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Liu C, Otsuka K, Kawai T. Recent advances in microscale separation techniques for glycome analysis. J Sep Sci 2024; 47:e2400170. [PMID: 38863084 DOI: 10.1002/jssc.202400170] [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: 03/04/2024] [Revised: 05/12/2024] [Accepted: 05/24/2024] [Indexed: 06/13/2024]
Abstract
The glycomic analysis holds significant appeal due to the diverse roles that glycans and glycoconjugates play, acting as modulators and mediators in cellular interactions, cell/organism structure, drugs, energy sources, glyconanomaterials, and more. The glycomic analysis relies on liquid-phase separation technologies for molecular purification, separation, and identification. As a miniaturized form of liquid-phase separation technology, microscale separation technologies offer various advantages such as environmental friendliness, high resolution, sensitivity, fast speed, and integration capabilities. For glycan analysis, microscale separation technologies are continuously evolving to address the increasing challenges in their unique manners. This review discusses the fundamentals and applications of microscale separation technologies for glycomic analysis. It covers liquid-phase separation technologies operating at scales generally less than 100 µm, including capillary electrophoresis, nanoflow liquid chromatography, and microchip electrophoresis. We will provide a brief overview of glycomic analysis and describe new strategies in microscale separation and their applications in glycan analysis from 2014 to 2023.
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Affiliation(s)
- Chenchen Liu
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Koji Otsuka
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- Research Administration Center, Osaka Metropolitan University, Osaka, Japan
| | - Takayuki Kawai
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka, Japan
- RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
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2
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Cheng CN, Liao HW, Lin CH, Chang WC, Chen IC, Lu YS, Kuo CH. Quantifying payloads of antibody‒drug conjugates using a postcolumn infused-internal standard strategy with LC‒MS. Anal Chim Acta 2024; 1303:342537. [PMID: 38609272 DOI: 10.1016/j.aca.2024.342537] [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: 11/17/2023] [Revised: 03/19/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024]
Abstract
BACKGROUND Antibody‒drug conjugates (ADCs) are innovative biopharmaceutics consisting of a monoclonal antibody, linkers, and cytotoxic payloads. Monitoring circulating payload concentrations has the potential to identify ADC toxicity; however, accurate quantification faces challenges, including low plasma concentrations, severe matrix effects, and the absence of stable isotope-labeled internal standards (SIL-IS) for payloads and their derivatives. Previous studies used structural analogs as internal standards, but different retention times between structural analogs and target analytes may hinder effective matrix correction. Therefore, a more flexible approach is required for precise payload quantification. RESULTS We developed an LC‒MS/MS method incorporating a postcolumn-infused internal standard (PCI-IS) strategy for quantifying payloads and their derivatives of trastuzumab emtansine, trastuzumab deruxtecan, and sacituzumab govitecan, including DM1, MCC-DM1, DXd, SN-38, and SN-38G. Structural analogs (maytansine, Lys-MCC-DM1, and exatecan) were selected as PCI-IS candidates, and their accuracy performance was evaluated based on the percentage of samples within 80%-120% quantification accuracy. Compared to the approach without PCI-IS correction, exatecan enhanced the accuracy performance from 30-40%-100% for SN-38 and DXd, while maytansine and Lys-MCC-DM1 showed comparable accuracy for DM1 and MCC-DM1. This validated PCI-IS analytical method showed superior normalization of matrix effect in all analytes compared to the conventional internal standard approach. The clinical application of this approach showed pronounced differences in DXd and SN-38 concentrations before and after PCI-IS correction. Moreover, only DXd concentrations after PCI-IS correction were significantly higher in patients with thrombocytopenia (p = 0.037). SIGNIFICANCE This approach effectively addressed the issue of unavailability of SIL-IS for novel ADC payloads and provided more accurate quantification, potentially yielding more robust statistical outcomes for understanding the exposure-toxicity relationship in ADCs. It is anticipated that this PCI-IS strategy may be extrapolated to quantify payloads and derivatives in diverse ADCs, thereby providing invaluable insights into drug toxicity and fortifying patient safety in ADC usage.
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Affiliation(s)
- Chih-Ning Cheng
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsiao-Wei Liao
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ching-Hung Lin
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan; Department of Medical Oncology, National Taiwan University Hospital, Cancer Center Branch, Taipei, Taiwan
| | - Wen-Chi Chang
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - I-Chun Chen
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan; Department of Medical Oncology, National Taiwan University Hospital, Cancer Center Branch, Taipei, Taiwan
| | - Yen-Shen Lu
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ching-Hua Kuo
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan; The Metabolomics Core Laboratory, Centers of Genomic and Precision Medicine, National Taiwan University, Taiwan; Department of Pharmacy, National Taiwan University Hospital, Taipei, Taiwan.
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3
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Wojtkiewicz M, Subramanian SP, Gundry RL. Multinozzle Emitter for Improved Negative Mode Analysis of Reduced Native N-Glycans by Microflow Porous Graphitized Carbon Liquid Chromatography Mass Spectrometry. Anal Chem 2024; 96:5746-5751. [PMID: 38556995 PMCID: PMC11024887 DOI: 10.1021/acs.analchem.3c03649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/13/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Microflow porous graphitized carbon liquid chromatography (PGC-LC) combined with negative mode ionization mass spectrometry (MS) provides high resolution separation and identification of reduced native N-glycan structural isomers. However, insufficient spray quality and low ionization efficiency of N-glycans present challenges for negative mode electrospray. Here, we evaluated the performance of a recently developed multinozzle electrospray source (MnESI) and accompanying M3 emitter for microflow PGC-LC-MS analysis of N-glycans in negative mode. In comparison to a standard electrospray ionization source, the MnESI with an M3 emitter improves signal intensity, identification, quantification, and resolution of structural isomers to accommodate low-input samples.
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Affiliation(s)
- Melinda Wojtkiewicz
- CardiOmics
Program, Center for Heart and Vascular Research, and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Sabarinath Peruvemba Subramanian
- CardiOmics
Program, Center for Heart and Vascular Research, and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Rebekah L. Gundry
- CardiOmics
Program, Center for Heart and Vascular Research, and Department of
Cellular and Integrative Physiology, University
of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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4
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Houlahan CB, Kong Y, Johnston B, Cielesh M, Chau TH, Fenwick J, Coleman PR, Hao H, Haltiwanger RS, Thaysen-Andersen M, Passam FH, Larance M. Analysis of the Healthy Platelet Proteome Identifies a New Form of Domain-Specific O-Fucosylation. Mol Cell Proteomics 2024; 23:100717. [PMID: 38237698 PMCID: PMC10879016 DOI: 10.1016/j.mcpro.2024.100717] [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: 07/14/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 02/17/2024] Open
Abstract
Platelet activation induces the secretion of proteins that promote platelet aggregation and inflammation. However, detailed analysis of the released platelet proteome is hampered by platelets' tendency to preactivate during their isolation and a lack of sensitive protocols for low abundance releasate analysis. Here, we detail the most sensitive analysis to date of the platelet releasate proteome with the detection of >1300 proteins. Unbiased scanning for posttranslational modifications within releasate proteins highlighted O-glycosylation as being a major component. For the first time, we detected O-fucosylation on previously uncharacterized sites including multimerin-1 (MMRN1), a major alpha granule protein that supports platelet adhesion to collagen and is a carrier for platelet factor V. The N-terminal elastin microfibril interface (EMI) domain of MMRN1, a key site for protein-protein interaction, was O-fucosylated at a conserved threonine within a new domain context. Our data suggest that either protein O-fucosyltransferase 1, or a novel protein O-fucosyltransferase, may be responsible for this modification. Mutating this O-fucose site on the EMI domain led to a >50% reduction of MMRN1 secretion, supporting a key role of EMI O-fucosylation in MMRN1 secretion. By comparing releasates from resting and thrombin-treated platelets, 202 proteins were found to be significantly released after high-dose thrombin stimulation. Complementary quantification of the platelet lysates identified >3800 proteins, which confirmed the platelet origin of releasate proteins by anticorrelation analysis. Low-dose thrombin treatment yielded a smaller subset of significantly regulated proteins with fewer secretory pathway enzymes. The extensive platelet proteome resource provided here (larancelab.com/platelet-proteome) allows identification of novel regulatory mechanisms for drug targeting to address platelet dysfunction and thrombosis.
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Affiliation(s)
- Callum B Houlahan
- The Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Yvonne Kong
- Central Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Bede Johnston
- The Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Michelle Cielesh
- Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - The Huong Chau
- School of Natural Sciences, Macquarie University, Macquarie Park, New South Wales, Australia
| | - Jemma Fenwick
- The Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia; Central Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Paul R Coleman
- The Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Huilin Hao
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Robert S Haltiwanger
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Macquarie University, Macquarie Park, New South Wales, Australia; Institute for Glyco-Core Research, Nagoya University, Nagoya, Aichi, Japan
| | - Freda H Passam
- The Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia; Central Clinical School, The University of Sydney, Sydney, New South Wales, Australia.
| | - Mark Larance
- Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia.
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5
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Chernykh A, Abrahams JL, Grant OC, Kambanis L, Sumer-Bayraktar Z, Ugonotti J, Kawahara R, Corcilius L, Payne RJ, Woods RJ, Thaysen-Andersen M. Position-specific N- and O-glycosylation of the reactive center loop impacts neutrophil elastase-mediated proteolysis of corticosteroid-binding globulin. J Biol Chem 2024; 300:105519. [PMID: 38042488 PMCID: PMC10784704 DOI: 10.1016/j.jbc.2023.105519] [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: 03/21/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/04/2023] Open
Abstract
Corticosteroid-binding globulin (CBG) delivers anti-inflammatory cortisol to inflamed tissues through proteolysis of an exposed reactive center loop (RCL) by neutrophil elastase (NE). We previously demonstrated that RCL-localized Asn347-linked N-glycans impact NE proteolysis, but a comprehensive structure-function characterization of the RCL glycosylation is still required to better understand CBG glycobiology. Herein, we first performed RCL-centric glycoprofiling of serum-derived CBG to elucidate the Asn347-glycans and then used molecular dynamics simulations to study their impact on NE proteolysis. Importantly, we also identified O-glycosylation (di/sialyl T) across four RCL sites (Thr338/Thr342/Thr345/Ser350) of serum CBG close to the NE-targeted Val344-Thr345 cleavage site. A restricted N- and O-glycan co-occurrence pattern on the RCL involving exclusively Asn347 and Thr338 glycosylation was experimentally observed and supported in silico by modeling of a CBG-GalNAc-transferase (GalNAc-T) complex with various RCL glycans. GalNAc-T2 and GalNAc-T3 abundantly expressed by liver and gall bladder, respectively, showed in vitro a capacity to transfer GalNAc (Tn) to multiple RCL sites suggesting their involvement in RCL O-glycosylation. Recombinant CBG was then used to determine roles of RCL O-glycosylation through longitudinal NE-centric proteolysis experiments, which demonstrated that both sialoglycans (disialyl T) and asialoglycans (T) decorating Thr345 inhibit NE proteolysis. Synthetic RCL O-glycopeptides expanded on these findings by showing that Thr345-Tn and Thr342-Tn confer strong and moderate protection against NE cleavage, respectively. Molecular dynamics substantiated that short Thr345-linked O-glycans abrogate NE interactions. In conclusion, we report on biologically relevant CBG RCL glycosylation events, which improve our understanding of mechanisms governing cortisol delivery to inflamed tissues.
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Affiliation(s)
- Anastasia Chernykh
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Jodie L Abrahams
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Lucas Kambanis
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Zeynep Sumer-Bayraktar
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Glycometabolic Biochemistry Team, Cluster of Pioneering Research, RIKEN, Wako, Saitama, Japan
| | - Julian Ugonotti
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Rebeca Kawahara
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| | - Leo Corcilius
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan.
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6
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Delafield DG, Miles HN, Ricke WA, Li L. Inclusion of Porous Graphitic Carbon Chromatography Yields Greater Protein Identification and Compartment and Process Coverage and Enables More Reflective Protein-Level Label-Free Quantitation. J Proteome Res 2023; 22:3508-3518. [PMID: 37815119 PMCID: PMC10732698 DOI: 10.1021/acs.jproteome.3c00373] [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] [Indexed: 10/11/2023]
Abstract
The ubiquity of mass spectrometry-based bottom-up proteomic analyses as a component of biological investigation mandates the validation of methodologies that increase acquisition efficiency, improve sample coverage, and enhance profiling depth. Chromatographic separation is often ignored as an area of potential improvement, with most analyses relying on traditional reversed-phase liquid chromatography (RPLC); this consistent reliance on a single chromatographic paradigm fundamentally limits our view of the observable proteome. Herein, we build upon early reports and validate porous graphitic carbon chromatography (PGC) as a facile means to substantially enhance proteomic coverage without changes to sample preparation, instrument configuration, or acquisition methods. Analysis of offline fractionated cell line digests using both separations revealed an increase in peptide and protein identifications by 43% and 24%, respectively. Increased identifications provided more comprehensive coverage of cellular components and biological processes independent of protein abundance, highlighting the substantial quantity of proteomic information that may go undetected in standard analyses. We further utilize these data to reveal that label-free quantitative analyses using RPLC separations alone may not be reflective of actual protein constituency. Together, these data highlight the value and comprehension offered through PGC-MS proteomic analyses. RAW proteomic data have been uploaded to the MassIVE repository with the primary accession code MSV000091495.
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Affiliation(s)
- Daniel G. Delafield
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Hannah N. Miles
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075
| | - William A. Ricke
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- George M. O’Brien Urology Research Center of Excellence, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
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7
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Carnielli CM, Melo de Lima Morais T, Malta de Sá Patroni F, Prado Ribeiro AC, Brandão TB, Sobroza E, Matos LL, Kowalski LP, Paes Leme AF, Kawahara R, Thaysen-Andersen M. Comprehensive glycoprofiling of oral tumours associates N-glycosylation with lymph node metastasis and patient survival. Mol Cell Proteomics 2023:100586. [PMID: 37268159 PMCID: PMC10336694 DOI: 10.1016/j.mcpro.2023.100586] [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: 02/01/2023] [Revised: 05/08/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023] Open
Abstract
While altered protein glycosylation is regarded a trait of oral squamous cell carcinoma (OSCC), the heterogeneous and dynamic glycoproteome of tumour tissues from OSCC patients remain unmapped. To this end, we here employ an integrated multi-omics approach comprising unbiased and quantitative glycomics and glycoproteomics applied to a cohort of resected primary tumour tissues from OSCC patients with (n = 19) and without (n = 12) lymph node metastasis. While all tumour tissues displayed relatively uniform N-glycome profiles suggesting overall stable global N-glycosylation during disease progression, altered expression of six sialylated N-glycans was found to correlate with lymph node metastasis. Notably, glycoproteomics and advanced statistical analyses uncovered altered site-specific N-glycosylation revealing previously unknown associations with several clinicopathological features. Importantly, the glycomics and glycoproteomics data unveiled that comparatively high abundance of two core-fucosylated and sialylated N-glycans (Glycan 40a and Glycan 46a) and one N-glycopeptide from fibronectin were associated with low patient survival, while a relatively low abundance of N-glycopeptides from both afamin and CD59 were also associated with poor survival. This study provides novel insight into the complex OSCC tissue N-glycoproteome forming an important resource to further explore the underpinning disease mechanisms and uncover new prognostic glyco-markers for OSCC.
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Affiliation(s)
- Carolina Moretto Carnielli
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 SP, Brazil
| | | | | | - Ana Carolina Prado Ribeiro
- Serviço de Odontologia Oncológica, Instituto do Câncer do Estado de São Paulo, ICESP-FMUSP, São Paulo, 01246-000 SP, Brazil; Universidade Brasil, Fernandópolis, 15600-000 SP, Brazil
| | - Thaís Bianca Brandão
- Serviço de Odontologia Oncológica, Instituto do Câncer do Estado de São Paulo, ICESP-FMUSP, São Paulo, 01246-000 SP, Brazil
| | - Evandro Sobroza
- Serviço de Odontologia Oncológica, Instituto do Câncer do Estado de São Paulo, ICESP-FMUSP, São Paulo, 01246-000 SP, Brazil
| | - Leandro Luongo Matos
- Serviço de Cirurgia de Cabeça e Pescoço, Instituto do Câncer do Estado de São Paulo, ICESP-FMUSP, São Paulo, 01246-000 SP, Brazil
| | - Luiz Paulo Kowalski
- Departamento de Cirurgia de Cabeça e Pescoço e Otorrinolaringologia, A.C. Camargo Cancer Center, São Paulo, SP, 01509-900, Brazil; Departamento de Cirurgia de Cabeça e Pescoço, Faculdade de Medicina, Universidade de São Paulo - USP, São Paulo, SP, 01246-903, Brazil
| | - Adriana Franco Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, 13083-970 SP, Brazil.
| | - Rebeca Kawahara
- School of Natural Sciences, Macquarie University, Sydney, NSW-2109, Australia; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8601, Japan.
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Macquarie University, Sydney, NSW-2109, Australia; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, 464-8601, Japan.
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8
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Chau TH, Chernykh A, Ugonotti J, Parker BL, Kawahara R, Thaysen-Andersen M. Glycomics-Assisted Glycoproteomics Enables Deep and Unbiased N-Glycoproteome Profiling of Complex Biological Specimens. Methods Mol Biol 2023; 2628:235-263. [PMID: 36781790 DOI: 10.1007/978-1-0716-2978-9_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Mass spectrometry-driven glycomics and glycoproteomics, the system-wide profiling of detached glycans and intact glycopeptides from biological samples, respectively, are powerful approaches to interrogate the heterogenous glycoproteome. Efforts to develop integrated workflows employing both glycomics and glycoproteomics have been invested since the concerted application of these complementary approaches enables a deeper exploration of the glycoproteome. This protocol paper outlines, step-by-step, an integrated -omics technology, the "glycomics-assisted glycoproteomics" method, that first establishes the N-glycan fine structures and their quantitative distribution pattern of protein extracts via porous graphitized carbon-LC-MS/MS. The N-glycome information is then used to augment and guide the challenging reversed-phase LC-MS/MS-based profiling of intact N-glycopeptides from the same protein samples. Experimental details and considerations relating to the sample preparation and the N-glycomics and N-glycoproteomics data collection, analysis, and integration are discussed. Benefits of the glycomics-assisted glycoproteomics method, which can be readily applied to both simple and complex biological specimens such as protein extracts from cells, tissues, and bodily fluids (e.g., serum), include quantitative information of the protein carriers and site(s) of glycosylation, site occupancy, and the site-specific glycan structures directly from biological samples. The glycomics-assisted glycoproteomics method therefore facilitates a comprehensive view of the complexity and dynamics of the heterogenous glycoproteome.
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Affiliation(s)
- The Huong Chau
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Anastasia Chernykh
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Julian Ugonotti
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Benjamin L Parker
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Rebeca Kawahara
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia.
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia.
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Aichi, Japan.
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9
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. MASS SPECTROMETRY REVIEWS 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
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10
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Lageveen‐Kammeijer GSM, Kuster B, Reusch D, Wuhrer M. High sensitivity glycomics in biomedicine. MASS SPECTROMETRY REVIEWS 2022; 41:1014-1039. [PMID: 34494287 PMCID: PMC9788051 DOI: 10.1002/mas.21730] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 05/15/2023]
Abstract
Many analytical challenges in biomedicine arise from the generally high heterogeneity and complexity of glycan- and glycoconjugate-containing samples, which are often only available in minute amounts. Therefore, highly sensitive workflows and detection methods are required. In this review mass spectrometric workflows and detection methods are evaluated for glycans and glycoproteins. Furthermore, glycomic methodologies and innovations that are tailored for enzymatic treatments, chemical derivatization, purification, separation, and detection at high sensitivity are highlighted. The discussion is focused on the analysis of mammalian N-linked and GalNAc-type O-linked glycans.
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Affiliation(s)
| | - Bernhard Kuster
- Chair for Proteomics and BioanalyticsTechnical University of MunichFreisingGermany
| | - Dietmar Reusch
- Pharma Technical Development EuropeRoche Diagnostics GmbHPenzbergGermany
| | - Manfred Wuhrer
- Leiden University Medical CenterCenter for Proteomics and MetabolomicsLeidenThe Netherlands
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11
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Sui X, Wu Q, Cui X, Wang X, Zhang L, Deng N, Bian Y, Xu R, Tian R. Robust Capillary- and Micro-Flow Liquid Chromatography-Tandem Mass Spectrometry Methods for High-Throughput Proteome Profiling. J Proteome Res 2022; 21:2472-2480. [PMID: 36040778 DOI: 10.1021/acs.jproteome.2c00405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Capillary- and micro-flow liquid chromatography-tandem mass spectrometry (capLC-MS/MS and μLC-MS/MS) is becoming a valuable alternative to nano-flow LC-MS/MS due to its high robustness and throughput. The systematic comparison of capLC-MS/MS and μLC-MS/MS systems for global proteome profiling has not been reported yet. Here, the capLC-MS/MS (150 μm i.d. column, 1 μL/min) and μLC-MS/MS (1 mm i.d. column, 50 μL/min) systems were both established based on UltiMate 3000 RSLCnano coupled to an Orbitrap Exploris 240 by integrating with different flowmeters. We evaluated both systems in terms of sensitivity, analysis throughput, separation efficiency, and robustness. capLC-MS/MS was about 10 times more sensitive than μLC-MS/MS at different gradient lengths. Compared with capLC-MS/MS, μLC-MS/MS was able to achieve higher analysis throughput and separation efficiency. During the 7 days' long-term performance test, both systems showed good reproducibility of chromatographic full width (RSD < 3%), retention time (RSD < 0.4%), and protein identification (RSD < 3%). These results demonstrate that capLC-MS/MS is more suitable for high-throughput analysis of clinical samples with a limited starting material. When enough samples are available, μLC-MS/MS is preferred. Together, capLC and μLC coupled to Orbitrap Exploris 240 with moderate sensitivity should well meet the needs of large-cohort clinical proteomic analysis.
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Affiliation(s)
- Xintong Sui
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Qiong Wu
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiaozhen Cui
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xi Wang
- Department of Oncology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen 518020, China
| | - Luobin Zhang
- Department of Oncology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen 518020, China
| | - Nan Deng
- Instrumental Analysis Center, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yangyang Bian
- The College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ruilian Xu
- Department of Oncology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen 518020, China
| | - Ruijun Tian
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
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12
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Increased levels of acidic free-N-glycans, including multi-antennary and fucosylated structures, in the urine of cancer patients. PLoS One 2022; 17:e0266927. [PMID: 35413075 PMCID: PMC9004742 DOI: 10.1371/journal.pone.0266927] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/29/2022] [Indexed: 12/01/2022] Open
Abstract
We recently reported increased levels of urinary free-glycans in some cancer patients. Here, we focused on cancer related alterations in the levels of high molecular weight free-glycans. The rationale for this study was that branching, elongation, fucosylation and sialylation, which lead to increases in the molecular weight of glycans, are known to be up-regulated in cancer. Urine samples from patients with gastric cancer, pancreatic cancer, cholangiocarcinoma and colorectal cancer and normal controls were analyzed. The extracted free-glycans were fluorescently labeled with 2-aminopyridine and analyzed by multi-step liquid chromatography. Comparison of the glycan profiles revealed increased levels of glycans in some cancer patients. Structural analysis of the glycans was carried out by performing chromatography and mass spectrometry together with enzymatic or chemical treatments. To compare glycan levels between samples with high sensitivity and selectivity, simultaneous measurements by reversed-phase liquid chromatography-selected ion monitoring of mass spectrometry were also performed. As a result, three lactose-core glycans and 78 free-N-glycans (one phosphorylated oligomannose-type, four sialylated hybrid-type and 73 bi-, tri- and tetra-antennary complex-type structures) were identified. Among them, glycans with α1,3-fucosylation ((+/− sialyl) Lewis X), triply α2,6-sialylated tri-antennary structures and/or a (Man3)GlcNAc1-core displayed elevated levels in cancer patients. However, simple α2,3-sialylation and α1,6-core-fucosylation did not appear to contribute to the observed increase in the level of glycans. Interestingly, one tri-antennary free-N-glycan that showed remarkable elevation in some cancer patients contained a unique Glcβ1-4GlcNAc-core instead of the common GlcNAc2-core at the reducing end. This study provides further insights into free-glycans as potential tumor markers and their processing pathways in cancer.
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13
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Guo L, Nayak S, Mao Y, Li N. Glycine additive enhances sensitivity for N- and O-glycan analysis with hydrophilic interaction chromatography-electrospray ionization-mass spectrometry. Anal Biochem 2021; 635:114447. [PMID: 34742721 DOI: 10.1016/j.ab.2021.114447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/01/2021] [Indexed: 11/30/2022]
Abstract
Glycosylation is critical for many biological processes and biotherapeutic development. One of the most powerful approaches for analyzing released glycans is hydrophilic interaction chromatography coupled with electrospray ionization mass spectrometry (HILIC-ESI-MS). The high sensitivity of MS is crucial for detecting low-abundance glycans and elucidating their structures. In this study, we presented a simple solution to boost MS response of procainamide (ProcA) labeled glycans for 2- to over 60-fold by including 1 mM glycine in ammonium formate mobile phases for HILIC-ESI-MS. The glycine additive increased charge states, enhanced ion intensities and signal-to-noise ratios, and improved tandem MS spectral quality of various N- and O-glycans without affecting chromatographic performance. Furthermore, more homogeneous ionization among different ProcA labeled glycans was achieved by using the glycine additive, resulting in more comparable quantitative results relative to fluorescence-based quantification. We demonstrated that ammonium formate caused ion suppression to ProcA labeled glycans, which were likely mitigated by glycine with enhanced ESI ionization. Overall, simple addition of glycine to mobile phases during HILIC-ESI-MS analysis significantly improves MS detection sensitivity and will facilitate future profiling and quantitation of glycans released from N- and O-glycoproteins.
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Affiliation(s)
- Lili Guo
- Analytical Chemistry, Regeneron Pharmaceuticals Inc, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, United States
| | - Shruti Nayak
- Analytical Chemistry, Regeneron Pharmaceuticals Inc, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, United States
| | - Yuan Mao
- Analytical Chemistry, Regeneron Pharmaceuticals Inc, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, United States.
| | - Ning Li
- Analytical Chemistry, Regeneron Pharmaceuticals Inc, 777 Old Saw Mill River Road, Tarrytown, NY, 10591, United States
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14
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Ugonotti J, Kawahara R, Loke I, Zhu Y, Chatterjee S, Tjondro HC, Sumer-Bayraktar Z, Neelamegham S, Thaysen-Andersen M. N-acetyl-β-D-hexosaminidases mediate the generation of paucimannosidic proteins via a putative noncanonical truncation pathway in human neutrophils. Glycobiology 2021; 32:218-229. [PMID: 34939086 DOI: 10.1093/glycob/cwab108] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/26/2022] Open
Abstract
We recently discovered that human neutrophils express immunomodulatory glycoproteins carrying unusual and highly truncated paucimannosidic N-glycans (Man1-3GlcNAc2Fuc0-1), but their biosynthesis remains elusive. Guided by the well-characterized truncation pathway in invertebrates and plants in which the N-acetyl-β-D-hexosaminidase (Hex) isoenzymes catalyze paucimannosidic protein (PMP) formation, we here set out to test if the homologous human Hex α and β subunits encoded by HEXA and HEXB drive a similar truncation pathway in human neutrophils. To this end, we performed quantitative glycomics and glycoproteomics of several CRISPR-Cas9-edited Hex-disrupted neutrophil-like HL-60 mutants (HEXA-KO and HEXB-KO) and matching unedited cell lines. Hex disruption was validated using next-generation sequencing, enzyme-linked immunosorbent assay (ELISA), quantitative proteomics and Hex activity assays. Excitingly, all Hex-disrupted mutants displayed significantly reduced levels of paucimannosylation, particularly Man2-3GlcNAc2Fuc1, relative to unedited HL-60 suggesting that both HEXA and HEXB contribute to PMP formation via a hitherto unexplored truncation pathway in neutrophils. Quantitative N-glycomics indeed demonstrated reduced utilization of a putative noncanonical truncation pathway in favor of the canonical elongation pathway in all Hex-disrupted mutants relative to unedited controls. Quantitative glycoproteomics recapitulated the truncation-to-elongation switch in all Hex-disrupted mutants and showed a greater switch for N-glycoproteins cotrafficking with Hex to the azurophilic granules of neutrophils such as myeloperoxidase. Finally, we supported the Hex-PMP relationship by documenting that primary neutrophils isolated from an early-onset Sandhoff disease patient (HEXB-/-) displayed dramatically reduced paucimannosylation relative to neutrophils from an age-matched unaffected donor. We conclude that both human Hex α and β mediate PMP formation via a putative noncanonical truncation pathway in neutrophils.
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Affiliation(s)
- Julian Ugonotti
- Department of Molecular Sciences, Macquarie University, Balaclava Road, Macquarie Park, Sydney, NSW 2109, Australia
| | - Rebeca Kawahara
- Department of Molecular Sciences, Macquarie University, Balaclava Road, Macquarie Park, Sydney, NSW 2109, Australia
| | - Ian Loke
- Cordlife Group Limited, 1 Yishun Industrial Street, Singapore 768160, Singapore
| | - Yuqi Zhu
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, USA
| | - Sayantani Chatterjee
- Department of Molecular Sciences, Macquarie University, Balaclava Road, Macquarie Park, Sydney, NSW 2109, Australia
| | - Harry C Tjondro
- Department of Molecular Sciences, Macquarie University, Balaclava Road, Macquarie Park, Sydney, NSW 2109, Australia
| | - Zeynep Sumer-Bayraktar
- Department of Molecular Sciences, Macquarie University, Balaclava Road, Macquarie Park, Sydney, NSW 2109, Australia
| | - Sriram Neelamegham
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, USA
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Balaclava Road, Macquarie Park, Sydney, NSW 2109, Australia.,Biomolecular Discovery Research Centre, Macquarie University, Balaclava Road, Macquarie Park, Sydney, NSW 2109, Australia
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15
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Chatterjee S, Ugonotti J, Lee LY, Everest-Dass A, Kawahara R, Thaysen-Andersen M. Trends in oligomannosylation and α1,2-mannosidase expression in human cancers. Oncotarget 2021; 12:2188-2205. [PMID: 34676051 PMCID: PMC8522845 DOI: 10.18632/oncotarget.28064] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/18/2021] [Indexed: 02/05/2023] Open
Abstract
Aberrant protein glycosylation is a prominent cancer feature. While many tumour-associated glycoepitopes have been reported, advances in glycoanalytics continue to uncover new associations between glycosylation and cancer. Guided by a comprehensive literature survey suggesting that oligomannosylation (Man5–9 GlcNAc2) is a widespread and often regulated glycosignature in human cancers, we here revisit a valuable compilation of nearly 500 porous graphitized carbon LC-MS/MS N-glycomics datasets acquired across 11 human cancer types to systematically test for oligomannose-cancer associations. Firstly, the quantitative glycomics data obtained across 34 cancerous cell lines demonstrated that oligomannosylation is a pan-cancer feature spanning in a wide abundance range. In keeping with literature, our quantitative glycomics data of tumour and matching control tissues and new MALDI-MS imaging data of tissue microarrays showed a strong cancer-associated elevation of oligomannosylation in both basal cell (p = 1.78 × 10–12) and squamous cell (p = 1.23 × 10–11) skin cancer and colorectal cancer (p = 8.0 × 10–4). The glycomics data also indicated that some cancer types including gastric and liver cancer exhibit unchanged or reduced oligomannose levels, observations also supported by literature and MALDI-MS imaging data. Finally, expression data from public cancer repositories indicated that several α1,2-mannosidases are regulated in tumour tissues suggesting that these glycan-processing enzymes may contribute to the cancer-associated modulation of oligomannosylation. This omics-centric study has compiled robust glycomics and enzyme expression data revealing interesting molecular trends that open avenues to better understand the role of oligomannosylation in human cancers.
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Affiliation(s)
| | - Julian Ugonotti
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Ling Y Lee
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | | | - Rebeca Kawahara
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Joint senior authors
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Biomolecular Discovery Research Centre (BDRC), Macquarie University, Sydney, Australia.,Joint senior authors
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16
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Moh ESX, Nishtala K, Iqbal S, Staikopoulos V, Kapur D, Hutchinson MR, Packer NH. Long-term intrathecal administration of morphine vs. baclofen: Differences in CSF glycoconjugate profiles using multiglycomics. Glycobiology 2021; 32:50-59. [PMID: 34969075 DOI: 10.1093/glycob/cwab098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/29/2021] [Accepted: 08/29/2021] [Indexed: 11/13/2022] Open
Abstract
Opioid use for treatment of persistent pain has increased dramatically over the past two decades, but it has not resulted in improved pain management outcomes. To understand the molecular mechanisms of opioids, molecular signatures that arise from opioid exposure are often sought after, using various analytical methods. In this study, we performed proteomics, and multiglycomics via sequential analysis of polysialic acids, glycosaminoglycans, N-glycans and O-glycans, using the same cerebral spinal fluid (CSF) sample from patients that had long-term (>2 years), intrathecal morphine or baclofen administered via an indwelling pump. Proteomics and N-glycomics signatures between the two treatment groups were highly conserved, while significant differences were observed in polysialic acid, heparan sulfate glycosaminoglycan and O-glycan profiles between the two treatment groups. This represents the first study to investigate the potential relationships between diverse CSF conjugated glycans and long-term intrathecal drug exposure. The unique changes, observed by a sequential analytical workflow, reflect previously undescribed molecular effects of opioid administration and pain management.
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Affiliation(s)
- Edward S X Moh
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, New South Wales, 2109, Australia.,Department of Molecular Science, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Krishnatej Nishtala
- Department of Molecular Science, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Sameera Iqbal
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, New South Wales, 2109, Australia.,Department of Molecular Science, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Vasiliki Staikopoulos
- ARC Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, South Australia, 5000, Australia.,Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, 5000, Australia
| | - Dilip Kapur
- Pain Management Unit, Flinders Medical Centre, Adelaide, South Australia, 5042, Australia
| | - Mark R Hutchinson
- ARC Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, South Australia, 5000, Australia.,Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, 5000, Australia
| | - Nicolle H Packer
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, New South Wales, 2109, Australia.,Department of Molecular Science, Macquarie University, Sydney, New South Wales, 2109, Australia
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17
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Madunić K, Wagt S, Zhang T, Wuhrer M, Lageveen-Kammeijer GSM. Dopant-Enriched Nitrogen Gas for Enhanced Electrospray Ionization of Released Glycans in Negative Ion Mode. Anal Chem 2021; 93:6919-6923. [PMID: 33914523 PMCID: PMC8153384 DOI: 10.1021/acs.analchem.1c00023] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
The desolvation and
ionization process of analytes can significantly
be improved by enriching the nebulizing gas with a dopant (dopant
enriched nitrogen (DEN) gas) in the electrospray source. However,
for the analysis of released glycans in negative ion mode, the usage
of DEN gas remains largely unexplored. For this purpose, we investigated
the effect of different polar protic solvents (methanol, ethanol,
and isopropanol) as well as using solely the nebulizing gas or ambient
air on the ionization and charge state distribution of released N- and O-glycans. Compared to the standard
acetonitrile enriched nitrogen gas, isopropanol showed the highest
increase in regards to peak areas. Moreover, it showed large benefits
for the identification of glycan structures at high sensitivity as
the increased precursor intensities subsequently resulted in higher
intensities in tandem MS mode. While similar effects are noted for
both neutral and sialylated species, the most significant effect was
observed for early eluting glycans where very low acetonitrile concentrations
were present in the eluent. The best results in terms of S/N ratios
were obtained with methanol, with less effect on the MS/MS signal
enhancement. Therefore, the use of this dopant would be particularly
beneficial for high sensitivity MS-mode applications. In conclusion,
isopropanol enriched DEN gas greatly improves the detection of both N-and O-glycan species and their tandem
mass spectra, particularly for the early eluting species whose ionization
in the absence of DEN gas is hindered by low organic concentrations.
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Affiliation(s)
- Katarina Madunić
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Sander Wagt
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Tao Zhang
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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18
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Pralow A, Hoffmann M, Nguyen-Khuong T, Pioch M, Hennig R, Genzel Y, Rapp E, Reichl U. Comprehensive N-glycosylation analysis of the influenza A virus proteins HA and NA from adherent and suspension MDCK cells. FEBS J 2021; 288:4869-4891. [PMID: 33629527 DOI: 10.1111/febs.15787] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/04/2021] [Accepted: 02/22/2021] [Indexed: 12/25/2022]
Abstract
Glycosylation is considered as a critical quality attribute for the production of recombinant biopharmaceuticals such as hormones, blood clotting factors, or monoclonal antibodies. In contrast, glycan patterns of immunogenic viral proteins, which differ significantly between the various expression systems, are hardly analyzed yet. The influenza A virus (IAV) proteins hemagglutinin (HA) and neuraminidase (NA) have multiple N-glycosylation sites, and alteration of N-glycan micro- and macroheterogeneity can have strong effects on virulence and immunogenicity. Here, we present a versatile and powerful glycoanalytical workflow that enables a comprehensive N-glycosylation analysis of IAV glycoproteins. We challenged our workflow with IAV (A/PR/8/34 H1N1) propagated in two closely related Madin-Darby canine kidney (MDCK) cell lines, namely an adherent MDCK cell line and its corresponding suspension cell line. As expected, N-glycan patterns of HA and NA from virus particles produced in both MDCK cell lines were similar. Detailed analysis of the HA N-glycan microheterogeneity showed an increasing variability and a higher complexity for N-glycosylation sites located closer to the head region of the molecule. In contrast, NA was found to be exclusively N-glycosylated at site N73. Almost all N-glycan structures were fucosylated. Furthermore, HA and NA N-glycan structures were exclusively hybrid- and complex-type structures, to some extent terminated with alpha-linked galactose(s) but also with blood group H type 2 and blood group A epitopes. In contrast to the similarity of the overall glycan pattern, differences in the relative abundance of individual structures were identified. This concerned, in particular, oligomannose-type, alpha-linked galactose, and multiantennary complex-type N-glycans.
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Affiliation(s)
- Alexander Pralow
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Marcus Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Terry Nguyen-Khuong
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Markus Pioch
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - René Hennig
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,glyXera GmbH, Magdeburg, Germany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,glyXera GmbH, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Chair of Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany
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19
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Serum N-Glycomics Stratifies Bacteremic Patients Infected with Different Pathogens. J Clin Med 2021; 10:jcm10030516. [PMID: 33535571 PMCID: PMC7867038 DOI: 10.3390/jcm10030516] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 01/08/2023] Open
Abstract
Bacteremia—i.e., the presence of pathogens in the blood stream—is associated with long-term morbidity and is a potential precursor condition to life-threatening sepsis. Timely detection of bacteremia is therefore critical to reduce patient mortality, but existing methods lack precision, speed, and sensitivity to effectively stratify bacteremic patients. Herein, we tested the potential of quantitative serum N-glycomics performed using porous graphitized carbon liquid chromatography tandem mass spectrometry to stratify bacteremic patients infected with Escherichia coli (n = 11), Staphylococcus aureus (n = 11), Pseudomonas aeruginosa (n = 5), and Streptococcus viridans (n = 5) from healthy donors (n = 39). In total, 62 N-glycan isomers spanning 41 glycan compositions primarily comprising complex-type core fucosylated, bisecting N-acetylglucosamine (GlcNAc), and α2,3-/α2,6-sialylated structures were profiled across all samples using label-free quantitation. Excitingly, unsupervised hierarchical clustering and principal component analysis of the serum N-glycome data accurately separated the patient groups. P. aeruginosa-infected patients displayed prominent N-glycome aberrations involving elevated levels of fucosylation and bisecting GlcNAcylation and reduced sialylation relative to other bacteremic patients. Notably, receiver operating characteristic analyses demonstrated that a single N-glycan isomer could effectively stratify each of the four bacteremic patient groups from the healthy donors (area under the curve 0.93–1.00). Thus, the serum N-glycome represents a new hitherto unexplored class of potential diagnostic markers for bloodstream infections.
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20
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A mass spectrometry-based glycotope-centric cellular glycomics is the more fruitful way forward to see the forest for the trees. Biochem Soc Trans 2021; 49:55-69. [PMID: 33492355 DOI: 10.1042/bst20190861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 02/08/2023]
Abstract
The nature of protein glycosylation renders cellular glycomics a very challenging task in having to deal with all the disparate glycans carried on membrane glycoproteins. Rapid mapping by mass spectrometry analysis provides only a coarse sketch of the glycomic complexity based primarily on glycosyl compositions, whereby the missing high-resolution structural details require a combination of multi-mode separations and multi-stages of induced fragmentation to gain sufficiently discriminative precision, often at the expenses of throughput and sensitivity. Given the available technology and foreseeable advances in the near future, homing in on resolving the terminal fucosylated, sialylated and/or sulfated structural units, or glycotopes, maybe a more pragmatic and ultimately more rewarding approach to gain insights into myriad biological processes mediated by these terminal coding units carried on important glycoproteins, to be decoded by a host of endogenous glycan-binding proteins and antibodies. A broad overview of recent technical advances and limitations in cellular glycomics is first provided as a backdrop to the propounded glycotope-centric approach based on advanced nanoLC-MS2/MS3 analysis of permethylated glycans. To prioritize analytical focus on the more tangible glycotopes is akin to first identifying the eye-catching and characteristic-defining flowers and fruits of the glyco-forest, to see the forest for the trees. It has the best prospects of attaining the much-needed balance in sensitivity, structural precision and analytical throughput to match advances in other omics.
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21
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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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22
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Tjondro HC, Ugonotti J, Kawahara R, Chatterjee S, Loke I, Chen S, Soltermann F, Hinneburg H, Parker BL, Venkatakrishnan V, Dieckmann R, Grant OC, Bylund J, Rodger A, Woods RJ, Karlsson-Bengtsson A, Struwe WB, Thaysen-Andersen M. Hyper-truncated Asn355- and Asn391-glycans modulate the activity of neutrophil granule myeloperoxidase. J Biol Chem 2021; 296:100144. [PMID: 33273015 PMCID: PMC7857493 DOI: 10.1074/jbc.ra120.016342] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 12/15/2022] Open
Abstract
Myeloperoxidase (MPO) plays essential roles in neutrophil-mediated immunity via the generation of reactive oxidation products. Complex carbohydrates decorate MPO at discrete sites, but their functional relevance remains elusive. To this end, we have characterised the structure-biosynthesis-activity relationship of neutrophil MPO (nMPO). Mass spectrometry demonstrated that nMPO carries both characteristic under-processed and hyper-truncated glycans. Occlusion of the Asn355/Asn391-glycosylation sites and the Asn323-/Asn483-glycans, located in the MPO dimerisation zone, was found to affect the local glycan processing, thereby providing a molecular basis of the site-specific nMPO glycosylation. Native mass spectrometry, mass photometry and glycopeptide profiling revealed significant molecular complexity of diprotomeric nMPO arising from heterogeneous glycosylation, oxidation, chlorination and polypeptide truncation variants and a previously unreported low-abundance monoprotomer. Longitudinal profiling of maturing, mature, granule-separated and pathogen-stimulated neutrophils demonstrated that nMPO is dynamically expressed during granulopoiesis, unevenly distributed across granules and degranulated upon activation. We also show that proMPO-to-MPO maturation occurs during early/mid-stage granulopoiesis. While similar global MPO glycosylation was observed across conditions, the conserved Asn355-/Asn391-sites displayed elevated glycan hyper-truncation, which correlated with higher enzyme activities of MPO in distinct granule populations. Enzymatic trimming of the Asn355-/Asn391-glycans recapitulated the activity gain and showed that nMPO carrying hyper-truncated glycans at these positions exhibits increased thermal stability, polypeptide accessibility and ceruloplasmin-mediated inhibition potential relative to native nMPO. Finally, molecular modelling revealed that hyper-truncated Asn355-glycans positioned in the MPO-ceruloplasmin interface are critical for uninterrupted inhibition. Here, through an innovative and comprehensive approach, we report novel functional roles of MPO glycans, providing new insight into neutrophil-mediated immunity.
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Affiliation(s)
- Harry C Tjondro
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - Julian Ugonotti
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - Rebeca Kawahara
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - Sayantani Chatterjee
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - Ian Loke
- Cordlife Group Limited, Singapore, Singapore
| | - Siyun Chen
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Fabian Soltermann
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Hannes Hinneburg
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - Benjamin L Parker
- Department of Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Vignesh Venkatakrishnan
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Regis Dieckmann
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Johan Bylund
- Department of Oral Microbiology and Immunology, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Alison Rodger
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, New South Wales, Australia
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Anna Karlsson-Bengtsson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Weston B Struwe
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, New South Wales, Australia.
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23
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Meyer EJ, Torpy DJ, Chernykh A, Thaysen-Andersen M, Nenke MA, Lewis JG, Rajapaksha H, Rankin W, Polyak SW. Pyrexia and acidosis act independently of neutrophil elastase reactive center loop cleavage to effect cortisol release from corticosteroid-binding globulin. Protein Sci 2020; 29:2495-2509. [PMID: 33085168 DOI: 10.1002/pro.3982] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 12/21/2022]
Abstract
Corticosteroid-binding globulin (CBG) transports cortisol and other steroids. High-affinity CBG (haCBG) undergoes proteolysis of the reactive center loop (RCL) by neutrophil elastase (NE) altering conformation to low-affinity CBG (laCBG). Elevated temperature reduces CBG:cortisol binding affinity. Surface plasmon resonance was used to determine binding profiles of 19 steroids to haCBG and laCBG at 25, 37, and 39°C mimicking pyrexia and pH 7.4 and 7.0 mimicking acidosis, pathophysiological conditions relevant to sepsis. An expected 4-8-fold reduction in affinity for cortisol, cortisone, corticosterone, 11-deoxycortisol, progesterone, 17-hydroxyprogesterone, and prednisolone occurred with NE-mediated haCBG-to-laCBG conversion. CBG:cortisol binding affinity was further reduced 3.5-fold at 39°C relative to 37°C, binding affinity was also reduced by acidosis for both haCBG and laCBG. Using a conformational antibody generated against the RCL, we confirmed RCL antibody binding was eliminated by NE cleavage, but preserved in pyrexia and acidosis. Molecular modeling studies performed at 40°C confirmed a critical role for Trp371, positioned within the steroid-binding pocket, in ligand binding. These studies demonstrated CBG binding affinity to range of steroids is ligand specific and is reduced with NE-mediated haCBG-to-laCBG transition. Reduced CBG:cortisol binding occurs with increased temperature and in acidosis. Increased flexibility of the Trp371 side chain is proposed in the thermo-coupling mechanism of cortisol release. The synergy of NE cleavage, pyrexia, and acidosis on CBG:cortisol binding may serve to enhance cortisol delivery to the interstitial space in inflammation.
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Affiliation(s)
- Emily J Meyer
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, South Australia, Australia.,Department of Endocrinology and Diabetes, The Queen Elizabeth Hospital, Adelaide, South Australia, Australia
| | - David J Torpy
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Anastasia Chernykh
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | | | - Marni A Nenke
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, South Australia, Australia.,Department of Endocrinology and Diabetes, The Queen Elizabeth Hospital, Adelaide, South Australia, Australia
| | - John G Lewis
- Steroid & Immunobiochemistry Laboratory, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Harinda Rajapaksha
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Wayne Rankin
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, South Australia, Australia.,Chemical Pathology Directorate, SA Pathology, Adelaide, South Australia, Australia
| | - Steven W Polyak
- Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
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24
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Pralow A, Cajic S, Alagesan K, Kolarich D, Rapp E. State-of-the-Art Glycomics Technologies in Glycobiotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 175:379-411. [PMID: 33112988 DOI: 10.1007/10_2020_143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Glycosylation affects the properties of biologics; thus regulatory bodies classified it as critical quality attribute and force biopharma industry to capture and control it throughout all phases, from R&D till end of product lifetime. The shift from originators to biosimilars further increases importance and extent of glycoanalysis, which thus increases the need for technology platforms enabling reliable high-throughput and in-depth glycan analysis. In this chapter, we will first summarize on established glycoanalytical methods based on liquid chromatography focusing on hydrophilic interaction chromatography, capillary electrophoresis focusing on multiplexed capillary gel electrophoresis, and mass spectrometry focusing on matrix-assisted laser desorption; we will then highlight two emerging technologies based on porous graphitized carbon liquid chromatography and on ion-mobility mass spectrometry as both are highly promising tools to deliver an additional level of information for in-depth glycan analysis; additionally we elaborate on the advantages and challenges of different glycoanalytical technologies and their complementarity; finally, we briefly review applications thereof to biopharmaceutical products. This chapter provides an overview of current state-of-the-art analytical approaches for glycan characterization of biopharmaceuticals that can be employed to capture glycoprotein heterogeneity in a biopharmaceutical context.
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Affiliation(s)
- Alexander Pralow
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Samanta Cajic
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Kathirvel Alagesan
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
- ARC Centre of Excellence in Nanoscale Biophotonics, Griffith University, Gold Coast, QLD, Australia
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
- glyXera GmbH, Magdeburg, Germany.
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25
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She YM, Tam RY, Li X, Rosu-Myles M, Sauvé S. Resolving Isomeric Structures of Native Glycans by Nanoflow Porous Graphitized Carbon Chromatography-Mass Spectrometry. Anal Chem 2020; 92:14038-14046. [PMID: 32960038 DOI: 10.1021/acs.analchem.0c02951] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Characterization of the structural diversity of glycans by liquid chromatography-tandem mass spectrometry (LC-MS/MS) remains an analytical challenge in large-scale glycomics applications because of the presence of heterogeneous composition, ubiquitous isomers, lability of post-translational glycan modifications, and complexity of data interpretation. High-resolution separation of glycan isomers differentiating from positional, linkage, branching, and anomeric structures is often a prerequisite to ensure the comprehensive glycan identification. Here, we developed a straightforward method using self-packed capillary porous graphitic carbon (PGC) columns for nanoflow LC-MS/MS analyses of native glycans released from glycoproteins. The technique enables highly resolved chromatographic separation of over 20 high-mannose glycan isomers in ribonuclease B and a diverse range of hybrid and complex-type sialoglycoforms of fetuin. The distinct structures of anomeric glycans and linkage sialoglycan isomers, α2,3 and α2,6, were identified by the characteristic MS/MS fragment ions. A glycan sequencing strategy utilizing diagnostic ions and complementary fragments specific to branching residues was established to simplify the MS/MS data interpretation of closely related isomeric structures. To promote the PGC-LC-MS/MS-based method for glycome-wide applications, we extended analyses to native sulfoglycans from the egg-propagated and cell culture-derived influenza vaccines and demonstrate the high-resolution separation and structural characterization of underivatized neutral and anionic glycoforms including oligomannosidic glycan anomers, sialoglycan linkage isomers, and regioisomers of afucosylated and fucosylated sulfoglycans containing sulfated-6-GlcNAc and sulfated-4-GalNAc residues.
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Affiliation(s)
- Yi-Min She
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Roger Y Tam
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Xuguang Li
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Michael Rosu-Myles
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Simon Sauvé
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
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26
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Sanders KL, Edwards JL. Nano-liquid chromatography-mass spectrometry and recent applications in omics investigations. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4404-4417. [PMID: 32901622 PMCID: PMC7530103 DOI: 10.1039/d0ay01194k] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Liquid chromatography coupled to mass spectrometry (LC-MS) is one of the most powerful tools in identifying and quantitating molecular species. Decreasing column diameter from the millimeter to micrometer scale is now a well-developed method which allows for sample limited analysis. Specific fabrication of capillary columns is required for proper implementation and optimization when working in the nanoflow regime. Coupling the capillary column to the mass spectrometer for electrospray ionization (ESI) requires reduction of the subsequent emitter tip. Reduction of column diameter to capillary scale can produce improved chromatographic efficiency and the reduction of emitter tip size increased sensitivity of the electrospray process. This improved sensitivity and ionization efficiency is valuable in analysis of precious biological samples where analytes vary in size, ion affinity, and concentration. In this review we will discuss common approaches and challenges in implementing nLC-MS methods and how the advantages can be leveraged to investigate a wide range of biomolecules.
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27
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Lan R, Xin M, Hao Z, You S, Xu Y, Wu J, Dang L, Zhang X, Sun S. Biological Functions and Large-Scale Profiling of Protein Glycosylation in Human Semen. J Proteome Res 2020; 19:3877-3889. [DOI: 10.1021/acs.jproteome.9b00795] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Rongxia Lan
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
| | - Miaomiao Xin
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
- Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Vodnany 38925, Czech Republic
| | - Zhifang Hao
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
| | - Shanshan You
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
| | - Yintai Xu
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
| | - Jingyu Wu
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
| | - Liuyi Dang
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
| | - Xinwen Zhang
- The Medical Genetics Centre, Xi 'an People's Hospital (Xi 'an Fourth Hospital), Xi’an Obstetrics and Gynecology Hospital, Xi’an, Shaanxi Province 710004, P. R. China
| | - Shisheng Sun
- College of Life Science, Northwest University, Xi’an, Shaanxi Province 710069, P. R. China
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28
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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.
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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.
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29
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Venkatakrishnan V, Dieckmann R, Loke I, Tjondro HC, Chatterjee S, Bylund J, Thaysen-Andersen M, Karlsson NG, Karlsson-Bengtsson A. Glycan analysis of human neutrophil granules implicates a maturation-dependent glycosylation machinery. J Biol Chem 2020; 295:12648-12660. [PMID: 32665399 DOI: 10.1074/jbc.ra120.014011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/15/2020] [Indexed: 12/12/2022] Open
Abstract
Protein glycosylation is essential to trafficking and immune functions of human neutrophils. During granulopoiesis in the bone marrow, distinct neutrophil granules are successively formed. Distinct receptors and effector proteins, many of which are glycosylated, are targeted to each type of granule according to their time of expression, a process called "targeting by timing." Therefore, these granules are time capsules reflecting different times of maturation that can be used to understand the glycosylation process during granulopoiesis. Herein, neutrophil subcellular granules were fractionated by Percoll density gradient centrifugation, and N- and O-glycans present in each compartment were analyzed by LC-MS. We found abundant paucimannosidic N-glycans and lack of O-glycans in the early-formed azurophil granules, whereas the later-formed specific and gelatinase granules and secretory vesicles contained complex N- and O-glycans with remarkably elongated N-acetyllactosamine repeats with Lewis epitopes. Immunoblotting and histochemical analysis confirmed the expression of Lewis X and sialyl-Lewis X in the intracellular granules and on the cell surface, respectively. Many glycans identified are unique to neutrophils, and their complexity increased progressively from azurophil granules to specific granules and then to gelatinase granules, suggesting temporal changes in the glycosylation machinery indicative of "glycosylation by timing" during granulopoiesis. In summary, this comprehensive neutrophil granule glycome map, the first of its kind, highlights novel granule-specific glycosylation features and is a crucial first step toward a better understanding of the mechanisms regulating protein glycosylation during neutrophil granulopoiesis and a more detailed understanding of neutrophil biology and function.
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Affiliation(s)
- Vignesh Venkatakrishnan
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Régis Dieckmann
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ian Loke
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Cordlife Group Limited, Singapore
| | - Harry C Tjondro
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | | | - Johan Bylund
- Department of Oral Microbiology and Immunology, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| | - Niclas G Karlsson
- Department of Medical Chemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Karlsson-Bengtsson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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30
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Sanda M, Benicky J, Goldman R. Low Collision Energy Fragmentation in Structure-Specific Glycoproteomics Analysis. Anal Chem 2020; 92:8262-8267. [PMID: 32441515 DOI: 10.1021/acs.analchem.0c00519] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glycosylation is a major post-translational modification of proteins that regulates many biological processes including protein folding, structure stability, receptor activation, and immune responses. The glycans attached to proteins represent an important determinant of the protein interaction-specificity and maintain the 3D structure of proteins. Mass spectrometry (MS) is one of the most efficient tools used in the current studies of glycoproteins and structure of their glycoforms. Collision energy (CE) is a crucial instrument parameter that can be exploited to improve structural resolution because different linkages of glycan units show different stabilities under CID/HCD fragmentation. Here we report the utility of CE modulation for qualitative and quantitative analysis of site- and structure-specific glycoforms of proteins. Using CE modulation, we were able to break selectively specific glycan linkages on intact glycopeptides and get, to some degree, structure-specific mass spectrometric signals. Structure- and CE-specific oxonium ions provide sufficient information for the resolution of outer arm structure motifs with recognized biological functions. The complementary Y-ions, generated under optimized low CE (soft) conditions, provide additional structural information including features specific to the chitobiose core. This methodology of multiple CE fragmentation without merging spectral information can significantly improve confidence of glycopeptide identification and structural resolution by providing additional information to the established glycopeptide-search algorithms and tools.
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Affiliation(s)
- Miloslav Sanda
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, United States.,Clinical and Translational Glycoscience Research Center, Georgetown University, Washington, DC 20057, United States
| | - Julius Benicky
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, United States.,Clinical and Translational Glycoscience Research Center, Georgetown University, Washington, DC 20057, United States
| | - Radoslav Goldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, United States.,Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, United States.,Clinical and Translational Glycoscience Research Center, Georgetown University, Washington, DC 20057, United States
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31
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Zhang T, Madunić K, Holst S, Zhang J, Jin C, Ten Dijke P, Karlsson NG, Stavenhagen K, Wuhrer M. Development of a 96-well plate sample preparation method for integrated N- and O-glycomics using porous graphitized carbon liquid chromatography-mass spectrometry. Mol Omics 2020; 16:355-363. [PMID: 32281997 DOI: 10.1039/c9mo00180h] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Changes in glycosylation signatures of cells have been associated with pathological processes in cancer as well as infectious and autoimmune diseases. The current protocols for comprehensive analysis of N-glycomics and O-glycomics derived from cells and tissues often require a large amount of biological material. They also only allow the processing of very limited numbers of samples at a time. Here we established a workflow for sequential release of N-glycans and O-glycans based on PVDF membrane immobilization in 96-well format from 5 × 105 cells. Released glycans are reduced, desalted, purified, and reconstituted, all in 96-well format plates, without additional staining or derivatization. Glycans are then analyzed with porous graphitized carbon nano-liquid chromatography coupled to tandem mass spectrometry using negative-mode electrospray ionization, enabling the chromatographic resolution and structural elucidation of glycan species including many compositional isomers. The approach was demonstrated using glycoprotein standards and further applied to analyze the glycosylation of the murine mammary gland NMuMG cell line. The developed protocol allows the analysis of N- and O-glycans from relatively large numbers of samples in a less time consuming way with high repeatability. Inter- and intraday repeatability of the fetuin N-glycan analysis showed two median intraday coefficients of variations (CVs) of 7.6% and 8.0%, and a median interday CV of 9.8%. Median CVs of 7.9% and 8.7% for the main peaks of N- and O-glycans released from the NMuMG cell line indicate a very good repeatability. The method is applicable to purified glycoproteins as well as to biofluids and cell- or tissue-based samples.
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Affiliation(s)
- Tao Zhang
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
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32
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Joe CCD, Chatterjee S, Lovrecz G, Adams TE, Thaysen-Andersen M, Walsh R, Locarnini SA, Smooker P, Netter HJ. Glycoengineered hepatitis B virus-like particles with enhanced immunogenicity. Vaccine 2020; 38:3892-3901. [PMID: 32284273 DOI: 10.1016/j.vaccine.2020.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 02/25/2020] [Accepted: 03/02/2020] [Indexed: 01/04/2023]
Abstract
Virus-like particles (VLP) represent biological platforms for the development of novel products such as vaccines and delivery platforms for foreign antigenic sequences. VLPs composed of the small surface antigen (HBsAgS) derived from the hepatitis B virus (HBV) are the immunogenic components of a licensed, preventative vaccine, which contains aluminum hydroxide as adjuvant. Herein, we report that glycoengineering of N-glycosylated HBsAgS to generate hyper-glycosylated VLPs display an enhanced immunogenicity relative to the wild type (WT) HBsAgS VLPs when expressed in FreeStyle HEK 293F cells. Comparative mass spectrometry-based N-glycan profiling, gel electrophoresis, and immunoassays demonstrated that WT and hyper-glycosylated HBsAgS VLPs contain the same type and distribution of N-glycan structures, but the latter shows a higher glycan abundance per protein mass. The antigenic integrity of the modified VLPs was also shown to be retained. To assess whether hyper-glycosylated VLPs induce an enhanced immune response in the presence of the adjuvant aluminum hydroxide, the anti-HBV surface antigen (anti-HBsAgS) antibody response was monitored in BALB/c mice, subcutaneously injected with different VLP derivatives. In the absence and presence of adjuvant, hyper-glycosylated VLPs showed an enhanced immunogenicity compared to WT VLPs. The ability of hyper-glycosylated VLPs to promote potent anti-HBsAgS immune responses compared to VLPs with a native N-glycan level as well as non-glycosylated, yeast-derived HBsAgS VLPs opens exciting avenues for generating more efficacious VLP-based vaccines against hepatitis B and improved HBsAgS VLP carrier platforms using glycoengineering.
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Affiliation(s)
- Carina C D Joe
- Royal Melbourne Institute of Technology (RMIT) University, School of Science, Melbourne, Victoria 3001, Australia; Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria 3169, Australia
| | - Sayantani Chatterjee
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - George Lovrecz
- Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria 3169, Australia
| | - Timothy E Adams
- Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria 3169, Australia
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Renae Walsh
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Melbourne Health, The Peter Doherty Institute, Melbourne, Victoria 3000, Australia
| | - Stephen A Locarnini
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Melbourne Health, The Peter Doherty Institute, Melbourne, Victoria 3000, Australia
| | - Peter Smooker
- Royal Melbourne Institute of Technology (RMIT) University, School of Science, Melbourne, Victoria 3001, Australia
| | - Hans J Netter
- Royal Melbourne Institute of Technology (RMIT) University, School of Science, Melbourne, Victoria 3001, Australia; Victorian Infectious Diseases Reference Laboratory (VIDRL), Melbourne Health, The Peter Doherty Institute, Melbourne, Victoria 3000, Australia.
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Hinneburg H, Pedersen JL, Bokil NJ, Pralow A, Schirmeister F, Kawahara R, Rapp E, Saunders BM, Thaysen-Andersen M. High-resolution longitudinal N- and O-glycoprofiling of human monocyte-to-macrophage transition. Glycobiology 2020; 30:679-694. [DOI: 10.1093/glycob/cwaa020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/18/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Abstract
Protein glycosylation impacts the development and function of innate immune cells. The glycophenotypes and the glycan remodelling associated with the maturation of macrophages from monocytic precursor populations remain incompletely described. Herein, label-free porous graphitised carbon–liquid chromatography–tandem mass spectrometry (PGC-LC-MS/MS) was employed to profile with high resolution the N- and O-glycome associated with human monocyte-to-macrophage transition. Primary blood-derived CD14+ monocytes were differentiated ex vivo in the absence of strong anti- and proinflammatory stimuli using a conventional 7-day granulocyte-macrophage colony-stimulating factor differentiation protocol with longitudinal sampling. Morphology and protein expression monitored by light microscopy and proteomics validated the maturation process. Glycomics demonstrated that monocytes and macrophages display similar N-glycome profiles, comprising predominantly paucimannosidic (Man1-3GlcNAc2Fuc0–1, 22.1–30.8%), oligomannosidic (Man5-9GlcNAc2, 29.8–35.7%) and α2,3/6-sialylated complex-type N-glycans with variable core fucosylation (27.6–39.1%). Glycopeptide analysis validated conjugation of these glycans to human proteins, while quantitative proteomics monitored the glycoenzyme expression levels during macrophage differentiation. Significant interperson glycome variations were observed suggesting a considerable physiology-dependent or heritable heterogeneity of CD14+ monocytes. Only few N-glycome changes correlated with the monocyte-to-macrophage transition across donors including decreased core fucosylation and reduced expression of mannose-terminating (paucimannosidic-/oligomannosidic-type) N-glycans in macrophages, while lectin flow cytometry indicated that more dramatic cell surface glycan remodelling occurs during maturation. The less heterogeneous core 1-rich O-glycome showed a minor decrease in core 2-type O-glycosylation but otherwise remained unchanged with macrophage maturation. This high-resolution glycome map underpinning normal monocyte-to-macrophage transition, the most detailed to date, aids our understanding of the molecular makeup pertaining to two vital innate immune cell types and forms an important reference for future glycoimmunological studies.
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Affiliation(s)
- Hannes Hinneburg
- Department of Molecular Sciences, Macquarie University, NSW 2109 Sydney, Australia
- Biomolecular Discovery Research Centre, Macquarie University, NSW 2109 Sydney, Australia
| | - Jessica L Pedersen
- School of Life Sciences, Faculty of Science, University of Technology, NSW 2007 Sydney, Australia
| | - Nilesh J Bokil
- School of Life Sciences, Faculty of Science, University of Technology, NSW 2007 Sydney, Australia
| | - Alexander Pralow
- Max Planck Institute for Dynamics of Complex Technical Systems (Bioprocess Engineering), 39106 Magdeburg, Germany
| | | | - Rebeca Kawahara
- Department of Molecular Sciences, Macquarie University, NSW 2109 Sydney, Australia
- Biomolecular Discovery Research Centre, Macquarie University, NSW 2109 Sydney, Australia
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems (Bioprocess Engineering), 39106 Magdeburg, Germany
- GlyXera GmbH, 39120 Magdeburg, Germany
| | - Bernadette M Saunders
- School of Life Sciences, Faculty of Science, University of Technology, NSW 2007 Sydney, Australia
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, NSW 2109 Sydney, Australia
- Biomolecular Discovery Research Centre, Macquarie University, NSW 2109 Sydney, Australia
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Ashwood C, Waas M, Weerasekera R, Gundry RL. Reference glycan structure libraries of primary human cardiomyocytes and pluripotent stem cell-derived cardiomyocytes reveal cell-type and culture stage-specific glycan phenotypes. J Mol Cell Cardiol 2020; 139:33-46. [PMID: 31972267 DOI: 10.1016/j.yjmcc.2019.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/23/2019] [Accepted: 12/27/2019] [Indexed: 12/16/2022]
Abstract
Cell surface glycoproteins play critical roles in maintaining cardiac structure and function in health and disease and the glycan-moiety attached to the protein is critical for proper protein folding, stability and signaling [1]. However, despite mounting evidence that glycan structures are key modulators of heart function and must be considered when developing cardiac biomarkers, we currently do not have a comprehensive view of the glycans present in the normal human heart. In the current study, we used porous graphitized carbon liquid chromatography interfaced with mass spectrometry (PGC-LC-MS) to generate glycan structure libraries for primary human heart tissue homogenate, cardiomyocytes (CM) enriched from human heart tissue, and human induced pluripotent stem cell derived CM (hiPSC-CM). Altogether, we established the first reference structure libraries of the cardiac glycome containing 265 N- and O-glycans. Comparing the N-glycome of CM enriched from primary heart tissue to that of heart tissue homogenate, the same pool of N-glycan structures was detected in each sample type but the relative signal of 21 structures significantly differed between samples, with the high mannose class increased in enriched CM. Moreover, by comparing primary CM to hiPSC-CM collected during 20-100 days of differentiation, dynamic changes in the glycan profile throughout in vitro differentiation were observed and differences between primary and hiPSC-CM were revealed. Namely, >30% of the N-glycome significantly changed across these time-points of differentiation and only 23% of the N-glycan structures were shared between hiPSC-CM and primary CM. These observations are an important complement to current genomic, transcriptomic, and proteomic profiling and reveal new considerations for the use and interpretation of hiPSC-CM models for studies of human development, disease, and drug testing. Finally, these data are expected to support future regenerative medicine efforts by informing targets for evaluating the immunogenic potential of hiPSC-CM and harnessing differences between immature, proliferative hiPSC-CM and adult primary CM.
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Affiliation(s)
- Christopher Ashwood
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ranjuna Weerasekera
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Center for Biomedical Mass Spectrometry Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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Wei J, Tang Y, Bai Y, Zaia J, Costello CE, Hong P, Lin C. Toward Automatic and Comprehensive Glycan Characterization by Online PGC-LC-EED MS/MS. Anal Chem 2020; 92:782-791. [PMID: 31829560 PMCID: PMC7082718 DOI: 10.1021/acs.analchem.9b03183] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Despite the recent advances in mass spectrometry (MS)-based methods for glycan structural analysis, characterization of glycomes remains a significant analytical challenge, in part due to the widespread presence of isomeric structures and the need to define the many structural variables for each glycan. Interpretation of the complex tandem mass spectra of glycans is often laborious and requires substantial expertise. Broad adoption of MS methods for glycomics, within and outside the glycoscience community, has been hindered by the shortage of bioinformatics tools for rapid and accurate glycan sequencing. Here, we developed an online porous graphitic carbon liquid chromatography (PGC-LC)-electronic excitation dissociation (EED) MS/MS method that takes advantage of the superior isomer resolving power of PGC and the structural details provided by EED MS/MS for characterization of glycan mixtures. We also made improvements to GlycoDeNovo, our de novo glycan sequencing algorithm, so that it can automatically and accurately identify glycan topologies from EED tandem mass spectra acquired online. The majority of linkages can also be determined de novo, although in some cases, biological insight may be needed to fully define the glycan structure. Application of this method to the analysis of N-glycans released from ribonuclease B not only revealed the presence of 18 high-mannose structures, including new isomers not previously reported, but also provided relative quantification for each isomeric structure. With fully automated data acquisition and topology analysis, the approach presented here holds great potential for automated and comprehensive glycan characterization.
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Affiliation(s)
- Juan Wei
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Yang Tang
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Yu Bai
- Beijing National Laboratory for Molecular Sciences, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Catherine E. Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Pengyu Hong
- Department of Computer Science, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
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Chatterjee S, Lee LY, Kawahara R, Abrahams JL, Adamczyk B, Anugraham M, Ashwood C, Sumer‐Bayraktar Z, Briggs MT, Chik JHL, Everest‐Dass A, Förster S, Hinneburg H, Leite KRM, Loke I, Möginger U, Moh ESX, Nakano M, Recuero S, Sethi MK, Srougi M, Stavenhagen K, Venkatakrishnan V, Wongtrakul‐Kish K, Diestel S, Hoffmann P, Karlsson NG, Kolarich D, Molloy MP, Muders MH, Oehler MK, Packer NH, Palmisano G, Thaysen‐Andersen M. Protein Paucimannosylation Is an EnrichedN‐Glycosylation Signature of Human Cancers. Proteomics 2019; 19:e1900010. [DOI: 10.1002/pmic.201900010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/25/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Sayantani Chatterjee
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
| | - Ling Y. Lee
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- ISGlobal, Barcelona Centre for International Health Research (CRESIB) Hospital Clínic–Universitat de Barcelona Barcelona 08193 Spain
| | - Rebeca Kawahara
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Department of Parasitology, Institute of Biomedical Sciences University of São Paulo São Paulo 01000 Brazil
| | - Jodie L. Abrahams
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Institute for Glycomics, Griffith University Gold Coast 4222 Australia
| | - Barbara Adamczyk
- Department of Medical Biochemistry and Cell Biology Institute of Biomedicine, Sahlgrenska Academy University of Gothenburg Gothenburg SE 405 30 Sweden
| | - Merrina Anugraham
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Institute of Biological Chemistry Academia Sinica Taipei 11529 Taiwan
| | - Christopher Ashwood
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Department of Biochemistry Medical College of Wisconsin Milwaukee WI 53226 USA
| | - Zeynep Sumer‐Bayraktar
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- School of Life and Environmental Sciences Charles Perkins Centre (CPC), The University of Sydney Sydney 2006 Australia
| | - Matthew T. Briggs
- Future Industries Institute Mawson Lakes Campus, University of South Australia Adelaide 5005 Australia
| | - Jenny H. L. Chik
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- International Collaboration on Repair Discoveries Vancouver Coastal Health Research Institute and Department of Pathology and Laboratory Medicine The University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Arun Everest‐Dass
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Institute for Glycomics, Griffith University Gold Coast 4222 Australia
| | - Sarah Förster
- Rudolf‐Becker‐Laboratory Institute of Pathology University Hospital Bonn Bonn 53127 Germany
| | - Hannes Hinneburg
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
| | - Katia R. M. Leite
- Laboratório de Investigação Médica da Disciplina de Urologia (LIM55) Faculdade de Medicina da FMUSP Universidade de Sao Paulo São Paulo 01000 Brazil
| | - Ian Loke
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Department of Biological Sciences National University of Singapore Singapore 119077 Singapore
| | - Uwe Möginger
- Department for Biochemistry and Molecular Biology University of Southern Denmark Odense 5230 Denmark
| | - Edward S. X. Moh
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- ARC Centre for Nanoscale Biophotonics Macquarie University Sydney 2109 Australia
| | - Miyako Nakano
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Graduate School of Advanced Sciences of Matter Hiroshima University Hiroshima 739‐8527 Japan
| | - Saulo Recuero
- Laboratório de Investigação Médica da Disciplina de Urologia (LIM55) Faculdade de Medicina da FMUSP Universidade de Sao Paulo São Paulo 01000 Brazil
| | - Manveen K. Sethi
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Center for Biomedical Mass Spectrometry Department of Biochemistry Boston University School of Medicine Boston University Boston MA 02215 USA
| | - Miguel Srougi
- Laboratório de Investigação Médica da Disciplina de Urologia (LIM55) Faculdade de Medicina da FMUSP Universidade de Sao Paulo São Paulo 01000 Brazil
| | - Kathrin Stavenhagen
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Beth Israel Deaconess Medical Center Department of Surgery and Harvard Medical School Center for Glycoscience Harvard Medical School Boston MA 02215 USA
| | - Vignesh Venkatakrishnan
- Department of Rheumatology and Inflammation Research Institute of Medicine, Sahlgrenska Academy University of Gothenburg Gothenburg SE 405 30 Sweden
| | - Katherine Wongtrakul‐Kish
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Bioprocessing Technology Institute A*STAR Singapore 13862 Singapore
| | - Simone Diestel
- Institute of Nutrition and Food Sciences University of Bonn Bonn 53127 Germany
| | - Peter Hoffmann
- Future Industries Institute Mawson Lakes Campus, University of South Australia Adelaide 5005 Australia
| | - Niclas G. Karlsson
- Department of Medical Biochemistry and Cell Biology Institute of Biomedicine, Sahlgrenska Academy University of Gothenburg Gothenburg SE 405 30 Sweden
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University Gold Coast 4222 Australia
| | - Mark P. Molloy
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Faculty of Medicine and Health Sydney School of Medicine Royal North Shore Hospital Sydney 2065 Australia
| | - Michael H. Muders
- Rudolf‐Becker‐Laboratory Institute of Pathology University Hospital Bonn Bonn 53127 Germany
| | - Martin K. Oehler
- Department of Gynaecological Oncology Royal Adelaide Hospital Adelaide 5000 Australia
| | - Nicolle H. Packer
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
- Institute for Glycomics, Griffith University Gold Coast 4222 Australia
- ARC Centre for Nanoscale Biophotonics Macquarie University Sydney 2109 Australia
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences University of São Paulo São Paulo 01000 Brazil
| | - Morten Thaysen‐Andersen
- Department of Molecular Sciences and Biomolecular Discovery and Design Research Centre (BDDRC) Macquarie University Sydney 2109 Australia
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Tjondro HC, Loke I, Chatterjee S, Thaysen-Andersen M. Human protein paucimannosylation: cues from the eukaryotic kingdoms. Biol Rev Camb Philos Soc 2019; 94:2068-2100. [PMID: 31410980 DOI: 10.1111/brv.12548] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 12/11/2022]
Abstract
Paucimannosidic proteins (PMPs) are bioactive glycoproteins carrying truncated α- or β-mannosyl-terminating asparagine (N)-linked glycans widely reported across the eukaryotic domain. Our understanding of human PMPs remains limited, despite findings documenting their existence and association with human disease glycobiology. This review comprehensively surveys the structures, biosynthetic routes and functions of PMPs across the eukaryotic kingdoms with the aim of synthesising an improved understanding on the role of protein paucimannosylation in human health and diseases. Convincing biochemical, glycoanalytical and biological data detail a vast structural heterogeneity and fascinating tissue- and subcellular-specific expression of PMPs within invertebrates and plants, often comprising multi-α1,3/6-fucosylation and β1,2-xylosylation amongst other glycan modifications and non-glycan substitutions e.g. O-methylation. Vertebrates and protists express less-heterogeneous PMPs typically only comprising variable core fucosylation of bi- and trimannosylchitobiose core glycans. In particular, the Manα1,6Manβ1,4GlcNAc(α1,6Fuc)β1,4GlcNAcβAsn glycan (M2F) decorates various human neutrophil proteins reportedly displaying bioactivity and structural integrity demonstrating that they are not degradation products. Less-truncated paucimannosidic glycans (e.g. M3F) are characteristic glycosylation features of proteins expressed by human cancer and stem cells. Concertedly, these observations suggest the involvement of human PMPs in processes related to innate immunity, tumorigenesis and cellular differentiation. The absence of human PMPs in diverse bodily fluids studied under many (patho)physiological conditions suggests extravascular residence and points to localised functions of PMPs in peripheral tissues. Absence of PMPs in Fungi indicates that paucimannosylation is common, but not universally conserved, in eukaryotes. Relative to human PMPs, the expression of PMPs in plants, invertebrates and protists is more tissue-wide and constitutive yet, similar to their human counterparts, PMP expression remains regulated by the physiology of the producing organism and PMPs evidently serve essential functions in development, cell-cell communication and host-pathogen/symbiont interactions. In most PMP-producing organisms, including humans, the N-acetyl-β-hexosaminidase isoenzymes and linkage-specific α-mannosidases are glycoside hydrolases critical for generating PMPs via N-acetylglucosaminyltransferase I (GnT-I)-dependent and GnT-I-independent truncation pathways. However, the identity and structure of many species-specific PMPs in eukaryotes, their biosynthetic routes, strong tissue- and development-specific expression, and diverse functions are still elusive. Deep exploration of these PMP features involving, for example, the characterisation of endogenous PMP-recognising lectins across a variety of healthy and N-acetyl-β-hexosaminidase-deficient human tissue types and identification of microbial adhesins reactive to human PMPs, are amongst the many tasks required for enhanced insight into the glycobiology of human PMPs. In conclusion, the literature supports the notion that PMPs are significant, yet still heavily under-studied biomolecules in human glycobiology that serve essential functions and create structural heterogeneity not dissimilar to other human N-glycoprotein types. Human PMPs should therefore be recognised as bioactive glycoproteins that are distinctly different from the canonical N-glycoprotein classes and which warrant a more dedicated focus in glycobiological research.
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Affiliation(s)
- Harry C Tjondro
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Ian Loke
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia.,Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Sayantani Chatterjee
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Morten Thaysen-Andersen
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
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