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Jang L, Kim A, Park CS, Moon C, Kim M, Kim J, Yang S, Jang JY, Jeong CM, Lee HS, Park J, Kim K, Byeon H, Kim HH. Fucosylation and galactosylation in N-glycans of bovine intestinal alkaline phosphatase and their role in its enzymatic activity. Arch Biochem Biophys 2024; 758:110069. [PMID: 38914216 DOI: 10.1016/j.abb.2024.110069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 06/26/2024]
Abstract
Bovine intestinal alkaline phosphatase (biALP), a membrane-bound plasma metalloenzyme, maintains intestinal homeostasis, regulates duodenal surface pH, and protects against infections caused by pathogenic bacteria. The N-glycans of biALP regulate its enzymatic activity, protein folding, and thermostability, but their structures are not fully reported. In this study, the structures and quantities of the N-glycans of biALP were analyzed by liquid chromatography-electrospray ionization-high energy collision dissociation-tandem mass spectrometry. In total, 48 N-glycans were identified and quantified, comprising high-mannose [6 N-glycans, 33.1 % (sum of relative quantities of each N-glycan)], hybrid (6, 11.9 %), and complex (36, 55.0 %) structures [bi- (13, 26.1 %), tri- (16, 21.5 %), and tetra-antennary (7, 7.4 %)]. These included bisecting N-acetylglucosamine (33, 56.6 %), mono-to tri-fucosylation (32, 53.3 %), mono-to tri-α-galactosylation (16, 20.7 %), and mono-to tetra-β-galactosylation (36, 58.5 %). No sialylation was identified. N-glycans with non-bisecting GlcNAc (9, 10.3 %), non-fucosylation (10, 13.6 %), non-α-galactosylation (26, 46.2 %), and non-β-galactosylation (6, 8.4 %) were also identified. The activity (100 %) of biALP was reduced to 37.3 ± 0.2 % (by de-fucosylation), 32.7 ± 2.9 % (by de-α-galactosylation), and 0.2 ± 0.2 % (by de-β-galactosylation), comparable to inhibition by 10-4 to 101 mM EDTA, a biALP inhibitor. These results indicate that fucosylated and galactosylated N-glycans, especially β-galactosylation, affected the activity of biALP. This study is the first to identify 48 diverse N-glycan structures and quantities of bovine as well as human intestinal ALP and to demonstrate the importance of the role of fucosylation and galactosylation for maintaining the activity of biALP.
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Affiliation(s)
- Leeseul Jang
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Ahyeon Kim
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Chi Soo Park
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Chulmin Moon
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Mirae Kim
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Jieun Kim
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Subin Yang
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Ji Yeon Jang
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Chang Myeong Jeong
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Han Seul Lee
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Juhee Park
- Department of Pharmaceutical Regulatory Sciences, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Kyuran Kim
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Haeun Byeon
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Ha Hyung Kim
- Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea; Department of Pharmaceutical Regulatory Sciences, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea.
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Chongsaritsinsuk J, Rangel-Angarita V, Mahoney KE, Lucas TM, Enny OM, Katemauswa M, Malaker SA. Quantification and site-specific analysis of co-occupied N- and O-glycopeptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.06.602348. [PMID: 39005468 PMCID: PMC11245114 DOI: 10.1101/2024.07.06.602348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Protein glycosylation is a complex post-translational modification that is generally classified as N- or O-linked. Site-specific analysis of glycopeptides is accomplished with a variety of fragmentation methods, depending on the type of glycosylation being investigated and the instrumentation available. For instance, collisional dissociation methods are frequently used for N-glycoproteomic analysis with the assumption that one N-sequon exists per tryptic peptide. Alternatively, electron-based methods are indispensable for O-glycosite localization. However, the presence of simultaneously N- and O-glycosylated peptides could suggest the necessity of electron-based fragmentation methods for N-glycoproteomics, which is not commonly performed. Thus, we quantified the prevalence of N- and O-glycopeptides in mucins and other glycoproteins. A much higher frequency of co-occupancy within mucins was detected whereas only a negligible occurrence occurred within non-mucin glycoproteins. This was demonstrated from analyses of recombinant and/or purified proteins, as well as more complex samples. Where co-occupancy occurred, O-glycosites were frequently localized to the Ser/Thr within the N-sequon. Additionally, we found that O-glycans in close proximity to the occupied Asn were predominantly unelaborated core 1 structures, while those further away were more extended. Overall, we demonstrate electron-based methods are required for robust site-specific analysis of mucins, wherein co-occupancy is more prevalent. Conversely, collisional methods are generally sufficient for analyses of other types of glycoproteins.
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DeBono NJ, Moh ESX, Packer NH. Experimentally Determined Diagnostic Ions for Identification of Peptide Glycotopes. J Proteome Res 2024; 23:2661-2673. [PMID: 38888225 DOI: 10.1021/acs.jproteome.3c00858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
The analysis of the structures of glycans present on glycoproteins is an essential component for determining glycoprotein function; however, detailed glycan structural assignment on glycopeptides from proteomics mass spectrometric data remains challenging. Glycoproteomic analysis by mass spectrometry currently can provide significant, yet incomplete, information about the glycans present, including the glycan monosaccharide composition and in some circumstances the site(s) of glycosylation. Advancements in mass spectrometric resolution, using high-mass accuracy instrumentation and tailored MS/MS fragmentation parameters, coupled with a dedicated definition of diagnostic fragmentation ions have enabled the determination of some glycan structural features, or glycotopes, expressed on glycopeptides. Here we present a collation of diagnostic glycan fragments produced by traditional positive-ion-mode reversed-phase LC-ESI MS/MS proteomic workflows and describe the specific fragmentation energy settings required to identify specific glycotopes presented on N- or O-linked glycopeptides in a typical proteomics MS/MS experiment.
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Affiliation(s)
- Nicholas J DeBono
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Edward S X Moh
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Nicolle H Packer
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
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Nilsson J, Rimkute I, Sihlbom C, Tenge VR, Lin SC, Atmar RL, Estes MK, Larson G. N-glycoproteomic analyses of human intestinal enteroids, varying in histo-blood group geno- and phenotypes, reveal a wide repertoire of fucosylated glycoproteins. Glycobiology 2024; 34:cwae029. [PMID: 38590172 PMCID: PMC11041853 DOI: 10.1093/glycob/cwae029] [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: 11/03/2023] [Revised: 03/12/2024] [Accepted: 04/03/2024] [Indexed: 04/10/2024] Open
Abstract
Human noroviruses, globally the main cause of viral gastroenteritis, show strain specific affinity for histo-blood group antigens (HBGA) and can successfully be propagated ex vivo in human intestinal enteroids (HIEs). HIEs established from jejunal stem cells of individuals with different ABO, Lewis and secretor geno- and phenotypes, show varying susceptibility to such infections. Using bottom-up glycoproteomic approaches we have defined and compared the N-linked glycans of glycoproteins of seven jejunal HIEs. Membrane proteins were extracted, trypsin digested, and glycopeptides enriched by hydrophilic interaction liquid chromatography and analyzed by nanoLC-MS/MS. The Byonic software was used for glycopeptide identification followed by hands-on verifications and interpretations. Glycan structures and attachment sites were identified from MS2 spectra obtained by higher-energy collision dissociation through analysis of diagnostic saccharide oxonium ions (B-ions), stepwise glycosidic fragmentation of the glycans (Y-ions), and peptide sequence ions (b- and y-ions). Altogether 694 unique glycopeptides from 93 glycoproteins were identified. The N-glycans encompassed pauci- and oligomannose, hybrid- and complex-type structures. Notably, polyfucosylated HBGA-containing glycopeptides of the four glycoproteins tetraspanin-8, carcinoembryonic antigen-related cell adhesion molecule 5, sucrose-isomaltase and aminopeptidase N were especially prominent and were characterized in detail and related to donor ABO, Lewis and secretor types of each HIE. Virtually no sialylated N-glycans were identified for these glycoproteins suggesting that terminal sialylation was infrequent compared to fucosylation and HBGA biosynthesis. This approach gives unique site-specific information on the structural complexity of N-linked glycans of glycoproteins of human HIEs and provides a platform for future studies on the role of host glycoproteins in gastrointestinal infectious diseases.
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Affiliation(s)
- Jonas Nilsson
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, Bruna Stråket 16, SE 413 45, Gothenburg, Sweden
- Department of Clinical Chemistry, Region Västra Götaland, Sahlgrenska University Hospital, Bruna Stråket 16, SE 413 45, Gothenburg, Sweden
- Proteomics Core Facilities, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 9E, SE 413 90, Gothenburg, Sweden
| | - Inga Rimkute
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, Bruna Stråket 16, SE 413 45, Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Medicinaregatan 7A, SE 413 90, Gothenburg, Sweden
| | - Carina Sihlbom
- Proteomics Core Facilities, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 9E, SE 413 90, Gothenburg, Sweden
| | - Victoria R Tenge
- Department of Molecular Virology, Baylor College School of Medicine, One Baylor Plaza, Houston, TX 770 30, United States
| | - Shih-Ching Lin
- Department of Molecular Virology, Baylor College School of Medicine, One Baylor Plaza, Houston, TX 770 30, United States
- Present address: Department of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Robert L Atmar
- Department of Molecular Virology, Baylor College School of Medicine, One Baylor Plaza, Houston, TX 770 30, United States
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX 770 30, United States
| | - Mary K Estes
- Department of Molecular Virology, Baylor College School of Medicine, One Baylor Plaza, Houston, TX 770 30, United States
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX 770 30, United States
| | - Göran Larson
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, Bruna Stråket 16, SE 413 45, Gothenburg, Sweden
- Department of Clinical Chemistry, Region Västra Götaland, Sahlgrenska University Hospital, Bruna Stråket 16, SE 413 45, Gothenburg, Sweden
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5
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Atanasova D, Mirgorodskaya E, Moparthi L, Koch S, Haarhaus M, Narisawa S, Millán JL, Landberg E, Magnusson P. Glycoproteomic profile of human tissue-nonspecific alkaline phosphatase expressed in osteoblasts. JBMR Plus 2024; 8:ziae006. [PMID: 38505526 PMCID: PMC10945725 DOI: 10.1093/jbmrpl/ziae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 03/21/2024] Open
Abstract
Tissue-nonspecific alkaline phosphatase (TNALP) is a glycoprotein expressed by osteoblasts that promotes bone mineralization. TNALP catalyzes the hydrolysis of the mineralization inhibitor inorganic pyrophosphate and ATP to provide inorganic phosphate, thus controlling the inorganic pyrophosphate/inorganic phosphate ratio to enable the growth of hydroxyapatite crystals. N-linked glycosylation of TNALP is essential for protein stability and enzymatic activity and is responsible for the presence of different bone isoforms of TNALP associated with functional and clinical differences. The site-specific glycosylation profiles of TNALP are, however, elusive. TNALP has 5 potential N-glycosylation sites located at the asparagine (N) residues 140, 230, 271, 303, and 430. The objective of this study was to reveal the presence and structure of site-specific glycosylation in TNALP expressed in osteoblasts. Calvarial osteoblasts derived from Alpl+/- expressing SV40 Large T antigen were transfected with soluble epitope-tagged human TNALP. Purified TNALP was analyzed with a lectin microarray, matrix-assisted laser desorption/ionization-time of flight mass spectrometry, and liquid chromatography with tandem mass spectrometry. The results showed that all sites (n = 5) were fully occupied predominantly with complex-type N-glycans. High abundance of galactosylated biantennary N-glycans with various degrees of sialylation was observed on all sites, as well as glycans with no terminal galactose and sialic acid. Furthermore, all sites had core fucosylation except site N271. Modelling of TNALP, with the protein structure prediction software ColabFold, showed possible steric hindrance by the adjacent side chain of W270, which could explain the absence of core fucosylation at N271. These novel findings provide evidence for N-linked glycosylation on all 5 sites of TNALP, as well as core fucosylation on 4 out of 5 sites. We anticipate that this new knowledge can aid in the development of functional and clinical assays specific for the TNALP bone isoforms.
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Affiliation(s)
- Diana Atanasova
- Department of Clinical Chemistry, and Department of Biomedical and Clinical Sciences, Linköping University, Linköping SE-58185, Sweden
| | - Ekaterina Mirgorodskaya
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-41346, Sweden
| | - Lavanya Moparthi
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping SE-58185, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping SE-58185, Sweden
| | - Stefan Koch
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping SE-58185, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping SE-58185, Sweden
| | - Mathias Haarhaus
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, Stockholm SE-14186, Sweden
| | - Sonoko Narisawa
- Sanford Children’s Health Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, United States
| | - José Luis Millán
- Sanford Children’s Health Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, United States
| | - Eva Landberg
- Department of Clinical Chemistry, and Department of Biomedical and Clinical Sciences, Linköping University, Linköping SE-58185, Sweden
| | - Per Magnusson
- Department of Clinical Chemistry, and Department of Biomedical and Clinical Sciences, Linköping University, Linköping SE-58185, Sweden
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He X, Wang B, Deng W, Cao J, Tan Z, Li X, Guan F. Impaired bisecting GlcNAc reprogrammed M1 polarization of macrophage. Cell Commun Signal 2024; 22:73. [PMID: 38279161 PMCID: PMC10811823 DOI: 10.1186/s12964-023-01432-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/09/2023] [Indexed: 01/28/2024] Open
Abstract
The functions of macrophages are governed by distinct polarization phenotypes, which can be categorized as either anti-tumor/M1 type or pro-tumor/M2 type. Glycosylation is known to play a crucial role in various cellular processes, but its influence on macrophage polarization is not well-studied. In this study, we observed a significant decrease in bisecting GlcNAc during M0-M1 polarization, and impaired bisecting GlcNAc was found to drive M0-M1 polarization. Using a glycoproteomics strategy, we identified Lgals3bp as a specific glycoprotein carrying bisecting GlcNAc. A high level of bisecting GlcNAc modification facilitated the degradation of Lgals3bp, while a low level of bisecting GlcNAc stabilized Lgals3bp. Elevated levels of Lgals3bp promoted M1 polarization through the activation of the NF-кB pathway. Conversely, the activated NF-кB pathway significantly repressed the transcription of MGAT3, leading to reduced levels of bisecting GlcNAc modification on Lgals3bp. Overall, our study highlights the impact of glycosylation on macrophage polarization and suggests the potential of engineered macrophages via glycosylated modification. Video Abstract.
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Affiliation(s)
- Xin He
- Key Laboratory of Resource Biology and Biotechnology Western China, Ministry of Education; Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, No, 229, Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Bowen Wang
- Key Laboratory of Resource Biology and Biotechnology Western China, Ministry of Education; Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, No, 229, Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Wenli Deng
- Key Laboratory of Resource Biology and Biotechnology Western China, Ministry of Education; Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, No, 229, Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Jinhua Cao
- Key Laboratory of Resource Biology and Biotechnology Western China, Ministry of Education; Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, No, 229, Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Zengqi Tan
- Key Laboratory of Resource Biology and Biotechnology Western China, Ministry of Education; Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, No, 229, Taibai North Road, Xi'an, Shaanxi, 710069, China
| | - Xiang Li
- Institute of Hematology, School of Medicine, Northwest University, Xi'an, 710069, China.
| | - Feng Guan
- Key Laboratory of Resource Biology and Biotechnology Western China, Ministry of Education; Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, No, 229, Taibai North Road, Xi'an, Shaanxi, 710069, China.
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7
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Ren W, Yang L, Feng J, Wang S, Hu Q, Liu H, Zhang J, Wang Z, Yan M, Yu H, Wang Y. A platform for qualitative and quantitative characterization of α-Gal and NeuGc at the oligosaccharide level. Anal Biochem 2023; 683:115362. [PMID: 37866525 DOI: 10.1016/j.ab.2023.115362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 10/24/2023]
Abstract
Glycosylation modification serves as a pivotal quality attribute in glycoprotein-based therapeutics, emphasizing its role in drug safety and efficacy. Prior studies have underscored the potential immunogenic risks posed by the presence of galactose-α-1,3-galactose (α-Gal) and N-glycolylneuraminic acid (NeuGc) in glycoprotein formulations. This accentuates the imperative for developing robust qualitative and quantitative analytical methods to monitor these immunogenic epitopes, thereby ensuring drug safety. In the present investigation, α-Gal and NeuGc were accurately quantified using UPLC-FLR-MS/MS at the oligosaccharide level. Remarkably, α-Gal could be identified when the ion intensity ratio or the mass-to-charge ratio (m/z) of 528.19 to 366.14 exceeded 1. Concurrently, NeuGc and N-acetylneuraminic acid (NeuAc) could be unambiguously identified through their respective fragment ions at m/z 673.23 and m/z 657.23. Furthermore, relative quantification of α-Gal and NeuGc was achieved using fluorescence signals. This study introduces a sensitive and reliable analytical approach for the qualitative and quantitative assessment of α-Gal and NeuGc in glycoprotein pharmaceuticals. The methodology offers significant potential for application in process control and optimization of glycoprotein production, aimed at minimizing immunogenicity and enhancing product quality.
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Affiliation(s)
- Weicheng Ren
- School of Life Sciences, Jilin University, Changchun, 130015, China
| | - Lan Yang
- GeneScience Pharmaceutical Co., Ltd., Changchun, 130012, China
| | - Jia Feng
- GeneScience Pharmaceutical Co., Ltd., Changchun, 130012, China
| | - Shuyue Wang
- GeneScience Pharmaceutical Co., Ltd., Changchun, 130012, China
| | - Qi Hu
- GeneScience Pharmaceutical Co., Ltd., Changchun, 130012, China
| | - Hailong Liu
- GeneScience Pharmaceutical Co., Ltd., Changchun, 130012, China
| | - Jinliang Zhang
- School of Life Sciences, Jilin University, Changchun, 130015, China; GeneScience Pharmaceutical Co., Ltd., Changchun, 130012, China
| | - Zhiwei Wang
- GeneScience Pharmaceutical Co., Ltd., Changchun, 130012, China
| | - Menghan Yan
- GeneScience Pharmaceutical Co., Ltd., Changchun, 130012, China
| | - Hongwei Yu
- GeneScience Pharmaceutical Co., Ltd., Changchun, 130012, China
| | - Yingwu Wang
- School of Life Sciences, Jilin University, Changchun, 130015, China.
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8
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Dang L, Li P, Dan W, Liu H, Shen J, Zhu B, Jia L, Sun S. Glycoproteomic analysis of regulatory effects of bisecting N-glycans on N-glycan biosynthesis and protein expressions in human HK-2 cells. Carbohydr Res 2023; 531:108894. [PMID: 37421876 DOI: 10.1016/j.carres.2023.108894] [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: 09/27/2022] [Revised: 06/02/2023] [Accepted: 07/01/2023] [Indexed: 07/10/2023]
Abstract
Bisecting N-glycan is known to be a metastasis suppressor and plays a regulatory role in the biosynthesis of N-glycans. Previous studies have shown that bisecting N-glycans are capable of modulating both the branching and terminal modifications of glycans. However, these effects have been investigated mainly by glycomic approaches and it remains unclear how they alter when glycans are attached to different glycosites of proteins. Here, we systematically investigated the regulatory roles of bisecting N-glycans in human HK-2 cells using StrucGP, a strategy we developed for structural interpretation of site-specific N-glycans on glycoproteins. The glycoproteomics analysis showed that most of bisecting N-glycans are complex type and often occur in company with core fucosylation. With the overexpression and knockdown of MGAT3, the only enzyme responsible for bisecting N-glycan synthesis, we found that bisecting N-glycans can impact the biosynthesis of N-glycans from multiple aspects, including glycan types, branching, sialylation, fucosylation (different effects for core and terminal fucosylation) as well as the presence of terminal N-acetylglucosamine. Furthermore, gene ontology analysis suggested that most proteins with bisecting N-glycans located in the extracellular region or membrane, where they function mostly in cell adhesion, extracellular matrix regulation and cell signaling. Finally, we showed that overexpression of bisecting N-glycans had a broad impact on the protein expressions of HK-2 cells, involving multiple biological processes. Taken together, our work systematically demonstrated the expression profiles of bisecting N-glycans, and their regulatory effects on the biosynthesis of N-glycans and protein expressions, which provide valuable information for the functional elucidation of bisecting N-glycans.
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Affiliation(s)
- Liuyi Dang
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China
| | - Pengfei Li
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China
| | - Wei Dan
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China
| | - Huanhuan Liu
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China
| | - Jiechen Shen
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China
| | - Bojing Zhu
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China
| | - Li Jia
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China
| | - Shisheng Sun
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, China.
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9
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Shipman J, Sommers C, Keire DA, Chen K, Zhu H. Comprehensive N-Glycan Mapping using Parallel Reaction Monitoring LC-MS/MS. Pharm Res 2023; 40:1399-1410. [PMID: 36513905 DOI: 10.1007/s11095-022-03453-1] [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: 07/05/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
PURPOSE Glycan composition can impact a biotherapeutic's safety and efficacy. For example, changes in the relative abundance of different glycan attributes like afucosylation, galactosylation or high-mannose content can change the properties or functions of a monoclonal antibody (mAb). While established methods can effectively characterize major glycan species in biotherapeutic drug products, there is still a need for more sensitive and specific methods that can effectively monitor low abundance species which may impact mAb function. METHODS Glycans released from two mAbs, adalimumab and trastuzumab, were derivatized with Rapifluor-MS™. Glycans were separated using HILIC and detected using either fluorescence (FLD) or mass spectrometry (MS). A parallel reaction monitoring (PRM) workflow was used for the MS analysis. RESULTS AND CONCLUSION FLD analysis identified 18 and 19 glycan peaks in adalimumab and trastuzumab, respectively. Glycan identities were determined using MS-analysis and a high number of FLD peaks containing co-eluting glycan species were observed. PRM analysis quantified 38 and 39 glycan species in adalimumab and trastuzumab, respectively, and the increase in glycans that could be identified was due to superior sensitivity and selectivity compared to FLD. Notably, many low abundance glycans identified by PRM included species that were not reported in other studies. PRM also offered several additional advantages; unique structural features could be identified using the collected MS/MS spectra and de-coupling MS acquisition and data processing simplified the transfer of methods between instruments. The results established PRM as a precise, informative tool for glycan analysis and quantitation.
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Affiliation(s)
- Joshua Shipman
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO, 63110, USA
| | - Cynthia Sommers
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO, 63110, USA
| | - David A Keire
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO, 63110, USA
| | - Kang Chen
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO, 63110, USA.
| | - Hongbin Zhu
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO, 63110, USA.
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10
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Dan W, Li C, Li J, Li P, Xin M, Chen Z, Dang L, Yu Z, Li J, Shen J, Hu L, Sun S. Glycoproteomic analysis reveals the effects of bisecting GlcNAc in intrahepatic cholangiocarcinoma. Glycoconj J 2022; 39:737-745. [PMID: 36322335 DOI: 10.1007/s10719-022-10085-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/26/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022]
Abstract
Intrahepatic cholangiocarcinoma (ICC) is the second major subtype of primary liver cancer and has caused more and more attention with increasing incidence and mortality worldwide. Our previous study found that bisecting N-glycans are commonly increased in ICC, while the effects and potential functions of bisecting GlcNAc in ICC are still largely unclear. In this study, we further confirmed that the structures of bisecting GlcNAc were significantly up-regulated in ICC compared with paracancer tissues by glycoproteomic data and lectin histochemistry. The expression of its glycosyltransferase MGAT3 was also up-regulated in ICC tissues at both mRNA and protein levels, and expression of MGAT3 is negatively correlated with overall survival explored by bioinformatic analyses and published datasets from 255 patients. Next, the silencing of MGAT3 could inhibit the growth and invasion of ICC cells, and overexpressing of MGAT3 only promoted ICC cell invasion. Further glycoproteomic analysis showed that the commonly glycoproteins modified by bisecting GlcNAc after MGAT3-overexpression in two ICC cell lines were mainly involved in cell movement-related biological processes, such as cell adhesion, integrin-related and ECM-receptor interaction. This study sheds light on the potential effects of bisecting GlcNAc in ICC cells and suggests that MGAT3 might be used as a potential target in the therapy of ICC.
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Affiliation(s)
- Wei Dan
- College of Life Sciences, Northwest University, 710069, Xi'an, Shaanxi Province, P. R. China
| | - Cheng Li
- College of Life Sciences, Northwest University, 710069, Xi'an, Shaanxi Province, P. R. China
| | - Jun Li
- College of Life Sciences, Northwest University, 710069, Xi'an, Shaanxi Province, P. R. China
| | - Pengfei Li
- College of Life Sciences, Northwest University, 710069, Xi'an, Shaanxi Province, P. R. China
| | - Miaomiao Xin
- College of Life Sciences, Northwest University, 710069, Xi'an, Shaanxi Province, P. R. China
| | - Zexuan Chen
- College of Life Sciences, Northwest University, 710069, Xi'an, Shaanxi Province, P. R. China
| | - Liuyi Dang
- College of Life Sciences, Northwest University, 710069, Xi'an, Shaanxi Province, P. R. China
| | - Zihao Yu
- College of Life Sciences, Northwest University, 710069, Xi'an, Shaanxi Province, P. R. China
| | - Jing Li
- College of Life Sciences, Northwest University, 710069, Xi'an, Shaanxi Province, P. R. China
| | - Jiechen Shen
- College of Life Sciences, Northwest University, 710069, Xi'an, Shaanxi Province, P. R. China
| | - Liangshuo Hu
- Department of Hepatobiliary Surgery, Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shisheng Sun
- College of Life Sciences, Northwest University, 710069, Xi'an, Shaanxi Province, P. R. China.
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11
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Chen Q, Zhang Y, Zhang K, Liu J, Pan H, Wang X, Li S, Hu D, Lin Z, Zhao Y, Hou G, Guan F, Li H, Liu S, Ren Y. Profiling the Bisecting N-acetylglucosamine Modification in Amniotic Membrane via Mass Spectrometry. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:648-656. [PMID: 35123071 PMCID: PMC9880894 DOI: 10.1016/j.gpb.2021.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/30/2021] [Accepted: 10/11/2021] [Indexed: 01/31/2023]
Abstract
Bisecting N-acetylglucosamine (GlcNAc), a GlcNAc linked to the core β-mannose residue via a β1,4 linkage, is a special type of N-glycosylation that has been reported to be involved in various biological processes, such as cell adhesion and fetal development. This N-glycan structure is abundant in human trophoblasts, which is postulated to be resistant to natural killer cell-mediated cytotoxicity, enabling a mother to nourish a fetus without rejection. In this study, we hypothesized that the human amniotic membrane, which serves as the last barrier for the fetus, may also express bisected-type glycans. To test this hypothesis, glycomic analysis of the human amniotic membrane was performed, and bisected N-glycans were detected. Furthermore, our proteomic data, which have been previously employed to explore human missing proteins, were analyzed and the presence of bisecting GlcNAc-modified peptides was confirmed. A total of 41 glycoproteins with 43 glycopeptides were found to possess a bisecting GlcNAc, and 25 of these glycoproteins were reported to exhibit this type of modification for the first time. These results provide insights into the potential roles of bisecting GlcNAc modification in the human amniotic membrane, and can be beneficial to functional studies on glycoproteins with bisecting GlcNAc modifications and functional studies on immune suppression in human placenta.
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Affiliation(s)
| | | | | | - Jie Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Siqi Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Dandan Hu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Yun Zhao
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Feng Guan
- Joint International Research Laboratory of Glycobiology and Medical Chemistry, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Hong Li
- Shenzhen Seventh People's Hospital, Shenzhen 518081, China
| | - Siqi Liu
- BGI-Shenzhen, Shenzhen 518083, China,Corresponding authors.
| | - Yan Ren
- BGI-Shenzhen, Shenzhen 518083, China,Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China,Corresponding authors.
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12
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Ma S, Chen F, Zhang M, Yuan H, Ouyang G, Zhao W, Zhang S, Zhao Y. Carboxyl-Based CPMP Tag for Ultrasensitive Analysis of Disaccharides by Negative Tandem Mass Spectrometry. Anal Chem 2022; 94:9557-9563. [PMID: 35759693 DOI: 10.1021/acs.analchem.2c00287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here, we develop a sensitive method for glucose-containing disaccharide analysis by 1-(4-carboxyphenyl)-3-methyl-5-pyrazolone (CPMP) derivatization using mass spectrometry. The intense anion of [M - H]- (m/z 759) was observed for CPMP-labeled disaccharides in a negative mode. After derivatization, its sensitivity was significantly increased with the limits of detection (LODs) and limits of quantification (LOQ) ranging from 3.90 to 8.67 ng L-1 and 12.99 to 28.92 ng L-1, respectively. During CID-MS/MS analysis, the fragment patterns of CPMP derivatized disaccharides in the negative mode were simpler and clearer than their counterparts in a positive mode, which further could be applied to distinct and relatively quantitative isomeric disaccharides with ultrahigh sensitivity and good reproducibility. The great linear relationships could be achieved under wider concentration ratios from 0.01 to 20 compared to the previous report. Eventually, the developed methodology was applicable to identify isomeric disaccharides in beers. No sucrose was discovered. All beers contain 1,4- and 1,6-linked disaccharides. Some of them also have a mixture of 1,2- and 1,3-linked disaccharides. Through the integration of statistical analysis, beers with different production processes were finally discriminated, and the relative quantification of isomaltose and maltose was realized. In general, this method is sensitive, fast, and reliable for the discrimination and relative quantification of isomeric disaccharides in complex matrices. This study provides a new idea for the structural analysis of oligosaccharides in food, plants, and animals and an important theoretical basis for the exploration of new functions of oligosaccharides.
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Affiliation(s)
- Shanshan Ma
- College of Chemistry, Zhengzhou University, Henan 450001, China
| | - Fangya Chen
- School of Ecology and Environment, Zhengzhou University, Henan 450001, China
| | - Meng Zhang
- College of Chemistry, Zhengzhou University, Henan 450001, China
| | - Hang Yuan
- College of Chemistry, Zhengzhou University, Henan 450001, China
| | - Gangfeng Ouyang
- College of Chemistry, Zhengzhou University, Henan 450001, China.,KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wuduo Zhao
- College of Chemistry, Zhengzhou University, Henan 450001, China
| | - Shusheng Zhang
- College of Chemistry, Zhengzhou University, Henan 450001, China
| | - Yufen Zhao
- College of Chemistry, Zhengzhou University, Henan 450001, China.,Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
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13
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Cao X, Wang S, Gadi MR, Liu D, Wang PG, Wan XF, Zhang J, Chen X, Pepi LE, Azadi P, Li L. Systematic synthesis of bisected N-glycans and unique recognitions by glycan-binding proteins. Chem Sci 2022; 13:7644-7656. [PMID: 35872821 PMCID: PMC9241959 DOI: 10.1039/d1sc05435j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 05/29/2022] [Indexed: 12/13/2022] Open
Abstract
Bisected N-glycans represent a unique class of protein N-glycans that play critical roles in many biological processes. Herein, we describe the systematic synthesis of these structures. A bisected N-glycan hexasaccharide was chemically assembled with two orthogonal protecting groups attached at the C2 of the branching mannose residues, followed by sequential installation of GlcNAc and LacNAc building blocks to afford two asymmetric bisecting "cores". Subsequent enzymatic modular extension of the "cores" yielded a comprehensive library of biantennary N-glycans containing the bisecting GlcNAc and presenting 6 common glycan determinants in a combinatorial fashion. These bisected N-glycans and their non-bisected counterparts were used to construct a distinctive glycan microarray to study their recognition by a wide variety of glycan-binding proteins (GBPs), including plant lectins, animal lectins, and influenza A virus hemagglutinins. Significantly, the bisecting GlcNAc could bestow (PHA-L, rDCIR2), enhance (PHA-E), or abolish (ConA, GNL, anti-CD15s antibody, etc.) N-glycan recognition of specific GBPs, and is tolerated by many others. In summary, synthesized compounds and the unique glycan microarray provide ideal standards and tools for glycoanalysis and functional glycomic studies. The microarray data provide new information regarding the fine details of N-glycan recognition by GBPs, and in turn improve their applications.
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Affiliation(s)
- Xuefeng Cao
- Department of Chemistry, Georgia State UniversityAtlantaGAUSA
| | - Shuaishuai Wang
- Department of Chemistry, Georgia State UniversityAtlantaGAUSA
| | | | - Ding Liu
- Department of Chemistry, Georgia State UniversityAtlantaGAUSA
| | - Peng G. Wang
- Department of Chemistry, Georgia State UniversityAtlantaGAUSA
| | - Xiu-Feng Wan
- MU Center for Research on Influenza Systems Biology (CRISB), University of MissouriColumbiaMOUSA,Department of Molecular Microbiology and Immunology, School of Medicine, University of MissouriColumbiaMOUSA,Bond Life Sciences Center, University of MissouriColumbiaMOUSA,Department of Electrical Engineering & Computer Science, College of Engineering, University of MissouriColumbiaMOUSA
| | | | - Xi Chen
- Department of Chemistry, University of CaliforniaOne Shields AvenueDavisCAUSA
| | - Lauren E. Pepi
- Complex Carbohydrate Research Center, University of GeorgiaAthensGAUSA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of GeorgiaAthensGAUSA
| | - Lei Li
- Department of Chemistry, Georgia State UniversityAtlantaGAUSA
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14
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Role and therapeutic implications of protein glycosylation in neuroinflammation. Trends Mol Med 2022; 28:270-289. [PMID: 35120836 DOI: 10.1016/j.molmed.2022.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 12/13/2022]
Abstract
The importance of glycosylation (post-translational attachment of glycan residues to proteins) in the context of neuroinflammation is only now beginning to be understood. Although the glycome is challenging to investigate due to its complexity, this field is gaining interest because of the emergence of novel analytical methods. These investigations offer the possibility of further understanding the molecular signature of disorders with underlying neuroinflammatory cascades. In this review, we portray the clinically relevant trends in glyconeurobiology and suggest glyco-related paths that could be targeted therapeutically to decrease neuroinflammation. A combinatorial insight from glycobiology and neurology can be harnessed to better understand neuroinflammatory-related conditions to identify relevant molecular targets.
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15
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Hoek M, Demmers LC, Wu W, Heck AJR. Allotype-Specific Glycosylation and Cellular Localization of Human Leukocyte Antigen Class I Proteins. J Proteome Res 2021; 20:4518-4528. [PMID: 34415762 PMCID: PMC8419865 DOI: 10.1021/acs.jproteome.1c00466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Presentation of antigens
by human leukocyte antigen (HLA) complexes
at the cell surface is a key process in the immune response. The α-chain,
containing the peptide-binding groove, is one of the most polymorphic
proteins in the proteome. All HLA class I α-chains carry a conserved
N-glycosylation site, but little is known about its nature and function.
Here, we report an in-depth characterization of N-glycosylation features
of HLA class I molecules. We observe that different HLA-A α-chains
carry similar glycosylation, distinctly different from the HLA-B,
HLA-C, and HLA-F α-chains. Although HLA-A displays the broadest
variety of glycan characteristics, HLA-B α-chains carry mostly
mature glycans, and HLA-C and HLA-F α-chains carry predominantly
high-mannose glycans. We expected these glycosylation features to
be directly linked to cellular localization of the HLA complexes.
Indeed, analyzing HLA class I complexes from crude plasma and inner
membrane-enriched fractions confirmed that most HLA-B complexes can
be found at the plasma membrane, while most HLA-C and HLA-F molecules
reside in the endoplasmic reticulum and Golgi membrane, and HLA-A
molecules are more equally distributed over these cellular compartments.
This allotype-specific cellular distribution of HLA molecules should
be taken into account when analyzing peptide antigen presentation
by immunopeptidomics.
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Affiliation(s)
- Max Hoek
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Laura C Demmers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, 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 Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
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16
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Cao L, Zhou Y, Li X, Lin S, Tan Z, Guan F. Integrating transcriptomics, proteomics, glycomics and glycoproteomics to characterize paclitaxel resistance in breast cancer cells. J Proteomics 2021; 243:104266. [PMID: 34000456 DOI: 10.1016/j.jprot.2021.104266] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/24/2021] [Accepted: 05/07/2021] [Indexed: 12/24/2022]
Abstract
Chemoresistance is a major factor driving breast cancer (BC) relapse and the high rates of cancer-related deaths. Aberrant levels of glycans are closely correlated with chemoresistance. The essential functions of glycans in chemoresistance is not systematically studied. In this study, an integrated strategy with a combination of transcriptomics, proteomics, glycomics and glycoproteomics was applied to explore the dysregulation of glycogenes, glycan structures and glycoproteins in chemoresistance of breast cancer cells. In paclitaxel (PTX) resistant MCF7 cells, 19 differentially expressed N-glycan-related proteins were identified, of which MGAT4A was the most significantly down-regulated, consistent with decrease in MGAT4A expression at mRNA level in PTX treated BC cells. Glycomic analysis consistently revealed suppressed levels of multi-antennary branching structures using MALDI-TOF/TOF-MS and lectin microarray. Several target glycoproteins bearing suppressed levels of multi-antennary branching structures were identified, and ERK signaling pathway was strongly suppressed in PTX resistant MCF7 cells. Our findings demonstrated the aberrant levels of multi-antennary branching structures and their target glycoproteins on PTX resistance. Systematically integrative multi-omic analysis is expected to facilitate the discovery of the aberrant glycosyltransferases, N-glycosylation and glycoproteins in tumor progression and chemoresistance. SIGNIFICANCE: An integrated strategy with a combination of transcriptomics, proteomics, glycomics and glycoproteomics is crucial to understand the association between glycans and chemoresistance in BC. In this multi-omic analysis, we identified unique glycan-related protein, glycan and glycoprotein signatures defining PTX chemoresistance in BC. This study might provide valuable information to understand molecular mechanisms underlying chemoresistance in BC.
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Affiliation(s)
- Lin Cao
- International Research Laboratory of Glycobiology and Medicinal Chemistry, College of Life Science, Northwest University, Xi'an 710069, PR China
| | - Yue Zhou
- International Research Laboratory of Glycobiology and Medicinal Chemistry, College of Life Science, Northwest University, Xi'an 710069, PR China; The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiang Li
- Institute of Hematology, School of Medicine, Northwest University, Xi'an 710069, PR China
| | - Shuai Lin
- Department of Oncology, The second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Zengqi Tan
- International Research Laboratory of Glycobiology and Medicinal Chemistry, College of Life Science, Northwest University, Xi'an 710069, PR China
| | - Feng Guan
- International Research Laboratory of Glycobiology and Medicinal Chemistry, College of Life Science, Northwest University, Xi'an 710069, PR China.
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17
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Towards structure-focused glycoproteomics. Biochem Soc Trans 2021; 49:161-186. [PMID: 33439247 PMCID: PMC7925015 DOI: 10.1042/bst20200222] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023]
Abstract
Facilitated by advances in the separation sciences, mass spectrometry and informatics, glycoproteomics, the analysis of intact glycopeptides at scale, has recently matured enabling new insights into the complex glycoproteome. While diverse quantitative glycoproteomics strategies capable of mapping monosaccharide compositions of N- and O-linked glycans to discrete sites of proteins within complex biological mixtures with considerable sensitivity, quantitative accuracy and coverage have become available, developments supporting the advancement of structure-focused glycoproteomics, a recognised frontier in the field, have emerged. Technologies capable of providing site-specific information of the glycan fine structures in a glycoproteome-wide context are indeed necessary to address many pending questions in glycobiology. In this review, we firstly survey the latest glycoproteomics studies published in 2018–2020, their approaches and their findings, and then summarise important technological innovations in structure-focused glycoproteomics. Our review illustrates that while the O-glycoproteome remains comparably under-explored despite the emergence of new O-glycan-selective mucinases and other innovative tools aiding O-glycoproteome profiling, quantitative glycoproteomics is increasingly used to profile the N-glycoproteome to tackle diverse biological questions. Excitingly, new strategies compatible with structure-focused glycoproteomics including novel chemoenzymatic labelling, enrichment, separation, and mass spectrometry-based detection methods are rapidly emerging revealing glycan fine structural details including bisecting GlcNAcylation, core and antenna fucosylation, and sialyl-linkage information with protein site resolution. Glycoproteomics has clearly become a mainstay within the glycosciences that continues to reach a broader community. It transpires that structure-focused glycoproteomics holds a considerable potential to aid our understanding of systems glycobiology and unlock secrets of the glycoproteome in the immediate future.
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18
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Kawahara R, Recuero S, Srougi M, Leite KRM, Thaysen-Andersen M, Palmisano G. The Complexity and Dynamics of the Tissue Glycoproteome Associated With Prostate Cancer Progression. Mol Cell Proteomics 2021; 20:100026. [PMID: 33127837 PMCID: PMC8010466 DOI: 10.1074/mcp.ra120.002320] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/19/2020] [Accepted: 10/30/2020] [Indexed: 12/30/2022] Open
Abstract
The complexity and dynamics of the immensely heterogeneous glycoproteome of the prostate cancer (PCa) tumor microenvironment remain incompletely mapped, a knowledge gap that impedes our molecular-level understanding of the disease. To this end, we have used sensitive glycomics and glycoproteomics to map the protein-, cell-, and tumor grade-specific N- and O-glycosylation in surgically removed PCa tissues spanning five histological grades (n = 10/grade) and tissues from patients with benign prostatic hyperplasia (n = 5). Quantitative glycomics revealed PCa grade-specific alterations of the oligomannosidic-, paucimannosidic-, and branched sialylated complex-type N-glycans, and dynamic remodeling of the sialylated core 1- and core 2-type O-glycome. Deep quantitative glycoproteomics identified ∼7400 unique N-glycopeptides from 500 N-glycoproteins and ∼500 unique O-glycopeptides from nearly 200 O-glycoproteins. With reference to a recent Tissue and Blood Atlas, our data indicate that paucimannosidic glycans of the PCa tissues arise mainly from immune cell-derived glycoproteins. Furthermore, the grade-specific PCa glycosylation arises primarily from dynamics in the cellular makeup of the PCa tumor microenvironment across grades involving increased oligomannosylation of prostate-derived glycoproteins and decreased bisecting GlcNAcylation of N-glycans carried by the extracellular matrix proteins. Furthermore, elevated expression of several oligosaccharyltransferase subunits and enhanced N-glycoprotein site occupancy were observed associated with PCa progression. Finally, correlations between the protein-specific glycosylation and PCa progression were observed including increased site-specific core 2-type O-glycosylation of collagen VI. In conclusion, integrated glycomics and glycoproteomics have enabled new insight into the complexity and dynamics of the tissue glycoproteome associated with PCa progression generating an important resource to explore the underpinning disease mechanisms.
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Affiliation(s)
- Rebeca Kawahara
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, USP, São Paulo, Brazil; Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Saulo Recuero
- Laboratório de Investigação Médica da Disciplina de Urologia da Faculdade de Medicina da USP, São Paulo, Brazil
| | - Miguel Srougi
- Laboratório de Investigação Médica da Disciplina de Urologia da Faculdade de Medicina da USP, São Paulo, Brazil
| | - Katia R M Leite
- Laboratório de Investigação Médica da Disciplina de Urologia da Faculdade de Medicina da USP, São Paulo, Brazil
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia.
| | - Giuseppe Palmisano
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, USP, São Paulo, Brazil.
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19
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Wongtrakul-Kish K, Herbert BR, Packer NH. Bisecting GlcNAc Protein N-Glycosylation Is Characteristic of Human Adipogenesis. J Proteome Res 2020; 20:1313-1327. [PMID: 33383989 DOI: 10.1021/acs.jproteome.0c00702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human adipose tissue contains a major source of adipose-derived stem cells (ADSCs) that have the ability to differentiate into various cell types: in vitro, ADSCs can differentiate into mesenchymal lineages including adipocytes, while in vivo, ADSCs become mature adipocytes. Protein glycosylation has been shown to change in stem cell differentiation, and while ADSCs have been acknowledged for their therapeutic potential, little is known about protein glycosylation during human ADSC adipogenic differentiation. In the present study, the global membrane protein glycosylation of native adipocytes was compared to ADSCs from the same individuals as a model of in vivo adipogenesis. For in vitro adipogenesis, ADSCs were adipogenically differentiated in cell culture using an optimized, large-scale differentiation procedure. The membrane glycome of the differentiated ADSCs (dADSCs) was compared with mature adipocytes and the progenitor ADSCs. A total of 137 glycan structures were characterized across the three cell types using PGC-LC coupled with negative-ion electrospray ionization mass spectrometry (ESI-MS)/MS. Significantly higher levels of bisecting GlcNAc-type N-glycans were detected in mature adipocytes (32.1% of total glycans) and in in vitro dADSC progeny (1.9% of total glycans) compared to ADSCs. This was further correlated by the mRNA expression of the MGAT3 gene responsible for the enzymatic synthesis of this structural type. The bisecting GlcNAc structures were found on the majority of human native adipocyte membrane proteins, suggesting an important role in human adipocyte biology. Core fucosylation was also significantly increased during in vivo adipogenesis but did not correlate with an increase in Fut8 gene transcript. Unexpectedly, low abundance structures carrying rare β-linked Gal-Gal termini were also detected. Overall, the N-glycan profiles of the in vitro differentiated progeny did not reflect native adipocytes, and the results show that bisecting GlcNAc structures are a characteristic feature of human adipocyte membrane protein N-glycosylation. Raw MS files are available on GlycoPOST (ID: GPST000153 https://glycopost.glycosmos.org/).
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Affiliation(s)
- Katherine Wongtrakul-Kish
- Biomolecular Discovery Research Centre, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.,ARC Centre for Nanoscale BioPhotonics, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Benjamin R Herbert
- Biomolecular Discovery Research Centre, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Nicolle H Packer
- Biomolecular Discovery Research Centre, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.,ARC Centre for Nanoscale BioPhotonics, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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20
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Thaysen-Andersen M, Kolarich D, Packer NH. Glycomics & Glycoproteomics: From Analytics to Function. Mol Omics 2020; 17:8-10. [PMID: 33295916 DOI: 10.1039/d0mo90019b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Morten Thaysen-Andersen, Daniel Kolarich and Nicolle H. Packer introduce the Molecular Omics themed issue on Glycomics & Glycoproteomics: From Analytics to Function.
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21
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Tan Z, Cao L, Wu Y, Wang B, Song Z, Yang J, Cheng L, Yang X, Zhou X, Dai Z, Li X, Guan F. Bisecting GlcNAc modification diminishes the pro-metastatic functions of small extracellular vesicles from breast cancer cells. J Extracell Vesicles 2020; 10:e12005. [PMID: 33304474 PMCID: PMC7710122 DOI: 10.1002/jev2.12005] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/21/2020] [Accepted: 09/29/2020] [Indexed: 12/19/2022] Open
Abstract
Small extracellular vesicles (sEVs) are enriched in glycoconjugates and display specific glycosignatures. Aberrant expression of surface glycoconjugates is closely correlated with cancer progression and metastasis. The essential functions of glycoconjugates in sEVs are poorly understood. In this study, we observed significantly reduced levels of bisecting GlcNAc in breast cancer. Introduction of bisecting GlcNAc into breast cancer cells altered the bisecting GlcNAc status on sEVs, and sEVs with diverse bisecting GlcNAc showed differing functions on recipient cells. Carcinogenesis and metastasis of recipient cells were enhanced by sEVs with low bisecting GlcNAc, and the pro‐metastatic functions of sEVs was diminished by high bisecting GlcNAc modification. We further identified vesicular integrin β1 as a target protein bearing bisecting GlcNAc. Metastasis of recipient cells was strongly suppressed by high bisecting GlcNAc levels on vesicular β1. Our findings demonstrate the important roles of glycoconjugates on sEVs. Modification of sEV glycosylation may contribute to development of novel targets in breast cancer therapy.
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Affiliation(s)
- Zengqi Tan
- Joint International Research Laboratory of Glycobiology and Medicinal Chemistry College of Life Science Northwest University Xi'an P.R. China
| | - Lin Cao
- Joint International Research Laboratory of Glycobiology and Medicinal Chemistry College of Life Science Northwest University Xi'an P.R. China
| | - Yurong Wu
- Joint International Research Laboratory of Glycobiology and Medicinal Chemistry College of Life Science Northwest University Xi'an P.R. China
| | - Bowen Wang
- Joint International Research Laboratory of Glycobiology and Medicinal Chemistry College of Life Science Northwest University Xi'an P.R. China
| | - Zhihui Song
- Joint International Research Laboratory of Glycobiology and Medicinal Chemistry College of Life Science Northwest University Xi'an P.R. China
| | - Juhong Yang
- Joint International Research Laboratory of Glycobiology and Medicinal Chemistry College of Life Science Northwest University Xi'an P.R. China
| | - Lanming Cheng
- Joint International Research Laboratory of Glycobiology and Medicinal Chemistry College of Life Science Northwest University Xi'an P.R. China
| | - Xiaomin Yang
- Department of Breast Surgery The First Affiliated Hospital of Xi'an Jiaotong University Xi'an P.R. China.,Department of Breast Surgery Tumor Hospital of Shaanxi Province Xi'an P.R. China
| | - Xiaoman Zhou
- Joint International Research Laboratory of Glycobiology and Medicinal Chemistry College of Life Science Northwest University Xi'an P.R. China
| | - Zhijun Dai
- Department of Breast Surgery The First Affiliated Hospital College of Medicine Zhejiang University Hangzhou P.R. China.,Department of Oncology The Second Affiliated Hospital of Xi'an Jiaotong Xi'an P.R. China
| | - Xiang Li
- School of Medicine Northwest University Xi'an P.R. China
| | - Feng Guan
- Joint International Research Laboratory of Glycobiology and Medicinal Chemistry College of Life Science Northwest University Xi'an P.R. China
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22
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Lee HK, Ha DI, Kang JG, Park GW, Lee JY, Cho K, Bin Moon S, Shin JH, Kim YS, An HJ, Kim JY, Yoo JS, Ko JH. Selective Identification of α-Galactosyl Epitopes in N-Glycoproteins Using Characteristic Fragment Ions from Higher-Energy Collisional Dissociation. Anal Chem 2020; 92:13144-13154. [PMID: 32902264 DOI: 10.1021/acs.analchem.0c02276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The α-galactosyl epitope is a terminal N-glycan moiety of glycoproteins found in mammals except in humans, and thus, it is recognized as an antigen that provokes an immunogenic response in humans. Accordingly, it is necessary to analyze the α-galactosyl structure in biopharmaceuticals or organ transplants. Due to an identical glycan composition and molecular mass between α-galactosyl N-glycans and hybrid/high-mannose-type N-glycans, it is challenging to characterize α-galactosyl epitopes in N-glycoproteins using mass spectrometry. Here, we describe a method to identify α-galactosyl N-glycopeptides in mice glycoproteins using liquid chromatography with tandem mass spectrometry with higher-energy collisional dissociation (HCD). The first measure was an absence of [YHM] ion peaks in the HCD spectra, which was exclusively observed in hybrid and/or high-mannose-type N-glycopeptides. The second complementary criterion was the ratio of an m/z 528.19 (Hex2HexNAc1) ion to m/z 366.14 (Hex1HexNAc1) ion (Im/z528/Im/z366). The measure of [Im/z528/Im/z366 > 0.3] enabled a clear-cut determination of α-galactosyl N-glycopeptides with high accuracy. In Ggta1 knockout mice, we could not find any α-galactosyl N-glycoproteins identified in WT mice plasma. Using this method, we could screen for α-galactosyl N-glycoproteins from mice spleen, lungs, and plasma samples in a highly sensitive and specific manner. Conclusively, we suggest that this method will provide a robust analytical tool for determination of α-galactosyl epitopes in pharmaceuticals and complex biological samples.
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Affiliation(s)
- Hyun Kyoung Lee
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Ochang-eup, Cheongju 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Dae-In Ha
- Genome Editing Research Center, KRIBB, 125 Gwahak-ro, Daejeon 34141, Republic of Korea.,Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon 34113, Republic of Korea
| | - Jeong Gu Kang
- Genome Editing Research Center, KRIBB, 125 Gwahak-ro, Daejeon 34141, Republic of Korea
| | - Gun Wook Park
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Ochang-eup, Cheongju 28119, Republic of Korea
| | - Ju Yeon Lee
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Ochang-eup, Cheongju 28119, Republic of Korea
| | - Kun Cho
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Ochang-eup, Cheongju 28119, Republic of Korea
| | - Su Bin Moon
- Genome Editing Research Center, KRIBB, 125 Gwahak-ro, Daejeon 34141, Republic of Korea.,Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon 34113, Republic of Korea
| | - Jong Hwan Shin
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Ochang-eup, Cheongju 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Yong-Sam Kim
- Genome Editing Research Center, KRIBB, 125 Gwahak-ro, Daejeon 34141, Republic of Korea.,Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon 34113, Republic of Korea
| | - Hyun Joo An
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Ochang-eup, Cheongju 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jin Young Kim
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Ochang-eup, Cheongju 28119, Republic of Korea
| | - Jong Shin Yoo
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Ochang-eup, Cheongju 28119, Republic of Korea.,Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jeong-Heon Ko
- Genome Editing Research Center, KRIBB, 125 Gwahak-ro, Daejeon 34141, Republic of Korea.,Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Daejeon 34113, Republic of Korea
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23
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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.
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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
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24
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Riley NM, Malaker SA, Driessen MD, Bertozzi CR. Optimal Dissociation Methods Differ for N- and O-Glycopeptides. J Proteome Res 2020; 19:3286-3301. [PMID: 32500713 PMCID: PMC7425838 DOI: 10.1021/acs.jproteome.0c00218] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
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Site-specific
characterization of glycosylation requires intact
glycopeptide analysis, and recent efforts have focused on how to best
interrogate glycopeptides using tandem mass spectrometry (MS/MS).
Beam-type collisional activation, i.e., higher-energy collisional
dissociation (HCD), has been a valuable approach, but stepped collision
energy HCD (sceHCD) and electron transfer dissociation with HCD supplemental
activation (EThcD) have emerged as potentially more suitable alternatives.
Both sceHCD and EThcD have been used with success in large-scale glycoproteomic
experiments, but they each incur some degree of compromise. Most progress
has occurred in the area of N-glycoproteomics. There
is growing interest in extending this progress to O-glycoproteomics, which necessitates comparisons of method performance
for the two classes of glycopeptides. Here, we systematically explore
the advantages and disadvantages of conventional HCD, sceHCD, ETD,
and EThcD for intact glycopeptide analysis and determine their suitability
for both N- and O-glycoproteomic
applications. For N-glycopeptides, HCD and sceHCD
generate similar numbers of identifications, although sceHCD generally
provides higher quality spectra. Both significantly outperform EThcD
methods in terms of identifications, indicating that ETD-based methods
are not required for routine N-glycoproteomics even
if they can generate higher quality spectra. Conversely, ETD-based
methods, especially EThcD, are indispensable for site-specific analyses
of O-glycopeptides. Our data show that O-glycopeptides cannot be robustly characterized with HCD-centric
methods that are sufficient for N-glycopeptides,
and glycoproteomic methods aiming to characterize O-glycopeptides must be constructed accordingly.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California 94305-6104, United States
| | - Stacy A Malaker
- Department of Chemistry, Stanford University, Stanford, California 94305-6104, United States
| | - Marc D Driessen
- Department of Chemistry, Stanford University, Stanford, California 94305-6104, United States
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305-6104, United States.,Howard Hughes Medical Institute, Stanford, California 94305-6104, United States
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25
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Cheng L, Cao L, Wu Y, Xie W, Li J, Guan F, Tan Z. Bisecting N-Acetylglucosamine on EGFR Inhibits Malignant Phenotype of Breast Cancer via Down-Regulation of EGFR/Erk Signaling. Front Oncol 2020; 10:929. [PMID: 32612952 PMCID: PMC7308504 DOI: 10.3389/fonc.2020.00929] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/12/2020] [Indexed: 12/27/2022] Open
Abstract
Glycosylation, the most prevalent and diverse post-translational modification of protein, plays crucial biological roles in many physiological and pathological events. Alteration of N-glycan has been detected during breast cancer progression. Among the specific N-glycan structures, bisecting N-Acetylglucosamine (GlcNAc) is a β1,4-linked GlcNAc attached to the core β-mannose residue, and is catalyzed by glycosyltransferase MGAT3. Bisecting GlcNAc levels were commonly dysregulated in different types of cancer. In this study, we utilized mass spectrometry and lectin microarray analysis to investigate aberrant N-glycans in breast cancer cells. Our data showed the decreased levels of bisecting GlcNAc and down-regulated expression of MGAT3 in breast cancer cells than normal epithelial cells. Using PHA-E (a plant lectin recognizing and combining bisecting GlcNAc) based enrichment coupled with nanoLC-MS/MS, we analyzed the glycoproteins bearing bisecting GlcNAc in various breast cancer cells. Among the differentially expressed glycoproteins, levels of bisecting GlcNAc on EGFR were significantly decreased in breast cancer cells, confirmed by immunostaining and immunoprecipitation. We overexpressed MGAT3 in breast cancer MDA-MB-231 cells, and overexpression of MGAT3 significantly enhanced the bisecting N-GlcNAc on EGFR and suppressed the EGFR/Erk signaling, which further resulted in the reduction of migratory ability, cell proliferation, and clonal formation. Taken together, we conclude that bisecting N-GlcNAc on EGFR inhibits malignant phenotype of breast cancer via down-regulation of EGFR/Erk signaling.
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Affiliation(s)
- Lanming Cheng
- Shaanxi Provincial Key Laboratory of Biotechnology, Joint International Research Laboratory of Glycobiology and Medicinal Chemistry, College of Life Science, Northwest University, Xi'an, China
| | - Lin Cao
- Shaanxi Provincial Key Laboratory of Biotechnology, Joint International Research Laboratory of Glycobiology and Medicinal Chemistry, College of Life Science, Northwest University, Xi'an, China
| | - Yurong Wu
- Shaanxi Provincial Key Laboratory of Biotechnology, Joint International Research Laboratory of Glycobiology and Medicinal Chemistry, College of Life Science, Northwest University, Xi'an, China
| | - Wenjie Xie
- Shaanxi Provincial Key Laboratory of Biotechnology, Joint International Research Laboratory of Glycobiology and Medicinal Chemistry, College of Life Science, Northwest University, Xi'an, China
| | - Jiaqi Li
- Shaanxi Provincial Key Laboratory of Biotechnology, Joint International Research Laboratory of Glycobiology and Medicinal Chemistry, College of Life Science, Northwest University, Xi'an, China
| | - Feng Guan
- Shaanxi Provincial Key Laboratory of Biotechnology, Joint International Research Laboratory of Glycobiology and Medicinal Chemistry, College of Life Science, Northwest University, Xi'an, China
| | - Zengqi Tan
- Shaanxi Provincial Key Laboratory of Biotechnology, Joint International Research Laboratory of Glycobiology and Medicinal Chemistry, College of Life Science, Northwest University, Xi'an, China
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26
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Zhao X, Yu Z, Huang Y, Liu C, Wang M, Li X, Qian X, Ying W. Integrated Strategy for Large-Scale Investigation on Protein Core Fucosylation Stoichiometry Based on Glycan-Simplification and Paired-Peaks-Extraction. Anal Chem 2020; 92:2896-2901. [PMID: 31986883 DOI: 10.1021/acs.analchem.9b05276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Core fucosylation (CF) is a special form of N-glycosylation and plays an important role in pathological and biological processes. Increasing efforts in this area are focused on the identification of CF glycosites, whereas evidence showed that the stoichiometry of CF occupancy is functionally important. Here, an integrated strategy based on "Glycan-Simplification and Paired-Peaks-extraction" (GSPPE) for detecting large-scale stoichiometries of CF was developed. After HILIC enrichment of intact glycopeptides, sequential cleavages by endoglycosidases H and endoglycosidases F3 were performed to generate simplified glycopeptide forms (SGFs), i.e., peptide-GlcNAc (pep-HN) and peptide-GlcNAc-Fucose (pep-CF). These paired SGFs were found to be eluted consecutively on a reversed-phase chromatography column, which allowed us to obtain peak areas of SGF pairs, even if only one of the peaks was captured by the mass spectrometer (MS), by introducing the Paired-Peaks-Extraction algorithm. Thus, the missing value dilemma of random data-dependent MS/MS acquisition was reduced and the stoichiometry of site-specific CF could be calculated. We systematically evaluated the feasibility of this strategy using standard glycoproteins and then explored urinary samples from healthy individuals and hepatocellular carcinoma (HCC) patients. In total, 1449 highly reliable core fucose glycosites and their corresponding CF stoichiometries were obtained. Dozens of glycosites that differed significantly in the urine of healthy individuals and HCC patients were disclosed. The developed approach and program presented here may promote studies on core fucosylation and lead to a deeper understanding of their dysregulation in physiological- or pathological processes.
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Affiliation(s)
- Xinyuan Zhao
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China
| | - Zixiang Yu
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China.,Department of Pathology, Zhongshan Hospital , Fudan University , Shanghai 200032 , P. R. China.,Anhui Medical University , No. 81, Meishan Road , Hefei , Anhui 230032 , P. R. China
| | - Yi Huang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China.,Anhui Medical University , No. 81, Meishan Road , Hefei , Anhui 230032 , P. R. China
| | - Chang Liu
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China.,College of Life Science and Bioengineering , Beijing University of Technology , No. 100, Pingleyuan, Chaoyang District , Beijing 100124 , P. R. China
| | - Mingchao Wang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China
| | - Xiaoyu Li
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China.,College of Life Science and Bioengineering , Beijing University of Technology , No. 100, Pingleyuan, Chaoyang District , Beijing 100124 , P. R. China
| | - Xiaohong Qian
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China
| | - Wantao Ying
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing 102206 , P. R. China
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27
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Qi H, Li Z, Zheng H, Fu L, Jia Q. Facile preparation of hydrophilic glutathione modified magnetic nanomaterials for specific enrichment of glycopeptides. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.06.046] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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