecting GlcNAc modification on proteins has been proven, with many implications for immune biology. Due to the essential functions of bisecting GlcNAc structures, analytical approaches to this modification are highly required. The traditional approach that has been used for bisecting GlcNAc determinations is based on the lectin recognition of Phaseolus vulgaris erythroagglutinin (PHA-E); however, poor binding specificity hinders the application of this method. With the development of mass spectrometry (MS) with high resolution and improved sensitivity and accuracy, MS-based glycomic analysis has provided precise characterization and quantification for glycosylation modification. In this review, we first provide an overview of the bisecting GlcNAc structure and its biological importance in neurological systems, immune tolerance, immunoglobulin G (IgG), and tumor metastasis and development and then summarize approaches to its determination by MS for performing precise functional studies. This review is valuable for those readers who are interested in the importance of bisecting GlcNAc in cell biology.
Collapse
Affiliation(s)
- Qiushi Chen
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Zengqi Tan
- Joint International Research Laboratory of Glycobiology and Medical Chemistry, College of Life Sciences, Northwest University, Xi'an, China
| | - Feng Guan
- Joint International Research Laboratory of Glycobiology and Medical Chemistry, College of Life Sciences, Northwest University, Xi'an, China
| | - Yan Ren
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| |
Collapse
|
38
|
Feng G, Hao Y, Wu L, Chen S. A visible-light activated [2 + 2] cycloaddition reaction enables pinpointing carbon-carbon double bonds in lipids. Chem Sci 2020; 11:7244-7251. [PMID: 34123010 PMCID: PMC8159383 DOI: 10.1039/d0sc01149e] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/20/2020] [Indexed: 12/11/2022] Open
Abstract
The precise location of C[double bond, length as m-dash]C bonds in bioactive molecules is critical for a deep understanding of the relationship between their structures and biological roles. However, the traditional ultraviolet light-based approaches exhibited great limitations. Here, we discovered a new type of visible-light activated [2 + 2] cycloaddition of carbonyl with C[double bond, length as m-dash]C bonds. We found that carbonyl in anthraquinone showed great reactivities towards C[double bond, length as m-dash]C bonds in lipids to form oxetanes under the irradiation of visible-light. Combined with tandem mass spectrometry, this site-specific dissociation of oxetane enabled precisely locating the C[double bond, length as m-dash]C bonds in various kinds of monounsaturated and polyunsaturated lipids. The proof-of-concept applicability of this new type of [2 + 2] photocycloaddition was validated in the global identification of unsaturated lipids in a complex human serum sample. 86 monounsaturated and polyunsaturated lipids were identified with definitive positions of C[double bond, length as m-dash]C bonds, including phospholipids and fatty acids even with up to 6 C[double bond, length as m-dash]C bonds. This study provides new insights into both the photocycloaddition reactions and the structural lipidomics.
Collapse
Affiliation(s)
- Guifang Feng
- Institute for Advanced Studies, Wuhan University Wuhan Hubei 430072 China
| | - Yanhong Hao
- Institute for Advanced Studies, Wuhan University Wuhan Hubei 430072 China
| | - Liang Wu
- Institute for Advanced Studies, Wuhan University Wuhan Hubei 430072 China
| | - Suming Chen
- Institute for Advanced Studies, Wuhan University Wuhan Hubei 430072 China
| |
Collapse
|
39
|
Plant-Derived Lectins as Potential Cancer Therapeutics and Diagnostic Tools. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1631394. [PMID: 32509848 PMCID: PMC7245692 DOI: 10.1155/2020/1631394] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/27/2020] [Indexed: 12/19/2022]
Abstract
Cancer remains a global health challenge, with high morbidity and mortality, despite the recent advances in diagnosis and treatment. Multiple compounds assessed as novel potential anticancer drugs derive from natural sources, including microorganisms, plants, and animals. Lectins, a group of highly diverse proteins of nonimmune origin with carbohydrate-binding abilities, have been detected in virtually all kingdoms of life. These proteins can interact with free and/or cell surface oligosaccharides and might differentially bind cancer cells, since malignant transformation is tightly associated with altered cell surface glycans. Therefore, lectins could represent a valuable tool for cancer diagnosis and be developed as anticancer therapeutics. Indeed, several plant lectins exert cytotoxic effects mainly by inducing apoptotic and autophagic pathways in malignant cells. This review summarizes the current knowledge regarding the basis for the use of lectins in cancer diagnosis and therapy, providing a few examples of plant-derived carbohydrate-binding proteins with demonstrated antitumor effects.
Collapse
|
40
|
Zheng H, Jia J, Li Z, Jia Q. Bifunctional Magnetic Supramolecular-Organic Framework: A Nanoprobe for Simultaneous Enrichment of Glycosylated and Phosphorylated Peptides. Anal Chem 2020; 92:2680-2689. [DOI: 10.1021/acs.analchem.9b04691] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
41
|
Affiliation(s)
| | | | - Ronghu Wu
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| |
Collapse
|
42
|
Yang SS, Wang C, Xiao J, Yu X, Shang W, Chen DDY, Gu ZY. Highly efficient enrichment of N-glycopeptides by two-dimensional Hf-based metal–organic framework nanosheets. Analyst 2020; 145:4432-4435. [DOI: 10.1039/d0an00647e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
2-D Hf-BTB nanosheets were explored as efficient materials for the capture of glycopeptides from the biosamples in proteomics analysis.
Collapse
Affiliation(s)
- Shi-Shu Yang
- Jiangsu Key Laboratory of Biofunctional Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing 210023
| | - Chen Wang
- Jiangsu Key Laboratory of Biofunctional Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing 210023
| | - Jing Xiao
- Jiangsu Key Laboratory of Biofunctional Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing 210023
| | - Xizhong Yu
- Key Laboratory for Metabolic Diseases in Chinese Medicine
- First College of Clinical Medicine
- Nanjing University of Chinese Medicine
- Nanjing 210023
- China
| | - Wenbin Shang
- Key Laboratory for Metabolic Diseases in Chinese Medicine
- First College of Clinical Medicine
- Nanjing University of Chinese Medicine
- Nanjing 210023
- China
| | - David Da Yong Chen
- Jiangsu Key Laboratory of Biofunctional Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing 210023
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing 210023
| |
Collapse
|
43
|
Yang L, Zhang Q, Huang Y, Lin L, Schlüter H, Wang K, Zhang C, Yang P, Yu H. Boronic acid-functionalized mesoporous magnetic particles with a hydrophilic surface for the multimodal enrichment of glycopeptides for glycoproteomics. Analyst 2020; 145:5252-5259. [PMID: 32617538 DOI: 10.1039/d0an00648c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Boronic acid-functionalized mesoporous magnetic particles with a hydrophilic surface for multimodal enrichment of glycopeptides for glycoproteomics.
Collapse
Affiliation(s)
- Lujie Yang
- Institutes of Biomedical Sciences & Minhang hospital
- Fudan University
- Shanghai
- China
| | - Quanqing Zhang
- Institutes of Biomedical Sciences & Minhang hospital
- Fudan University
- Shanghai
- China
- Department of Chemistry and Environmental Toxicology Graduate Program
| | - Yuanyu Huang
- Institutes of Biomedical Sciences & Minhang hospital
- Fudan University
- Shanghai
- China
| | - Ling Lin
- Institutes of Biomedical Sciences & Minhang hospital
- Fudan University
- Shanghai
- China
| | - Hartmut Schlüter
- Institute of Clinical Chemistry & Laboratory Medicine
- University Medical Center Hamburg-Eppendorf
- Hamburg
- Germany
| | - Ke Wang
- Institutes of Biomedical Sciences & Minhang hospital
- Fudan University
- Shanghai
- China
| | - Cuiping Zhang
- Institutes of Biomedical Sciences & Minhang hospital
- Fudan University
- Shanghai
- China
| | - Pengyuan Yang
- Institutes of Biomedical Sciences & Minhang hospital
- Fudan University
- Shanghai
- China
| | - Hongxiu Yu
- Institutes of Biomedical Sciences & Minhang hospital
- Fudan University
- Shanghai
- China
| |
Collapse
|
44
|
Sajid MS, Jovcevski B, Pukala TL, Jabeen F, Najam-ul-Haq M. Fabrication of Piperazine Functionalized Polymeric Monolithic Tip for Rapid Enrichment of Glycopeptides/Glycans. Anal Chem 2019; 92:683-689. [DOI: 10.1021/acs.analchem.9b02068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Muhammad Salman Sajid
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Blagojce Jovcevski
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Tara Louise Pukala
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Fahmida Jabeen
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Muhammad Najam-ul-Haq
- Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan
| |
Collapse
|
45
|
Yang P, Tian ZL, Xie LP, Su L, He JY, Wu YP, Jia WH. Preparation of Boronic Acid-Functionalized Silica Nanocomposites for Selective Enrichment of Glycoproteins. Chem Biodivers 2019; 17:e1900436. [PMID: 31705573 DOI: 10.1002/cbdv.201900436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/08/2019] [Indexed: 11/09/2022]
Abstract
A facile method was developed for synthesis of boronic acid-functionalized silica nanocomposites (SiO2 -BA) by 'thiol-ene' click reaction, where silica nanoparticles were synthesized by using tetraethoxysilane (TEOS) and γ-mercaptopropyl trimethoxysilane (γ-MPTS) as precursors. The morphology and structure properties of the resultant SiO2 -BA were characterized by transmission electronic microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), and Brunner-Emmet-Teller measurements (BET). The adsorption behavior of the SiO2 -BA for glycoproteins was evaluated. Under the optimized conditions, the SiO2 -BA exhibited higher adsorption capacity towards glycoproteins (ovalbumin, OVA, 7.64 μmol/g) than non-glycoproteins (bovine serum albumin, BSA, 0.83 μmol/g). In addition, the practicality of the SiO2 -BA was further assessed by selective enrichment of glycoproteins from egg white samples.
Collapse
Affiliation(s)
- Peng Yang
- Sixth Hospital of Shanxi Medical University, Taiyuan, 030001, P. R. China
| | - Zeng-Lian Tian
- Sixth Hospital of Shanxi Medical University, Taiyuan, 030001, P. R. China
| | - Li-Ping Xie
- Sixth Hospital of Shanxi Medical University, Taiyuan, 030001, P. R. China
| | - Lin Su
- Sixth Hospital of Shanxi Medical University, Taiyuan, 030001, P. R. China
| | - Jun-Yi He
- Sixth Hospital of Shanxi Medical University, Taiyuan, 030001, P. R. China
| | - Yan-Ping Wu
- Sixth Hospital of Shanxi Medical University, Taiyuan, 030001, P. R. China
| | - Wei-Hua Jia
- Sixth Hospital of Shanxi Medical University, Taiyuan, 030001, P. R. China
| |
Collapse
|
46
|
Relating glycoprotein structural heterogeneity to function - insights from native mass spectrometry. Curr Opin Struct Biol 2019; 58:241-248. [PMID: 31326232 PMCID: PMC7104348 DOI: 10.1016/j.sbi.2019.05.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 05/23/2019] [Accepted: 05/23/2019] [Indexed: 01/08/2023]
Abstract
Glycosylation is the most complex and prevalent protein modification that influences attributes ranging from cellular localization and signaling to half-life and proteolysis. Glycoconjugates are fundamental for cellular function and alterations in their structure are often observed in pathological states. Most biotherapeutic proteins are glycosylated, which influences drug safety and efficacy. Therefore, the ability to characterize glycoproteins is important in all areas of biomolecular and medicinal research. Here we discuss recent advances in native mass spectrometry that have significantly improved our ability to characterize heterogeneous glycoproteins and to relate glycan structure to protein function.
Collapse
|