1
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Sanni A, Hakim MA, Goli M, Adeniyi M, Talih F, Lanuzza B, Kobeissy F, Plazzi G, Moresco M, Mondello S, Ferri R, Mechref Y. Serum N-Glycan Profiling of Patients with Narcolepsy Type 1 Using LC-MS/MS. ACS OMEGA 2024; 9:32628-32638. [PMID: 39100283 PMCID: PMC11292663 DOI: 10.1021/acsomega.4c01593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/17/2024] [Accepted: 05/27/2024] [Indexed: 08/06/2024]
Abstract
The neurological condition known as narcolepsy type 1 (NT1) is an uncommon condition marked by extreme daytime sleepiness, cataplexy, sleep paralysis, hallucinations, disrupted nocturnal sleep, and low or undetectable levels of orexin in the CSF fluid. NT1 has been hypothesized to be an immunological disorder; its treatment is currently only symptomatic, and misdiagnosis is not uncommon. This study compares the N-glycome of NT1 patients with healthy controls in search of potential glycan biomarkers using LC-MS/MS. A total of 121 candidate N-glycans were identified, 55 of which were isomeric N-glycan structures and 65 were not. Seventeen N-glycan biomarker candidates showed significant differences between the NT1 and control cohorts. All of the candidate glycan biomarkers were isomeric except HexNAc6Hex7Fuc0NeuAc1 (6701) and HexNAc6Hex7Fuc1NeuAc2 (6712). Therefore, with isomeric and nonisomeric structures, a total of 20 candidate N-glycan biomarkers are reported in this study, and interestingly, all are either sialylated or sialylated-fucosylated and upregulated in NT1 relative to the control. The distribution levels of all the identified N-glycans show that the sialylated glycan type is the most abundant in NT1 and is majorly disialylated, although the trisialylated subtype is three-fold higher in NT1 compared to the healthy control. The first isomers of HexNAc5Hex6Fuc0NeuAc3 (5603), HexNAc6Hex7Fuc0NeuAc2 (6702), and HexNAc6Hex7Fuc1NeuAc4 (6714) expressed a high level of fold changes (FC) of 1.62, 2.19, and 2.98, respectively. These results suggest a different N-glycome profile of NT1 and a relationship between sialylated glycan isomers in NT1 disease development or progression. The revelation of N-glycan expression alterations in this study may improve NT1 diagnostic methods, understanding of NT1 pathology, and the development of new targeted therapeutics.
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Affiliation(s)
- Akeem Sanni
- Chemistry
and Biochemistry Department, Texas Tech
University, Lubbock, Texas 79409, United States
| | - Md Abdul Hakim
- Chemistry
and Biochemistry Department, Texas Tech
University, Lubbock, Texas 79409, United States
| | - Mona Goli
- Chemistry
and Biochemistry Department, Texas Tech
University, Lubbock, Texas 79409, United States
| | - Moyinoluwa Adeniyi
- Chemistry
and Biochemistry Department, Texas Tech
University, Lubbock, Texas 79409, United States
| | - Farid Talih
- Department
of Psychiatry, Faculty of Medicine, American
University of Beirut, Beirut 1107 2020, Lebanon
| | - Bartolo Lanuzza
- Sleep
Research Centre, Department of Neurology IC, Oasi Research Institute-IRCCS, Troina 94018, Italy
| | - Firas Kobeissy
- Department
of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
- Department
of Neurobiology, Center for Neurotrauma, Multiomics and Biomarkers
(CNMB), Neuroscience Institute, Morehouse
School of Medicine (MSM), Atlanta, Georgia 30310-1458, United States
| | - Giuseppe Plazzi
- IRCCS, Istituto
delle Scienze Neurologiche di Bologna, Bologna 40138, Italy
- Department
of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena 41121, Italy
| | - Monica Moresco
- IRCCS, Istituto
delle Scienze Neurologiche di Bologna, Bologna 40138, Italy
| | - Stefania Mondello
- Department
of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina 98122, Italy
| | - Raffaele Ferri
- Sleep
Research Centre, Department of Neurology IC, Oasi Research Institute-IRCCS, Troina 94018, Italy
| | - Yehia Mechref
- Chemistry
and Biochemistry Department, Texas Tech
University, Lubbock, Texas 79409, United States
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2
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Greenwood M, Murciano-Martínez P, Berrington J, Flitsch SL, Austin S, Stewart C. Characterising glycosaminoglycans in human breastmilk and their potential role in infant health. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:221-234. [PMID: 38975022 PMCID: PMC11224681 DOI: 10.15698/mic2024.07.827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 07/09/2024]
Abstract
Human breastmilk is composed of many well researched bioactive components crucial for infant nutrition and priming of the neonatal microbiome and immune system. Understanding these components gives us crucial insight to the health and wellbeing of infants. Research surrounding glycosaminoglycans (GAGs) previously focused on those produced endogenously; however, recent efforts have shifted to understanding GAGs in human breastmilk. The structural complexity of GAGs makes detection and analysis complicated therefore, research is time consuming and limited to highly specialised teams experienced in carbohydrate analysis. In breastmilk, GAGs are present in varying quantities in four forms; chondroitin sulphate, heparin/heparan sulphate, dermatan sulphate and hyaluronic acid, and are hypothesised to behave similar to other bioactive components with suspected roles in pathogen defense and proliferation of beneficial gut bacteria. Chondroitin sulphate and heparin, being the most abundant, are expected to have the most impact on infant health. Their decreasing concentration over lactation further indicates their role and potential importance during early life.
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Affiliation(s)
- Melissa Greenwood
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastle Upon Tyne, NE2 4HHUnited Kingdom
- Analytical Sciences Department, Société des Produits Nestlé, Nestlé Research, Vers-Chez-Les-BlancLausanneSwitzerland
| | - Patricia Murciano-Martínez
- Department of Nutrient Technology, Société des Produits Nestlé, Nestlé Research, Vers-Chez-Les-BlancLausanneSwitzerland
| | - Janet Berrington
- Newcastle Neonatal Service, Royal Victoria Infirmary, Newcastle Upon TyneNE1 4LPUnited Kingdom
| | - Sabine L Flitsch
- School of Chemistry, Faculty of Medical Sciences, The University of Manchester, Manchester Institute of BiotechnologyM1 7DNUnited Kingdom
| | - Sean Austin
- Analytical Sciences Department, Société des Produits Nestlé, Nestlé Research, Vers-Chez-Les-BlancLausanneSwitzerland
| | - Christopher Stewart
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastle Upon Tyne, NE2 4HHUnited Kingdom
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3
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Kontodimas V, Yaman M, Greis K, Lettow M, Pagel K, Marianski M. Reinvestigation of the internal glycan rearrangement of Lewis a and blood group type H1 epitopes. Phys Chem Chem Phys 2024; 26:14160-14170. [PMID: 38712976 PMCID: PMC11147448 DOI: 10.1039/d3cp04491b] [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] [Indexed: 05/08/2024]
Abstract
Protonated ions of fucose-containing oligosaccharides are prone to undergo internal glycan rearrangement which results in chimeric fragments that obfuscate mass-spectrometric analysis. Lack of accessible tools that would facilitate systematic analysis of glycans in the gas phase limits our understanding of this phenomenon. In this work, we use density functional theory modeling to interpret cryogenic IR spectra of Lewis a and blood group type H1 trisaccharides and to establish whether these trisaccharides undergo the rearrangement during gas-phase analysis. Structurally unconstrained search reveals that none of the parent ions constitute a thermodynamic global minimum. In contrast, predicted collision cross sections and anharmonic IR spectra provide a good match to available experimental data which allowed us to conclude that fucose migration does not occur in these antigens. By comparing the predicted structures with those obtained for Lewis x and blood group type H2 epitopes, we demonstrate that the availability of the mobile proton and a large difference in the relative stability of the parent ions and rearrangement products constitute the prerequisites for the rearrangement reaction.
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Affiliation(s)
- Vasilis Kontodimas
- Department of Chemistry, Hunter College, The City University of New York, New York, NY 10065, USA.
| | - Murat Yaman
- Department of Chemistry, Hunter College, The City University of New York, New York, NY 10065, USA.
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Kim Greis
- Fritz-Haber-Intitut der Max Planck Gesellschaft, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Maike Lettow
- Fritz-Haber-Intitut der Max Planck Gesellschaft, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Kevin Pagel
- Fritz-Haber-Intitut der Max Planck Gesellschaft, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Mateusz Marianski
- Department of Chemistry, Hunter College, The City University of New York, New York, NY 10065, USA.
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, The City University of New York, New York, NY 10016, USA
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4
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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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5
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Atashi M, Reyes CDG, Sandilya V, Purba W, Ahmadi P, Hakim MA, Kobeissy F, Plazzi G, Moresco M, Lanuzza B, Ferri R, Mechref Y. LC-MS/MS Quantitation of HILIC-Enriched N-glycopeptides Derived from Low-Abundance Serum Glycoproteins in Patients with Narcolepsy Type 1. Biomolecules 2023; 13:1589. [PMID: 38002271 PMCID: PMC10669497 DOI: 10.3390/biom13111589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Glycoproteomic analysis is always challenging because of low abundance and complex site-specific heterogeneity. Glycoproteins are involved in various biological processes such as cell signaling, adhesion, and cell-cell communication and may serve as potential biomarkers when analyzing different diseases. Here, we investigate glycoproteins in narcolepsy type 1 (NT1) disease, a form of narcolepsy characterized by cataplexy-the sudden onset of muscle paralysis that is typically triggered by intense emotions. In this study, 27 human blood serum samples were analyzed, 16 from NT1 patients and 11 from healthy individuals serving as controls. We quantified hydrophilic interaction liquid chromatography (HILIC)-enriched glycopeptides from low-abundance serum samples of controls and NT1 patients via LC-MS/MS. Twenty-eight unique N-glycopeptides showed significant changes between the two studied groups. The sialylated N-glycopeptide structures LPTQNITFQTESSVAEQEAEFQSPK HexNAc6, Hex3, Neu5Ac2 (derived from the ITIH4 protein) and the structure IVLDPSGSMNIYLVLDGSDSIGASNFTGAK HexNAc5, Hex4, Fuc1 (derived from the CFB protein), with p values of 0.008 and 0.01, respectively, were elevated in NT1 samples compared with controls. In addition, the N-glycopeptide protein sources Ceruloplasmin, Complement factor B, and ITH4 were observed to play an important role in the complement activation and acute-phase response signaling pathways. This may explain the possible association between the biomarkers and pathophysiological effects.
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Affiliation(s)
- Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Cristian D. Gutierrez Reyes
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Vishal Sandilya
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Waziha Purba
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Parisa Ahmadi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Md. Abdul Hakim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
| | - Firas Kobeissy
- Department of biochemistry and molecular genetics, Faculty of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 11072020, Lebanon;
- Department of Neurobiology, Center for Neurotrauma, Multiomics & Biomarkers (CNMB), Neuroscience Institute, Morehouse School of Medicine, Atlanta, GE 30310, USA
| | - Giuseppe Plazzi
- IRCCS, Instituto delle Scienze Neurologiche di Bologna, 40124 Bologna, Italy; (G.P.); (M.M.)
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Monica Moresco
- IRCCS, Instituto delle Scienze Neurologiche di Bologna, 40124 Bologna, Italy; (G.P.); (M.M.)
| | - Bartolo Lanuzza
- Sleep Research Center, Department of Neurology IC, Oasi Research Institute-IRCCS, 94018 Tronia, Italy; (B.L.); (R.F.)
| | - Raffaele Ferri
- Sleep Research Center, Department of Neurology IC, Oasi Research Institute-IRCCS, 94018 Tronia, Italy; (B.L.); (R.F.)
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (M.A.); (C.D.G.R.); (V.S.); (W.P.); (P.A.); (M.A.H.)
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6
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Zedan H, Morimura K, Elguoshy A, Yamamoto T, Natsuka S. Microheterogeneity and Individual Differences of Human Urinary N-Glycome under Normal Physiological Conditions. Biomolecules 2023; 13:biom13050756. [PMID: 37238626 DOI: 10.3390/biom13050756] [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: 03/15/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Urine is considered an outstanding biological fluid for biomarker discovery, reflecting both systemic and urogenital physiology. However, analyzing the N-glycome in urine in detail has been challenging due to the low abundance of glycans attached to glycoproteins compared to free oligosaccharides. Therefore, this study aims to thoroughly analyze urinary N-glycome using LC-MS/MS. The N-glycans were released using hydrazine and labeled with 2-aminopyridine (PA), followed by anion-exchange fractionation before LC-MS/MS analysis. A total of 109 N-glycans were identified and quantified, of which 58 were identified and quantified repeatedly in at least 80% of samples and accounted for approximately 85% of the total urinary glycome signal. Interestingly, a comparison between urine and serum N-glycome revealed that approximately 50% of the urinary glycome could originate from the kidney and urinary tract, where they were exclusively identified in urine, while the remaining 50% were common in both. Additionally, a correlation was found between age/sex and the relative abundances of urinary N-glycome, with more age-related changes observed in women than men. The results of this study provide a reference for human urine N-glycome profiling and structural annotations.
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Affiliation(s)
- Hend Zedan
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Kousuke Morimura
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Amr Elguoshy
- Biofluid Biomarker Center, Niigata University, Niigata 950-2181, Japan
| | - Tadashi Yamamoto
- Biofluid Biomarker Center, Niigata University, Niigata 950-2181, Japan
| | - Shunji Natsuka
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
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7
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Peng W, Reyes CDG, Gautam S, Yu A, Cho BG, Goli M, Donohoo K, Mondello S, Kobeissy F, Mechref Y. MS-based glycomics and glycoproteomics methods enabling isomeric characterization. MASS SPECTROMETRY REVIEWS 2023; 42:577-616. [PMID: 34159615 PMCID: PMC8692493 DOI: 10.1002/mas.21713] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 05/03/2023]
Abstract
Glycosylation is one of the most significant and abundant posttranslational modifications in mammalian cells. It mediates a wide range of biofunctions, including cell adhesion, cell communication, immune cell trafficking, and protein stability. Also, aberrant glycosylation has been associated with various diseases such as diabetes, Alzheimer's disease, inflammation, immune deficiencies, congenital disorders, and cancers. The alterations in the distributions of glycan and glycopeptide isomers are involved in the development and progression of several human diseases. However, the microheterogeneity of glycosylation brings a great challenge to glycomic and glycoproteomic analysis, including the characterization of isomers. Over several decades, different methods and approaches have been developed to facilitate the characterization of glycan and glycopeptide isomers. Mass spectrometry (MS) has been a powerful tool utilized for glycomic and glycoproteomic isomeric analysis due to its high sensitivity and rich structural information using different fragmentation techniques. However, a comprehensive characterization of glycan and glycopeptide isomers remains a challenge when utilizing MS alone. Therefore, various separation methods, including liquid chromatography, capillary electrophoresis, and ion mobility, were developed to resolve glycan and glycopeptide isomers before MS. These separation techniques were coupled to MS for a better identification and quantitation of glycan and glycopeptide isomers. Additionally, bioinformatic tools are essential for the automated processing of glycan and glycopeptide isomeric data to facilitate isomeric studies in biological cohorts. Here in this review, we discuss commonly employed MS-based techniques, separation hyphenated MS methods, and software, facilitating the separation, identification, and quantitation of glycan and glycopeptide isomers.
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Affiliation(s)
- Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | | | - Sakshi Gautam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Byeong Gwan Cho
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Kaitlyn Donohoo
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | | | - Firas Kobeissy
- Program for Neurotrauma, Neuroproteomics & Biomarkers Research, Departments of Emergency Medicine, University of Florida, Gainesville, Florida, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
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8
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Hurst RD, Nieves A, Brichacek M. Expanding Glycomic Investigations through Thiol-Derivatized Glycans. Molecules 2023; 28:1956. [PMID: 36838944 PMCID: PMC9964202 DOI: 10.3390/molecules28041956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
N-(2-thioethyl)-2-aminobenzamide (TEAB), a novel glycan auxiliary, was synthesized and its utility was evaluated. The auxiliary was conjugated to glycans by reductive amination with the water-stable reagent 2-picoline borane complex. Glycan products, which ranged from 1 to 7 linked hexoses, were all isolated in yields ranging from 60% to 90% after purification by reverse-phase chromatography. The novel conjugate introduces a convenient, shelf-stable thiol directly onto the desired free glycans with purification advantages and direct modification with efficient reactions through alkenes, halides, epoxides, disulfides, and carboxylates in yields of 49% to 93%. Subsequently, a thiol-selective modification of the BSA protein was used to generate a neoglycoprotein with a bifunctional PEG-maleimide linker. To further illustrate the utility of a thiol motif, 2-thiopyridine activation of a thiol-containing support facilitated the covalent chromatographic purification of labeled glycans in yields up to 63%. Finally, initial proof of concept of implementation in a light printed microarray was explored and validated through FITC-labeled concanavalin A binding. In conclusion, the thiol-functionalized glycans produced greatly expand the diversity of bioconjugation tools that can be developed with glycans and enable a variety of biological investigations.
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9
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Dumoncel RFP, Xavier B, Cardoso Júnior CDA, da Silva FS, Motta LGJ, Cavalheiro TN, Dalmora SL. Analysis of Denosumab by a Validated CZE Method and Determination of Sialic Acids by the RP-HPLC Method. J Chromatogr Sci 2023; 61:177-185. [PMID: 35279712 DOI: 10.1093/chromsci/bmac019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Indexed: 11/14/2022]
Abstract
A capillary zone electrophoresis (CZE) method was developed and validated to quantitate the monoclonal antibody denosumab (DmAb) and its charge variants in pharmaceutical products, demonstrating excellent precision, linearity and accuracy. Separations were obtained with migration times of 11.3 min for DmAb and the calibration curve was linear in the range of 0.95-20 mg/mL. The analytical comparability of seven batches of Prolia® showed mean differences of the estimated content/potencies of 1.87% lower, and 0.84 and 1.21% higher compared with the size-exclusion and reversed-phase liquid chromatography (SE-HPLC and RP-HPLC) methods and the osteoclast antiproliferative bioassay, respectively, with non-significant differences (P > 0.05). An RP-HPLC method with fluorescence detection (RP-HPLC-F), performed on a Kinetex® EVO C18 column (5 μm, 100 Å, 250 mm × 4.6 mm), was optimized to determine the levels of sialic acids of DmAb biomolecules, giving mean concentrations of 0.16 and 0.17 μg N-acetylneuraminic acid/mg DmAb for Prolia® and Xgeva® pharmaceutical products, respectively. The results demonstrated the capability of each one of the methods, and their use in combination constitutes a strategy to monitor instability, thereby assuring the quality and the batch-to-batch consistency of the biotechnology-derived medicine.
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Affiliation(s)
- Rafaela Ferreira Perobelli Dumoncel
- Postgraduate Program in Pharmaceutical Sciences, Industrial Pharmacy Department, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
| | - Bruna Xavier
- Postgraduate Program in Pharmaceutical Sciences, Industrial Pharmacy Department, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
| | - Clóvis Dervil Appratto Cardoso Júnior
- Postgraduate Program in Pharmaceutical Sciences, Industrial Pharmacy Department, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
| | - Francielle Santos da Silva
- Postgraduate Program in Pharmaceutical Sciences, Industrial Pharmacy Department, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
| | - Luís Gustavo Jung Motta
- Industrial Pharmacy Department, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
| | - Thaís Neuhaus Cavalheiro
- Industrial Pharmacy Department, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
| | - Sérgio Luiz Dalmora
- Industrial Pharmacy Department, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
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10
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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11
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Tian T, Rumachik N, Sinrod AJG, Barile D, Liu Y. Coupling an ion chromatography to high resolution mass spectrometry (IC-MS) for the discovery of potentially prebiotic oligosaccharides in Chardonnay grape marc. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1214:123540. [PMID: 36462400 DOI: 10.1016/j.jchromb.2022.123540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022]
Abstract
Oligosaccharides are carbohydrates made of three to twenty monosaccharide units linked through glycosidic bonds. Emerging research into the potential prebiotic activity of oligosaccharides is creating opportunities to use industrial byproducts as value-added products. Grape marc is a residue left after winemaking and has been shown to provide health benefits to humans. In this study, we analyzed the oligosaccharides in Chardonnay grape marc by utilizing a hyphenated platform in which an ion chromatography (IC) system is coupled to an Orbitrap mass spectrometer (MS). With this platform, we obtained a structural library including 32 oligosaccharides with unique compositions of monosaccharides and 61 oligosaccharide structures. Notably, the ion chromatographic separation provided resolution of charged isomers while maintaining separation capacity for small, neutral oligosaccharides. High-quality tandem MS also facilitated the identification of oligosaccharides with structural modifications including methylation and the presence of sugar alditols and hexuronic acids. The data acquired by the IC-MS system were also compared with previously published LC-MS data. We found that these two platforms are largely complementary and, in combination, provide a more comprehensive characterization of oligosaccharides than either platform achieves alone.
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Affiliation(s)
- Tian Tian
- Thermo Fisher Scientific, 1228 Titan Way, Sunnyvale, CA 94086, United States; Amgen Research, Molecular Analytics, Biologics Therapeutic Discovery, 750 Gateway Blvd, South San Francisco, CA 94080, United States(1).
| | - Neil Rumachik
- Thermo Fisher Scientific, 1228 Titan Way, Sunnyvale, CA 94086, United States.
| | - Amanda J G Sinrod
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States; Mattson, 343 Hatch Dr, Foster City, CA 94404, United States(1).
| | - Daniela Barile
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States.
| | - Yan Liu
- Thermo Fisher Scientific, 1228 Titan Way, Sunnyvale, CA 94086, United States.
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12
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Development of a novel, label-free N-glycan method using charged aerosol detection. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1212:123502. [DOI: 10.1016/j.jchromb.2022.123502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022]
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13
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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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14
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Wagt S, de Haan N, Wang W, Zhang T, Wuhrer M, Lageveen-Kammeijer GSM. N-Glycan Isomer Differentiation by Zero Flow Capillary Electrophoresis Coupled to Mass Spectrometry. Anal Chem 2022; 94:12954-12959. [PMID: 36098998 PMCID: PMC9523619 DOI: 10.1021/acs.analchem.2c02840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Isomeric N-glycans often vastly differ
in their
biological activities, hence the need for methods that allow resolving
and structurally characterizing them in biological material. Here,
we established a zero flow approach using capillary electrophoresis
in combination with (tandem) mass spectrometry to allow structural
characterization of isomeric N-glycans at high sensitivity.
Additionally, diagnostic fragment ion ratios were identified, indicative
for the antenna carrying specifically linked sialic acids. In total,
208 N-glycans were characterized in human plasma,
with 57 compositions showing multiple isomers.
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Affiliation(s)
- Sander Wagt
- Leiden University Medical Center, Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | - Noortje de Haan
- Leiden University Medical Center, Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | - Wenjun Wang
- Leiden University Medical Center, Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | - Tao Zhang
- Leiden University Medical Center, Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | - Manfred Wuhrer
- Leiden University Medical Center, Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
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15
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Ben Faleh A, Warnke S, Bansal P, Pellegrinelli RP, Dyukova I, Rizzo TR. Identification of Mobility-Resolved N-Glycan Isomers. Anal Chem 2022; 94:10101-10108. [PMID: 35797429 PMCID: PMC9310030 DOI: 10.1021/acs.analchem.2c01181] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Glycan analysis has
evolved considerably during the last decade.
The advent of high-resolution ion-mobility spectrometry has enabled
the separation of isomers with only the slightest of structural differences.
However, the ability to separate such species raises the problem of
identifying all the mobility-resolved peaks that are observed, especially
when analytical standards are not available. In this work, we report
an approach based on the combination of IMSn with cryogenic
vibrational spectroscopy to identify N-glycan reducing-end
anomers. By identifying the reducing-end α and β anomers
of diacetyl-chitobiose, which is a disaccharide that forms part of
the common core of all N-glycans, we are able to
assign mobility peaks to reducing anomers of a selection of N-glycans of different sizes, starting from trisaccharides
such as Man-1 up to glycans containing nine monosaccharide units,
such as G2. By building an infrared fingerprint database of the identified N-glycans, our approach allows unambiguous identification
of mobility peaks corresponding to reducing-end anomers and distinguishes
them from positional isomers that might be present in a complex mixture.
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Affiliation(s)
- Ahmed Ben Faleh
- Laboratoire de Chimie Physique Moléculaire, EPFL SB ISIC LCPM, École Polytechnique Fédérale de Lausanne, Station 6, Lausanne CH-1015, Switzerland
| | - Stephan Warnke
- Laboratoire de Chimie Physique Moléculaire, EPFL SB ISIC LCPM, École Polytechnique Fédérale de Lausanne, Station 6, Lausanne CH-1015, Switzerland
| | - Priyanka Bansal
- Laboratoire de Chimie Physique Moléculaire, EPFL SB ISIC LCPM, École Polytechnique Fédérale de Lausanne, Station 6, Lausanne CH-1015, Switzerland
| | - Robert P Pellegrinelli
- Laboratoire de Chimie Physique Moléculaire, EPFL SB ISIC LCPM, École Polytechnique Fédérale de Lausanne, Station 6, Lausanne CH-1015, Switzerland
| | - Irina Dyukova
- Laboratoire de Chimie Physique Moléculaire, EPFL SB ISIC LCPM, École Polytechnique Fédérale de Lausanne, Station 6, Lausanne CH-1015, Switzerland
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire, EPFL SB ISIC LCPM, École Polytechnique Fédérale de Lausanne, Station 6, Lausanne CH-1015, Switzerland
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16
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Zhang H, Shi X, Liu Y, Wang B, Xu M, Welham NV, Li L. On-tissue amidation of sialic acid with aniline for sensitive imaging of sialylated N-glycans from FFPE tissue sections via MALDI mass spectrometry. Anal Bioanal Chem 2022; 414:5263-5274. [PMID: 35072748 PMCID: PMC9381140 DOI: 10.1007/s00216-022-03894-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/24/2021] [Accepted: 01/10/2022] [Indexed: 01/06/2023]
Abstract
Spatial visualization of glycans within clinical tissue samples is critical for discovery of disease-relevant glycan dysregulations. Herein, we develop an on-tissue derivatization strategy for sensitive spatial visualization of N-glycans from formalin-fixed paraffin-embedded (FFPE) tissue sections, based on amidation of sialic acid residues with aniline. The sialylated N-glycans were stabilized and given enhanced signal intensity owing to selective capping of a phenyl group to the sialic acid residue after aniline labeling. Proof-of-concept experiments, including determinations of sialylglycopeptide and N-glycans enzymatically released from glycoproteins, were performed. Further, mass spectrometry (MS) imaging of N-glycans on human laryngeal cancer FFPE tissue sections was conducted via matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), based on our strategy for on-tissue amidation of sialylated N-glycans. We obtained higher sialylated N-glycan coverages for both the glycoproteins and cancer tissue samples, demonstrating that the detection sensitivity for sialylated N-glycans is notably improved by amidation derivatization. We also characterized N-glycan heterogeneity across the human laryngeal cancer tissue section, showing N-glycan dysregulation in the tumor region.
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Affiliation(s)
- Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI, 53705, USA
| | - Xudong Shi
- Division of Otolaryngology, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Yuan Liu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI, 53705, USA
| | - Bin Wang
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI, 53705, USA
| | - Meng Xu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Nathan V Welham
- Division of Otolaryngology, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI, 53705, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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17
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Molnarova K, Cokrtova K, Tomnikova A, Krizek T, Kozlik P. Liquid chromatography and capillary electrophoresis in glycomic and glycoproteomic analysis. MONATSHEFTE FUR CHEMIE 2022; 153:659-686. [PMID: 35754790 PMCID: PMC9212196 DOI: 10.1007/s00706-022-02938-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/29/2022] [Indexed: 11/28/2022]
Abstract
Glycosylation is one of the most significant and abundant post-translational modifications in cells. Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycomic and glycoproteomic analysis is highly challenging because of the large diversity of structures, low abundance, site-specific heterogeneity, and poor ionization efficiency of glycans and glycopeptides in mass spectrometry (MS). MS is a key tool for characterization of glycans and glycopeptides. However, MS alone does not always provide full structural and quantitative information for many reasons, and thus MS is combined with some separation technique. This review focuses on the role of separation techniques used in glycomic and glycoproteomic analyses, liquid chromatography and capillary electrophoresis. The most important separation conditions and results are presented and discussed. Graphical abstract
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Affiliation(s)
- Katarina Molnarova
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Katerina Cokrtova
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Alice Tomnikova
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tomas Krizek
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Kozlik
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
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18
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Zhang S, Cao Z, Fan P, Wang Y, Jia W, Wang L, Wang K, Liu Y, Du X, Hu C, Zhang P, Chen HY, Huang S. A Nanopore‐Based Saccharide Sensor. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Yao Liu
- Nanjing University Chemistry CHINA
| | | | | | | | | | - Shuo Huang
- Nanjing University Chemistry 163 Xianlin AveSchool of Chemistry and Chemical EngineeringXixia District 210023 Nanjing CHINA
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19
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Zhang S, Cao Z, Fan P, Wang Y, Jia W, Wang L, Wang K, Liu Y, Du X, Hu C, Zhang P, Chen HY, Huang S. A Nanopore-Based Saccharide Sensor. Angew Chem Int Ed Engl 2022; 61:e202203769. [PMID: 35718742 DOI: 10.1002/anie.202203769] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Indexed: 12/19/2022]
Abstract
Saccharides play critical roles in many forms of cellular activities. Saccharide structures are however complicated and similar, setting a technical hurdle for direct identification. Nanopores, which are emerging single molecule tools sensitive to minor structural differences between analytes, can be engineered to identity saccharides. A hetero-octameric Mycobacterium smegmatis porin A nanopore containing a phenylboronic acid was prepared, and was able to clearly identify nine monosaccharide types, including D-fructose, D-galactose, D-mannose, D-glucose, L-sorbose, D-ribose, D-xylose, L-rhamnose and N-acetyl-D-galactosamine. Minor structural differences between saccharide epimers can also be distinguished. To assist automatic event classification, a machine learning algorithm was developed, with which a general accuracy score of 0.96 was achieved. This sensing strategy is generally suitable for other saccharide types and may bring new insights to nanopore saccharide sequencing.
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Affiliation(s)
- Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Zhenyuan Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Chengzhen Hu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
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20
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Technical pipeline for screening microbial communities as a function of substrate specificity through fluorescent labelling. Commun Biol 2022; 5:444. [PMID: 35545700 PMCID: PMC9095699 DOI: 10.1038/s42003-022-03383-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
The study of specific glycan uptake and metabolism is an effective tool in aiding with the continued unravelling of the complexities in the human gut microbiome. To this aim fluorescent labelling of glycans may provide a powerful route towards this target. Here, we successfully used the fluorescent label 2-aminobenzamide (2-AB) to monitor and study microbial degradation of labelled glycans. Both single strain and co-cultured fermentations of microbes from the common human-gut derived Bacteroides genus, are able to grow when supplemented with 2-AB labelled glycans of different monosaccharide composition, degrees of acetylation and polymerization. Utilizing a multifaceted approach that combines chromatography, mass spectrometry, microscopy and flow cytometry techniques, it is possible to better understand the metabolism of labelled glycans in both supernatants and at a single cell level. We envisage this combination of complementary techniques will help further the understanding of substrate specificity and the role it plays within microbial communities. A reductive amination-based fluorophore labelling of complex wood-derived glycans provides a proof-of-principle multi-modal platform for monitoring glycan uptake by bacteria.
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21
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Moran AB, Gardner RA, Wuhrer M, Lageveen-Kammeijer GSM, Spencer DIR. Sialic Acid Derivatization of Fluorescently Labeled N-Glycans Allows Linkage Differentiation by Reversed-Phase Liquid Chromatography-Fluorescence Detection-Mass Spectrometry. Anal Chem 2022; 94:6639-6648. [PMID: 35482581 PMCID: PMC9096788 DOI: 10.1021/acs.analchem.1c02610] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 04/15/2022] [Indexed: 12/14/2022]
Abstract
Sialic acids have diverse biological roles, ranging from promoting up to preventing protein and cellular recognition in health and disease. The various functions of these monosaccharides are owed, in part, to linkage variants, and as a result, linkage-specific analysis of sialic acids is an important aspect of glycomic studies. This has been addressed by derivatization strategies using matrix-assisted laser desorption/ionization mass spectrometry (MS) or sialidase digestion arrays followed by liquid chromatography (LC)-MS. Despite this, these approaches are unable to simultaneously provide unambiguous assignment of sialic acid linkages and assess further isomeric glycan features within a single measurement. Thus, for the first time, we present the combination of procainamide fluorescent labeling with sialic acid linkage-specific derivatization via ethyl esterification and amidation for the analysis of released plasma N-glycans using reversed-phase (RP)LC-fluorescence detection (FD)-MS. As a result, α2,3- and α2,6-sialylated N-glycans, with the same mass prior to derivatization, are differentiated based on retention time, precursor mass, and fragmentation spectra, and additional sialylated isomers were also separated. Furthermore, improved glycan coverage and protocol precision were found via the novel application using a combined FD-MS quantification approach. Overall, this platform achieved unambiguous assignment of N-glycan sialic acid linkages within a single RPLC-FD-MS measurement, and by improving their retention on RPLC, this technique can be used for future investigations of released N-glycans as an additional or orthogonal method to current analytical approaches.
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Affiliation(s)
- Alan B. Moran
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
- Ludger
Ltd., Culham Science
Centre, OX14 3EB Abingdon, United Kingdom
| | | | - Manfred Wuhrer
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
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22
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Grabarics M, Lettow M, Kirschbaum C, Greis K, Manz C, Pagel K. Mass Spectrometry-Based Techniques to Elucidate the Sugar Code. Chem Rev 2022; 122:7840-7908. [PMID: 34491038 PMCID: PMC9052437 DOI: 10.1021/acs.chemrev.1c00380] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/22/2022]
Abstract
Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.
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Affiliation(s)
- Márkó Grabarics
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Maike Lettow
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kim Greis
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Christian Manz
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
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23
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Trinh D, Gardner RA, Franciosi AN, McCarthy C, Keane MP, Soliman MG, O’Donnell JS, Meleady P, Spencer DIR, Monopoli MP. Nanoparticle Biomolecular Corona-Based Enrichment of Plasma Glycoproteins for N-Glycan Profiling and Application in Biomarker Discovery. ACS NANO 2022; 16:5463-5475. [PMID: 35341249 PMCID: PMC9047655 DOI: 10.1021/acsnano.1c09564] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/10/2022] [Indexed: 05/28/2023]
Abstract
Biomolecular corona formation has emerged as a recurring and important phenomenon in nanomedicine that has been investigated for potential applications in disease diagnosis. In this study, we have combined the "personalized protein corona" with the N-glycosylation profiling that has recently gained considerable interest in human plasma biomarker discovery as a powerful early warning diagnostic and patient stratification tool. We envisioned that the protein corona formation could be exploited as an enrichment step that is critically important in both proteomic and proteoglycomic workflows. By using silica nanoparticles, plasma fibrinogen was enriched to a level in which its proteomic and glycomic "fingerprints" could be traced with confidence. Despite being a more simplified glycan profile compared to full plasma, the corona glycan profile revealed a fibrinogen-derived glycan peak that was found to potentially distinguish lung cancer patients from controls in a pilot study.
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Affiliation(s)
- Duong
N. Trinh
- Department
of Chemistry, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Richard A. Gardner
- Ludger
Ltd., Culham Science Centre, Abingdon, Oxfordshire OX14 3EB, United Kingdom
| | - Alessandro N. Franciosi
- UBC
Faculty of Medicine, Department of Respiratory Medicine, University of British Columbia, Vancouver, British Columbia V6Z 1Y6, Canada
| | - Cormac McCarthy
- Department
of Respiratory Medicine, St. Vincent’s
University Hospital, Dublin 4, Ireland
- School
of Medicine, University College Dublin, Dublin 4, Ireland
| | - Michael P. Keane
- Department
of Respiratory Medicine, St. Vincent’s
University Hospital, Dublin 4, Ireland
- School
of Medicine, University College Dublin, Dublin 4, Ireland
| | - Mahmoud G. Soliman
- Department
of Chemistry, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin 2, Ireland
- Physics Department,
Faculty of Science, Al-Azhar University, Nasr City 11884, Cairo, Egypt
| | - James S. O’Donnell
- Irish
Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences,
Royal College of Surgeons in Ireland, University
of Medicine and Health Sciences, Dublin 2, Ireland
| | - Paula Meleady
- School
of
Biotechnology, Dublin City University, Dublin 9, Ireland
| | - Daniel I. R. Spencer
- Ludger
Ltd., Culham Science Centre, Abingdon, Oxfordshire OX14 3EB, United Kingdom
| | - Marco P. Monopoli
- Department
of Chemistry, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin 2, Ireland
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24
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Liu X, Wang Q, Lauber MA. High sensitivity acidic N-glycan profiling with MS-enhancing derivatization and mixed mode chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1191:123120. [DOI: 10.1016/j.jchromb.2022.123120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 11/16/2022]
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25
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Recent advances and trends in sample preparation and chemical modification for glycan analysis. J Pharm Biomed Anal 2022; 207:114424. [PMID: 34653745 DOI: 10.1016/j.jpba.2021.114424] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 12/26/2022]
Abstract
Growing significance of glycosylation in protein functions has accelerated the development of methodologies for detection, identification, and characterization of protein glycosylation. In the past decade, glycobiology research has been advanced by innovative techniques with further progression in the post-genome era. Although significant technical progress has been made in terms of analytical throughput, comprehensiveness, and sensitivity, most methods for glycosylation analysis still require laborious and time-consuming sample preparation tasks. Additionally, sample preparation methods that are focused on specific glycan(s) require an in-depth understanding of various issues in glycobiology. In this review, modern sample preparation and chemical modification methods for the structural and quantitative glycan analyses together with the challenges and advantages of recent sample preparation methods are summarized. The techniques presented herein can facilitate the exploration of biomarkers, understanding of unknown glycan functions, and development of biopharmaceuticals.
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26
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Warnke S, Ben Faleh A, Rizzo TR. Toward High-Throughput Cryogenic IR Fingerprinting of Mobility-Separated Glycan Isomers. ACS MEASUREMENT SCIENCE AU 2021; 1:157-164. [PMID: 34939078 PMCID: PMC8679095 DOI: 10.1021/acsmeasuresciau.1c00018] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 05/10/2023]
Abstract
Infrared (IR) spectroscopy is a powerful tool used to infer detailed structural information on molecules, often in conjunction with quantum-chemical calculations. When applied to cryogenically cooled ions, IR spectra provide unique fingerprints that can be used for biomolecular identification. This is particularly important in the analysis of isomeric biopolymers, which are difficult to distinguish using mass spectrometry. However, IR spectroscopy typically requires laser systems that need substantial user attention and measurement times of tens of minutes, which limits its analytical utility. We report here the development of a new high-throughput instrument that combines ultrahigh-resolution ion-mobility spectrometry with cryogenic IR spectroscopy and mass spectrometry, and we apply it to the analysis of isomeric glycans. The ion mobility step, which is based on structures for lossless ion manipulations (SLIM), separates glycan isomers, and an IR fingerprint spectrum identifies them. An innovative cryogenic ion trap allows multiplexing the acquisition of analyte IR fingerprints following mobility separation, and using a turn-key IR laser, we can obtain spectra and identify isomeric species in less than a minute. This work demonstrates the potential of IR fingerprinting methods to impact the analysis of isomeric biomolecules and more specifically glycans.
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27
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Gong Y, Qin S, Dai L, Tian Z. The glycosylation in SARS-CoV-2 and its receptor ACE2. Signal Transduct Target Ther 2021; 6:396. [PMID: 34782609 PMCID: PMC8591162 DOI: 10.1038/s41392-021-00809-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/10/2021] [Accepted: 10/24/2021] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis. Here we reviewed the detections, substrates, biological functions of the glycosylation in SARS-CoV-2 proteins as well as the human receptor ACE2, and also summarized the approved and undergoing SARS-CoV-2 therapeutics associated with glycosylation. This review may not only broad the understanding of viral glycobiology, but also provide key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.
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Affiliation(s)
- Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China
| | - Suideng Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China.
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28
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Donohoo KB, Wang J, Goli M, Yu A, Peng W, Hakim MA, Mechref Y. Advances in mass spectrometry-based glycomics-An update covering the period 2017-2021. Electrophoresis 2021; 43:119-142. [PMID: 34505713 DOI: 10.1002/elps.202100199] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 12/21/2022]
Abstract
The wide variety of chemical properties and biological functions found in proteins is attained via post-translational modifications like glycosylation. Covalently bonded to proteins, glycans play a critical role in cell activity. Complex structures with microheterogeneity, the glycan structures that are associated with proteins are difficult to analyze comprehensively. Recent advances in sample preparation methods, separation techniques, and MS have facilitated the quantitation and structural elucidation of glycans. This review focuses on highlighting advances in MS-based techniques for glycomic analysis that occurred over the last 5 years (2017-2021) as an update to the previous review on the subject. The topics of discussion will include progress in glycomic workflow such as glycan release, purification, derivatization, and separation as well as the topics of ionization, tandem MS, and separation techniques that can be coupled with MS. Additionally, bioinformatics tools used for the analysis of glycans will be described.
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Affiliation(s)
- Kaitlyn B Donohoo
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Junyao Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Md Abdul Hakim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas
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29
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Sánchez-Trasviña C, Flores-Gatica M, Enriquez-Ochoa D, Rito-Palomares M, Mayolo-Deloisa K. Purification of Modified Therapeutic Proteins Available on the Market: An Analysis of Chromatography-Based Strategies. Front Bioeng Biotechnol 2021; 9:717326. [PMID: 34490225 PMCID: PMC8417561 DOI: 10.3389/fbioe.2021.717326] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/09/2021] [Indexed: 02/02/2023] Open
Abstract
Proteins, which have inherent biorecognition properties, have long been used as therapeutic agents for the treatment of a wide variety of clinical indications. Protein modification through covalent attachment to different moieties improves the therapeutic's pharmacokinetic properties, affinity, stability, confers protection against proteolytic degradation, and increases circulation half-life. Nowadays, several modified therapeutic proteins, including PEGylated, Fc-fused, lipidated, albumin-fused, and glycosylated proteins have obtained regulatory approval for commercialization. During its manufacturing, the purification steps of the therapeutic agent are decisive to ensure the quality, effectiveness, potency, and safety of the final product. Due to the robustness, selectivity, and high resolution of chromatographic methods, these are recognized as the gold standard in the downstream processing of therapeutic proteins. Moreover, depending on the modification strategy, the protein will suffer different physicochemical changes, which must be considered to define a purification approach. This review aims to deeply analyze the purification methods employed for modified therapeutic proteins that are currently available on the market, to understand why the selected strategies were successful. Emphasis is placed on chromatographic methods since they govern the purification processes within the pharmaceutical industry. Furthermore, to discuss how the modification type strongly influences the purification strategy, the purification processes of three different modified versions of coagulation factor IX are contrasted.
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Affiliation(s)
- Calef Sánchez-Trasviña
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Biotecnología-FEMSA, Monterrey, Mexico
| | - Miguel Flores-Gatica
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Biotecnología-FEMSA, Monterrey, Mexico
| | - Daniela Enriquez-Ochoa
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Biotecnología-FEMSA, Monterrey, Mexico
| | - Marco Rito-Palomares
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - Karla Mayolo-Deloisa
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Biotecnología-FEMSA, Monterrey, Mexico
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30
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Nmagu D, Singh SK, Lee KH. Creation of monoclonal antibody expressing CHO cell lines grown with sodium butyrate and characterization of resulting antibody glycosylation. Methods Enzymol 2021; 660:267-295. [PMID: 34742393 DOI: 10.1016/bs.mie.2021.06.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Chinese hamster ovary (CHO) cells are the primary mammalian cell lines utilized to produce monoclonal antibodies (mAbs). The upsurge in biosimilar development and the proven health benefits of mAb treatments reinforces the need for innovative methods to generate robust CHO clones and enhance production, while maintaining desired product quality attributes. Among various product titer-enhancing approaches, the use of histone deacetylase inhibitors (HDACis) such as sodium butyrate (NaBu) has yielded promising results. The titer-enhancing effect of HDACi treatment has generally been observed in lower producer cell lines but those studies are typically done on individual clones. Here, we describe a cell line development (CLD) platform approach for creating clones with varying productivities. We then describe a method for selecting an optimal NaBu concentration to evaluate potential titer-enhancing capabilities in a fed-batch study. Finally, a method for purifying the mAb using protein A chromatography, followed by glycosylation analysis using mass spectrometry, is described. The proposed workflow can be applied for a robust CLD process optimization to generate robust clones, enhance product expression, and improve product quality attributes.
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Affiliation(s)
- Douglas Nmagu
- Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States
| | - Sumit K Singh
- Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States
| | - Kelvin H Lee
- Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States.
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31
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Paton B, Suarez M, Herrero P, Canela N. Glycosylation Biomarkers Associated with Age-Related Diseases and Current Methods for Glycan Analysis. Int J Mol Sci 2021; 22:5788. [PMID: 34071388 PMCID: PMC8198018 DOI: 10.3390/ijms22115788] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 12/23/2022] Open
Abstract
Ageing is a complex process which implies the accumulation of molecular, cellular and organ damage, leading to an increased vulnerability to disease. In Western societies, the increase in the elderly population, which is accompanied by ageing-associated pathologies such as cardiovascular and mental diseases, is becoming an increasing economic and social burden for governments. In order to prevent, treat and determine which subjects are more likely to develop these age-related diseases, predictive biomarkers are required. In this sense, some studies suggest that glycans have a potential role as disease biomarkers, as they modify the functions of proteins and take part in intra- and intercellular biological processes. As the glycome reflects the real-time status of these interactions, its characterisation can provide potential diagnostic and prognostic biomarkers for multifactorial diseases. This review gathers the alterations in protein glycosylation profiles that are associated with ageing and age-related diseases, such as cancer, type 2 diabetes mellitus, metabolic syndrome and several chronic inflammatory diseases. Furthermore, the review includes the available techniques for the determination and characterisation of glycans, such as liquid chromatography, electrophoresis, nuclear magnetic resonance and mass spectrometry.
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Affiliation(s)
- Beatrix Paton
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
| | - Manuel Suarez
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Pol Herrero
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
| | - Núria Canela
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
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32
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Molnarova K, Duris A, Jecmen T, Kozlik P. Comparison of human IgG glycopeptides separation using mixed-mode hydrophilic interaction/ion-exchange liquid chromatography and reversed-phase mode. Anal Bioanal Chem 2021; 413:4321-4328. [PMID: 34002272 DOI: 10.1007/s00216-021-03388-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/12/2021] [Accepted: 05/03/2021] [Indexed: 12/24/2022]
Abstract
Glycoproteomics is a challenging branch of proteomics because of the micro- and macro-heterogeneity of protein glycosylation. Hydrophilic interaction liquid chromatography (HILIC) is an advantageous alternative to reversed-phase chromatography for intact glycopeptide separation prior to their identification by mass spectrometry. Nowadays, several HILIC columns differing in used chemistries are commercially available. However, there is a lack of comparative studies assessing their performance, and thus providing guidance for the selection of an adequate stationary phase for different glycoproteomics applications. Here, we compare three HILIC columns recently developed by Advanced Chromatography Technologies (ACE)- with unfunctionalized (HILIC-A), polyhydroxy functionalized (HILIC-N), and aminopropyl functionalized (HILIC-B) silica- with a C18 reversed-phase column in the separation of human immunoglobulin G glycopeptides. HILIC-A and HILIC-B exhibit mixed-mode separation combining hydrophilic and ion-exchange interactions for analyte retention. Expectably, reversed-phase mode successfully separated clusters of immunoglobulin G1 and immunoglobulin G2 glycopeptides, which differ in amino acid sequence, but was not able to adequately separate different glycoforms of the same peptide. All ACE HILIC columns showed higher separation power for different glycoforms, and we show that each column separates a different group of glycopeptides more effectively than the others. Moreover, HILIC-A and HILIC-N columns separated the isobaric A2G1F1 glycopeptides of immunoglobulin G, and thus showed the potential for the elucidation of the structure of isomeric glycoforms. Furthermore, the possible retention mechanism for the HILIC columns is discussed on the basis of the determined chromatographic parameters.
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Affiliation(s)
- Katarina Molnarova
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Ales Duris
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Tomas Jecmen
- Department of Biochemistry, Faculty of Science, Charles University, 128 00, Prague 2, Czech Republic
| | - Petr Kozlik
- Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic.
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33
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Macedo-da-Silva J, Santiago VF, Rosa-Fernandes L, Marinho CRF, Palmisano G. Protein glycosylation in extracellular vesicles: Structural characterization and biological functions. Mol Immunol 2021; 135:226-246. [PMID: 33933815 DOI: 10.1016/j.molimm.2021.04.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 02/07/2023]
Abstract
Extracellular vesicles (EVs) are lipid bilayer-enclosed particles involved in intercellular communication, delivery of biomolecules from donor to recipient cells, cellular disposal and homeostasis, potential biomarkers and drug carriers. The content of EVs includes DNA, lipids, metabolites, proteins, and microRNA, which have been studied in various diseases, such as cancer, diabetes, pregnancy, neurodegenerative, and cardiovascular disorders. EVs are enriched in glycoconjugates and exhibit specific glycosignatures. Protein glycosylation is a co- and post-translational modification (PTM) that plays an important role in the expression and function of exosomal proteins. N- and O-linked protein glycosylation has been mapped in exosomal proteins. The purpose of this review is to highlight the importance of glycosylation in EVs proteins. Initially, we describe the main PTMs in EVs with a focus on glycosylation. Then, we explore glycan-binding proteins describing the main findings of studies that investigated the glycosylation of EVs in cancer, pregnancy, infectious diseases, diabetes, mental disorders, and animal fluids. We have highlighted studies that have developed innovative methods for studying the content of EVs. In addition, we present works related to lipid glycosylation. We explored the content of studies deposited in public databases, such as Exocarta and Vesiclepedia. Finally, we discuss analytical methods for structural characterization of glycoconjugates and present an overview of the critical points of the study of glycosylation EVs, as well as perspectives in this field.
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Affiliation(s)
- Janaina Macedo-da-Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Verônica F Santiago
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Claudio R F Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil.
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34
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Stantič M, Gunčar G, Kuzman D, Mravljak R, Cvijić T, Podgornik A. Application of lectin immobilized on polyHIPE monoliths for bioprocess monitoring of glycosylated proteins. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1174:122731. [PMID: 33971517 DOI: 10.1016/j.jchromb.2021.122731] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 02/04/2023]
Abstract
In-process monitoring of glycosylated protein concentration becomes very important with the introduction of perfusion bioprocesses. Affinity chromatography based on lectins allows selective monitoring when carbohydrates are accessible on the protein surface. In this work, we immobilized lectin on polyHIPE type of monoliths and implemented it for bioprocess monitoring. A spacer was introduced to lectin, which increased binding kinetics toward Fc-fusion protein, demonstrated by bio-layer interferometry. Furthermore, complete desorption using 0.25 M galactose was shown. Affinity column exhibited linearity in the range between 0.5 and 8 mg/ml and flow-unaffected binding for the flow-rates between 0.5 and 8 ml/min. Long-term stability over at least four months period was demonstrated. No unspecific binding of culture media components, including host cell proteins and DNA, was detected. Results obtained by affinity column matched concentration values obtained by a reference method.
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Affiliation(s)
- Metka Stantič
- Faculty for Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Gregor Gunčar
- Faculty for Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Drago Kuzman
- Technical development biosimilars, Global drug development, Novartis, Kolodvorska 27, 1234 Mengeš, Slovenia
| | - Rok Mravljak
- Faculty for Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Tamara Cvijić
- Technical development biosimilars, Global drug development, Novartis, Kolodvorska 27, 1234 Mengeš, Slovenia
| | - Aleš Podgornik
- Faculty for Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia; COBIK, Tovarniška 26, 5270 Ajdovščina, Slovenia.
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35
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Chen S, Qin R, Mahal LK. Sweet systems: technologies for glycomic analysis and their integration into systems biology. Crit Rev Biochem Mol Biol 2021; 56:301-320. [PMID: 33820453 DOI: 10.1080/10409238.2021.1908953] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Found in virtually every organism, glycans are essential molecules that play important roles in almost every aspect of biology. The composition of glycome, the repertoire of glycans in an organism or a biological sample, is often found altered in many diseases, including cancer, infectious diseases, metabolic and developmental disorders. Understanding how glycosylation and glycomic changes enriches our knowledge of the mechanisms of disease progression and sheds light on the development of novel therapeutics. However, the inherent diversity of glycan structures imposes challenges on the experimental characterization of glycomes. Advances in high-throughput glycomic technologies enable glycomic analysis in a rapid and comprehensive manner. In this review, we discuss the analytical methods currently used in high-throughput glycomics, including mass spectrometry, liquid chromatography and lectin microarray. Concomitant with the technical advances is the integration of glycomics into systems biology in the recent years. Herein we elaborate on some representative works from this recent trend to underline the important role of glycomics in such integrated approaches to disease.
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Affiliation(s)
- Shuhui Chen
- Department of Chemistry, New York University, New York City, NY, USA
| | - Rui Qin
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Lara K Mahal
- Department of Chemistry, New York University, New York City, NY, USA.,Department of Chemistry, University of Alberta, Edmonton, AB, Canada
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36
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Toward robust N-glycomics of various tissue samples that may contain glycans with unknown or unexpected structures. Sci Rep 2021; 11:6334. [PMID: 33737529 PMCID: PMC7973440 DOI: 10.1038/s41598-021-84668-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/16/2021] [Indexed: 12/13/2022] Open
Abstract
Glycans in tissues are structurally diverse and usually include a large number of isomers that cannot be easily distinguished by mass spectrometry (MS). To address this issue, we developed a combined method that can efficiently separate and identify glycan isomers. First, we separated 2-aminopyridine (PA)-derivatized N-glycans from chicken colon by reversed-phase liquid chromatography (LC) and directly analyzed them by electrospray ionization (ESI)-MS and MS/MS to obtain an overview of the structural features of tissue glycans. Next, we deduced the structures of isomers based on their elution positions, full MS, and MS/MS data, before or after digestions with several exoglycosidases. In this method, the elution position differed greatly depending on the core structure and branching pattern, allowing multiantennary N-glycan structures to be easily distinguished. To further determine linkages of branch sequences, we modified PA-N-glycans with sialic acid linkage-specific alkylamidation and/or permethylation, and analyzed the products by LC–MS and multistage MS. We determined the relative abundances of core structures, branching patterns, and branch sequences of N-glycans from chicken colon, and confirmed presence of characteristic branch sequences such as Lex, sialyl Lex, sulfated LacNAc, LacNAc repeat, and LacdiNAc. The results demonstrated that our method is useful for comparing N-glycomes among various tissue samples.
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37
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Dhakal R, Nieman R, Valente DCA, Cardozo TM, Jayee B, Aqdas A, Peng W, Aquino AJA, Mechref Y, Lischka H, Moussa H. A General New Method for Calculating the Molecular Nonpolar Surface for Analysis of LC-MS Data. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 461:116495. [PMID: 33424422 PMCID: PMC7789828 DOI: 10.1016/j.ijms.2020.116495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The accurate determination of the nonpolar surface area of glycans is vital when utilizing liquid chromatograph/mass spectrometry (LC-MS) for structural characterization. A new approach for defining and computing nonpolar surface areas based on continuum solvation models (CS-NPSA) is presented. It is based on the classification of individual surface elements representing the solvent accessible surface used for the description of the polarized charge density elements in the CS models. Each element can be classified as polar or nonpolar according to a threshold value. The summation of the nonpolar elements then results in the NPSA resulting in a very fine resolution of this surface. The further advantage of the CS-NPSA approach is the straightforward connection to standard quantum chemical methods and program packages. The method has been analyzed in terms of the contributions of different atoms to the NPSA. The analysis showed that not only atoms normally classified as nonpolar contributed to the NPSA, but at least partially also atoms next to polar atoms or N atoms. By virtue of the construction of the solvent accessible surface, atoms in the inner regions of a molecule can be automatically identified as not contributing to the NPSA. The method has been applied to a variety of examples such as the phenylbutanehydrazide series, model dextrans consisting of glucose units and biantennary glycans. Linear correlation of the CS-NPSA values with retention times obtained from liquid chromatographic separations measurements in the mentioned cases give excellent results and promise for more extended applications on a larger variety of compounds.
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Affiliation(s)
- Rabin Dhakal
- Department of Mechanical Engineering, Texas Tech
University, Lubbock, TX, 79409, USA
| | - Reed Nieman
- Department of Chemistry and Biochemistry, Texas Tech
University, Lubbock, TX, 79409-1061, USA
- Corresponding author.
(R. Nieman),
(A. A. J. Aquino), and
(H. Lischka)
| | - Daniel C. A. Valente
- Instituto de Química, Universidade Federal do Rio de
Janeiro, Rio de Janeiro – RJ, 21941-901, Brazil
| | - Thiago M. Cardozo
- Instituto de Química, Universidade Federal do Rio de
Janeiro, Rio de Janeiro – RJ, 21941-901, Brazil
| | - Bhumika Jayee
- Department of Chemistry and Biochemistry, Texas Tech
University, Lubbock, TX, 79409-1061, USA
| | - Amna Aqdas
- Department of Chemistry and Biochemistry, Texas Tech
University, Lubbock, TX, 79409-1061, USA
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech
University, Lubbock, TX, 79409-1061, USA
| | - Adelia J. A. Aquino
- Department of Mechanical Engineering, Texas Tech
University, Lubbock, TX, 79409, USA
- Corresponding author.
(R. Nieman),
(A. A. J. Aquino), and
(H. Lischka)
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech
University, Lubbock, TX, 79409-1061, USA
| | - Hans Lischka
- Department of Chemistry and Biochemistry, Texas Tech
University, Lubbock, TX, 79409-1061, USA
- Corresponding author.
(R. Nieman),
(A. A. J. Aquino), and
(H. Lischka)
| | - Hanna Moussa
- Department of Mechanical Engineering, Texas Tech
University, Lubbock, TX, 79409, USA
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38
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Li X, Zhao H, Chen X. Screening of Marine Bioactive Antimicrobial Compounds for Plant Pathogens. Mar Drugs 2021; 19:69. [PMID: 33525648 PMCID: PMC7912171 DOI: 10.3390/md19020069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 01/09/2023] Open
Abstract
Plant diseases have been threatening food production. Controlling plant pathogens has become an important strategy to ensure food security. Although chemical control is an effective disease control strategy, its application is limited by many problems, such as environmental impact and pathogen resistance. In order to overcome these problems, it is necessary to develop more chemical reagents with new functional mechanisms. Due to their special living environment, marine organisms have produced a variety of bioactive compounds with novel structures, which have the potential to develop new fungicides. In the past two decades, screening marine bioactive compounds to inhibit plant pathogens has been a hot topic. In this review, we summarize the screening methods of marine active substances from plant pathogens, the identification of marine active substances from different sources, and the structure and antibacterial mechanism of marine active natural products. Finally, the application prospect of marine bioactive substances in plant disease control was prospected.
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Affiliation(s)
- Xiaohui Li
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China; (X.L.); (H.Z.)
| | - Hejing Zhao
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China; (X.L.); (H.Z.)
| | - Xiaolin Chen
- State Key Laboratory of Agricultural Microbiology and Provincial Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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39
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Kurz S, Sheikh MO, Lu S, Wells L, Tiemeyer M. Separation and Identification of Permethylated Glycan Isomers by Reversed Phase NanoLC-NSI-MS n. Mol Cell Proteomics 2021; 20:100045. [PMID: 33376194 PMCID: PMC8724860 DOI: 10.1074/mcp.ra120.002266] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 01/18/2023] Open
Abstract
HPLC has been employed for decades to enhance detection sensitivity and quantification of complex analytes within biological mixtures. Among these analytes, glycans released from glycoproteins and glycolipids have been characterized as underivatized or fluorescently tagged derivatives by HPLC coupled to various detection methods. These approaches have proven extremely useful for profiling the structural diversity of glycoprotein and glycolipid glycosylation but require the availability of glycan standards and secondary orthogonal degradation strategies to validate structural assignments. A robust method for HPLC separation of glycans as their permethylated derivatives, coupled with in-line multidimensional ion fragmentation (MSn) to assign structural features independent of standards, would significantly enhance the depth of knowledge obtainable from biological samples. Here, we report an optimized workflow for LC-MS analysis of permethylated glycans that includes sample preparation, mobile phase optimization, and MSn method development to resolve structural isomers on-the-fly. We report baseline separation and MSn of isomeric N- and O-glycan structures, aided by supplementing mobile phases with Li+, which simplifies adduct heterogeneity and facilitates cross-ring fragmentation to obtain valuable monosaccharide linkage information. Our workflow has been adapted from standard proteomics-based workflows and, therefore, provides opportunities for laboratories with expertise in proteomics to acquire glycomic data with minimal deviation from existing buffer systems, chromatography media, and instrument configurations. Furthermore, our workflow does not require a mass spectrometer with high-resolution/accurate mass capabilities. The rapidly evolving appreciation of the biological significance of glycans for human health and disease requires the implementation of high-throughput methods to identify and quantify glycans harvested from sample sets of sufficient size to achieve appropriately powered statistical significance. The LC-MSn approach we report generates glycan isomeric separations and robust structural characterization and is amenable to autosampling with associated throughput enhancements.
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Affiliation(s)
- Simone Kurz
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - M Osman Sheikh
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Shan Lu
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
| | - Michael Tiemeyer
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
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40
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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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Habazin S, Štambuk J, Šimunović J, Keser T, Razdorov G, Novokmet M. Mass Spectrometry-Based Methods for Immunoglobulin G N-Glycosylation Analysis. EXPERIENTIA SUPPLEMENTUM (2012) 2021; 112:73-135. [PMID: 34687008 DOI: 10.1007/978-3-030-76912-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mass spectrometry and its hyphenated techniques enabled by the improvements in liquid chromatography, capillary electrophoresis, novel ionization, and fragmentation modes are truly a cornerstone of robust and reliable protein glycosylation analysis. Boost in immunoglobulin G (IgG) glycan and glycopeptide profiling demands for both applied biomedical and research applications has brought many new advances in the field in terms of technical innovations, sample preparation, improved throughput, and confidence in glycan structural characterization. This chapter summarizes mass spectrometry basics, focusing on IgG and monoclonal antibody N-glycosylation analysis on several complexity levels. Different approaches, including antibody enrichment, glycan release, labeling, and glycopeptide preparation and purification, are covered and illustrated with recent breakthroughs and examples from the literature omitting excessive theoretical frameworks. Finally, selected highly popular methodologies in IgG glycoanalytics such as liquid chromatography-mass spectrometry and matrix-assisted laser desorption ionization are discussed more thoroughly yet in simple terms making this text a practical starting point either for the beginner in the field or an experienced clinician trying to make sense out of the IgG glycomic or glycoproteomic dataset.
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Affiliation(s)
- Siniša Habazin
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | - Jerko Štambuk
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
| | | | - Toma Keser
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | | | - Mislav Novokmet
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia.
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Petrović T, Trbojević-Akmačić I. Lectin and Liquid Chromatography-Based Methods for Immunoglobulin (G) Glycosylation Analysis. EXPERIENTIA SUPPLEMENTUM (2012) 2021; 112:29-72. [PMID: 34687007 DOI: 10.1007/978-3-030-76912-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Immunoglobulin (Ig) glycosylation has been shown to dramatically affect its structure and effector functions. Ig glycosylation changes have been associated with different diseases and show a promising biomarker potential for diagnosis and prognosis of disease advancement. On the other hand, therapeutic biomolecules based on structural and functional features of Igs demand stringent quality control during the production process to ensure their safety and efficacy. Liquid chromatography (LC) and lectin-based methods are routinely used in Ig glycosylation analysis complementary to other analytical methods, e.g., mass spectrometry and capillary electrophoresis. This chapter covers analytical approaches based on LC and lectins used in low- and high-throughput N- and O-glycosylation analysis of Igs, with the focus on immunoglobulin G (IgG) applications. General principles and practical examples of the most often used LC methods for Ig purification are described, together with typical workflows for N- and O-glycan analysis on the level of free glycans, glycopeptides, subunits, or intact Igs. Lectin chromatography is a historical approach for the analysis of lectin-carbohydrate interactions and glycoprotein purification but is still being used as a valuable tool in Igs purification and glycan analysis. On the other hand, lectin microarrays have found their application in the rapid screening of glycan profiles on intact proteins.
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Affiliation(s)
- Tea Petrović
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
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43
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Gutierrez Reyes CD, Jiang P, Donohoo K, Atashi M, Mechref YS. Glycomics and glycoproteomics: Approaches to address isomeric separation of glycans and glycopeptides. J Sep Sci 2020; 44:403-425. [PMID: 33090644 DOI: 10.1002/jssc.202000878] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/29/2020] [Accepted: 10/06/2020] [Indexed: 11/11/2022]
Abstract
Changes in the glycome of human proteins and cells are associated with the progression of multiple diseases such as Alzheimer's, diabetes mellitus, many types of cancer, and those caused by viruses. Consequently, several studies have shown essential modifications to the isomeric glycan moieties for diseases in different stages. However, the elucidation of extensive isomeric glycan profiles remains challenging because of the lack of analytical techniques with sufficient resolution power to separate all glycan and glycopeptide iso-forms. Therefore, the development of sensitive and accurate approaches for the characterization of all the isomeric forms of glycans and glycopeptides is essential to tracking the progression of pathology in glycoprotein-related diseases. This review describes the isomeric separation achievements reported in glycomics and glycoproteomics in the last decade. It focuses on the mass spectrometry-based analytical strategies, stationary phases, and derivatization techniques that have been developed to enhance the separation mechanisms in liquid chromatography systems and the detection capabilities of mass spectrometry systems.
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Affiliation(s)
| | - Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Kaitlyn Donohoo
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Mojgan Atashi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Yehia S Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
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44
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Analysis of hyaluronan and its derivatives using chromatographic and mass spectrometric techniques. Carbohydr Polym 2020; 250:117014. [DOI: 10.1016/j.carbpol.2020.117014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/10/2020] [Accepted: 08/26/2020] [Indexed: 01/15/2023]
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45
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de Haan N, Wuhrer M, Ruhaak L. Mass spectrometry in clinical glycomics: The path from biomarker identification to clinical implementation. CLINICAL MASS SPECTROMETRY (DEL MAR, CALIF.) 2020; 18:1-12. [PMID: 34820521 PMCID: PMC8600986 DOI: 10.1016/j.clinms.2020.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 02/01/2023]
Abstract
Over the past decades, the genome and proteome have been widely explored for biomarker discovery and personalized medicine. However, there is still a large need for improved diagnostics and stratification strategies for a wide range of diseases. Post-translational modification of proteins by glycosylation affects protein structure and function, and glycosylation has been implicated in many prevalent human diseases. Numerous proteins for which the plasma levels are nowadays evaluated in clinical practice are glycoproteins. While the glycosylation of these proteins often changes with disease, their glycosylation status is largely ignored in the clinical setting. Hence, the implementation of glycomic markers in the clinic is still in its infancy. This is for a large part caused by the high complexity of protein glycosylation itself and of the analytical techniques required for their robust quantification. Mass spectrometry-based workflows are particularly suitable for the quantification of glycans and glycoproteins, but still require advances for their transformation from a biomedical research setting to a clinical laboratory. In this review, we describe why and how glycomics is expected to find its role in clinical tests and the status of current mass spectrometry-based methods for clinical glycomics.
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Affiliation(s)
- N. de Haan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - M. Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - L.R. Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
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46
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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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47
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Gautam S, Peng W, Cho BG, Huang Y, Banazadeh A, Yu A, Dong X, Mechref Y. Glucose unit index (GUI) of permethylated glycans for effective identification of glycans and glycan isomers. Analyst 2020; 145:6656-6667. [PMID: 32804173 PMCID: PMC7554265 DOI: 10.1039/d0an00314j] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Retention time is the most common and widely used criterion to report the separation of glycans using Liquid Chromatography (LC), but it varies widely across different columns, instruments and laboratories. This variation is problematic when inter-laboratory data is compared. Furthermore, it influences reproducibility and hampers efficient data interpretation. In our endeavor to overcome this variance, we propose the use of the Glucose Unit Index (GUI) on C18 and PGC column-based separation of reduced and permethylated glycans. GUI has previously been utilized for retention time normalization of native and labeled glycans. We evaluated this method with reduced and permethylated glycans derived from model glycoproteins fetuin and ribonuclease B (RNase B), and then implemented it to human blood serum to generate C18 and PGC column-based isomeric glycan libraries. GUI values for glycan compositions were calculated with respect to the glucose units derived from dextrin, which was employed as an elution standard. The GUI values were validated on three different LC systems (UltiMate 3000 Nano UHPLC systems) in two laboratories to ensure the reliability and reproducibility of the method. Applicability on real samples was demonstrated using human breast cancer cell lines. A total of 116 permethylated N-glycans separated on a C18 column and 134 glycans separated on a PGC column were compiled in a library. Overall, the established GUI method and the demonstration of reproducible inter- and intra-laboratory GUI values would aid the future development of automated glycan and isomeric glycan identification methods.
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Affiliation(s)
- Sakshi Gautam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA.
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48
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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: 31] [Impact Index Per Article: 7.8] [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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49
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Wei J, Tang Y, Ridgeway ME, Park MA, Costello CE, Lin C. Accurate Identification of Isomeric Glycans by Trapped Ion Mobility Spectrometry-Electronic Excitation Dissociation Tandem Mass Spectrometry. Anal Chem 2020; 92:13211-13220. [PMID: 32865981 DOI: 10.1021/acs.analchem.0c02374] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Ion mobility-mass spectrometry (IM-MS) has become a powerful tool for glycan structural characterization due to its ability to separate isomers and provide collision cross section (CCS) values that facilitate structural assignment. However, IM-based isomer analysis may be complicated by the presence of multiple gas-phase conformations of a single structure that not only increases difficulty in isomer separation but can also introduce the possibility for misinterpretation of conformers as isomers. Here, the ion mobility behavior of several sets of isomeric glycans, analyzed as their permethylated derivatives, in both nonreduced and reduced forms, was investigated by gated-trapped ion mobility spectrometry (G-TIMS). Notably, reducing-end reduction, commonly performed to remove anomerism-induced chromatographic peak splitting, did not eliminate the conformational heterogeneity of permethylated glycans in the gas phase. At a mobility resolving power of ∼100, 14 out of 22 structures showed more than one conformation. These results highlight the need to use IMS devices with high mobility resolving power for better separation of isomers and to acquire additional structural information that can differentiate isomers from conformers. Online electronic excitation dissociation (EED) MS/MS analysis of isomeric glycan mixtures following G-TIMS separation showed that EED can generate isomer-specific fragments while producing nearly identical tandem mass spectra for conformers, thus allowing confident identification of isomers with minimal evidence of any ambiguity resulting from the presence of conformers. G-TIMS EED MS/MS analysis of N-linked glycans released from ovalbumin revealed that several mobility features previously thought to arise from isomeric structures were conformers of a single structure. Finally, analysis of ovalbumin N-glycans from different sources showed that the G-TIMS EED MS/MS approach can accurately determine the batch-to-batch variations in glycosylation profiles at the isomer level, with confident assignment of each isomeric structure.
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Affiliation(s)
- Juan Wei
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States
| | - Yang Tang
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States.,Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Mark E Ridgeway
- Bruker Daltonics, Billerica, Massachusetts 01821, United States
| | - Melvin A Park
- Bruker Daltonics, Billerica, Massachusetts 01821, United States
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States.,Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States
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50
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Illiano A, Pinto G, Melchiorre C, Carpentieri A, Faraco V, Amoresano A. Protein Glycosylation Investigated by Mass Spectrometry: An Overview. Cells 2020; 9:E1986. [PMID: 32872358 PMCID: PMC7564411 DOI: 10.3390/cells9091986] [Citation(s) in RCA: 36] [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: 07/09/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022] Open
Abstract
The protein glycosylation is a post-translational modification of crucial importance for its involvement in molecular recognition, protein trafficking, regulation, and inflammation. Indeed, abnormalities in protein glycosylation are correlated with several disease states such as cancer, inflammatory diseases, and congenial disorders. The understanding of cellular mechanisms through the elucidation of glycan composition encourages researchers to find analytical solutions for their detection. Actually, the multiplicity and diversity of glycan structures bond to the proteins, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies make their detection much trickier than other kinds of biopolymers. An overview of the most prominent techniques based on mass spectrometry (MS) for protein glycosylation (glycoproteomics) studies is here presented. The tricks and pre-treatments of samples are discussed as a crucial step prodromal to the MS analysis to improve the glycan ionization efficiency. Therefore, the different instrumental MS mode is also explored for the qualitative and quantitative analysis of glycopeptides and the glycans structural composition, thus contributing to the elucidation of biological mechanisms.
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Affiliation(s)
- Anna Illiano
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 26, 80126 Napoles, Italy; (A.I.); (G.P.); (C.M.); (A.C.); (A.A.)
- CEINGE Advanced Biotechnology, University of Naples Federico II, Via Cinthia 26, 80126 Napoles, Italy
| | - Gabriella Pinto
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 26, 80126 Napoles, Italy; (A.I.); (G.P.); (C.M.); (A.C.); (A.A.)
| | - Chiara Melchiorre
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 26, 80126 Napoles, Italy; (A.I.); (G.P.); (C.M.); (A.C.); (A.A.)
| | - Andrea Carpentieri
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 26, 80126 Napoles, Italy; (A.I.); (G.P.); (C.M.); (A.C.); (A.A.)
| | - Vincenza Faraco
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 26, 80126 Napoles, Italy; (A.I.); (G.P.); (C.M.); (A.C.); (A.A.)
| | - Angela Amoresano
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 26, 80126 Napoles, Italy; (A.I.); (G.P.); (C.M.); (A.C.); (A.A.)
- Istituto Nazionale Biostrutture e Biosistemi—Consorzio Interuniversitario, Viale delle Medaglie d’Oro, 305, 00136 Rome, Italy
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