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Wang Y, Zhang P, Luo Z, Huang C. Insights into the role of glycosyltransferase in the targeted treatment of gastric cancer. Biomed Pharmacother 2024; 178:117194. [PMID: 39137647 DOI: 10.1016/j.biopha.2024.117194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/15/2024] [Accepted: 07/22/2024] [Indexed: 08/15/2024] Open
Abstract
Gastric cancer is a remarkably heterogeneous tumor. Despite some advances in the diagnosis and treatment of gastric cancer in recent years, the precise treatment and curative outcomes remain unsatisfactory. Poor prognosis continues to pose a major challenge in gastric cancer. Therefore, it is imperative to identify effective targets to improve the treatment and prognosis of gastric cancer patients. It should be noted that glycosylation, a novel form of posttranslational modification, is a process capable of regulating protein function and influencing cellular activities. Currently, numerous studies have shown that glycosylation plays vital roles in the occurrence and progression of gastric cancer. As crucial enzymes that regulate glycan synthesis in glycosylation processes, glycosyltransferases are potential targets for treating GC. Hence, investigating the regulation of glycosyltransferases and the expression of associated proteins in gastric cancer cells is highly important. In this review, the related glycosyltransferases and their related signaling pathways in gastric cancer, as well as the existing inhibitors of glycosyltransferases, provide more possibilities for targeted therapies for gastric cancer.
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Affiliation(s)
- Yueling Wang
- Wuxi School of Medicine, Jiangnan University, Wuxi 214028, China; Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Pengshan Zhang
- Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Zai Luo
- Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Chen Huang
- Wuxi School of Medicine, Jiangnan University, Wuxi 214028, China; Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China.
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Brockmöller S, Seeger T, Worek F, Rothmiller S. Cell-Sonar, a Novel Method for Intracellular Tracking of Secretory Pathways. Cells 2024; 13:1449. [PMID: 39273021 PMCID: PMC11394445 DOI: 10.3390/cells13171449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/14/2024] [Accepted: 08/26/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND Intracellular tracking is commonly used in trafficking research. Until today, the respective techniques have remained complex, and complicated, mostly transgenic target protein changes are necessary, often requiring expensive equipment and expert knowledge. METHODS We present a novel method, which we term "cell-sonar", that enables the user to track expression changes of specific protein markers that serve as points of interaction. Our study provides comparable analyses of expression changes of these marker proteins by in-cell Western analyses in two otherwise isogenic cell lines that only differ in the overexpression of the tracked target protein. Using the overexpressed human adult muscle-type nicotinic acetylcholine receptor as an example, we demonstrate that cell-sonar can cover multiple intracellular compartments such as the endoplasmic reticulum, the pathway between it and the Golgi apparatus, and the endocytic pathway. RESULTS We provide evidence for receptor maturation in the Golgi and storage in recycling endosomes, rather than the fate of increased insertion into the plasma membrane. Additionally, we demonstrate with the implementation of nicotine that the receptor's destiny is exasperated up to secondary degradation. CONCLUSIONS Cell-sonar is an affordable, easy-to-implement, and cheap method that can be adapted to a broad variety of proteins and cellular pathways of interest to researchers.
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Affiliation(s)
- Sabrina Brockmöller
- Bundeswehr Institute of Pharmacology and Toxicology, 80937 Munich, Bavaria, Germany
| | - Thomas Seeger
- Bundeswehr Institute of Pharmacology and Toxicology, 80937 Munich, Bavaria, Germany
| | - Franz Worek
- Bundeswehr Institute of Pharmacology and Toxicology, 80937 Munich, Bavaria, Germany
| | - Simone Rothmiller
- Bundeswehr Institute of Pharmacology and Toxicology, 80937 Munich, Bavaria, Germany
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3
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Kim KS, Lee JS, Park JH, Lee EY, Moon JS, Lee SK, Lee JS, Kim JH, Kim HS. Identification of Novel Biomarker for Early Detection of Diabetic Nephropathy. Biomedicines 2021; 9:biomedicines9050457. [PMID: 33922243 PMCID: PMC8146473 DOI: 10.3390/biomedicines9050457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/23/2022] Open
Abstract
Diabetic nephropathy (DN) is one of the most common complications of diabetes mellitus. After development of DN, patients will progress to end-stage renal disease, which is associated with high morbidity and mortality. Here, we developed early-stage diagnostic biomarkers to detect DN as a strategy for DN intervention. For the DN model, Zucker diabetic fatty rats were used for DN phenotyping. The results revealed that DN rats showed significantly increased blood glucose, blood urea nitrogen (BUN), and serum creatinine levels, accompanied by severe kidney injury, fibrosis and microstructural changes. In addition, DN rats showed significantly increased urinary excretion of kidney injury molecule-1 (KIM-1) and neutrophil gelatinase-associated lipocalin (NGAL). Transcriptome analysis revealed that new DN biomarkers, such as complementary component 4b (C4b), complementary factor D (CFD), C-X-C motif chemokine receptor 6 (CXCR6), and leukemia inhibitory factor (LIF) were identified. Furthermore, they were found in the urine of patients with DN. Since these biomarkers were detected in the urine and kidney of DN rats and urine of diabetic patients, the selected markers could be used as early diagnosis biomarkers for chronic diabetic nephropathy.
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Affiliation(s)
- Kyeong-Seok Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (K.-S.K.); (J.-S.L.); (J.-H.P.)
- Department of Pharmacology, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju 52727, Korea
| | - Jin-Sol Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (K.-S.K.); (J.-S.L.); (J.-H.P.)
| | - Jae-Hyeon Park
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (K.-S.K.); (J.-S.L.); (J.-H.P.)
| | - Eun-Young Lee
- Department of Internal Medicine, Soonchunhyang University Cheonan Hospital, Cheonan 31151, Korea;
- BK21 Four Project, College of Medicine, Soonchunhyang University, Cheonan 31151, Korea
- Institute of Tissue Regeneration, College of Medicine, Soonchunhyang University, Cheonan 31151, Korea
| | - Jong-Seok Moon
- Department of Integrated Biomedical Science, Soonchunhyang Institute of Medi-Bio Science, Soonchunhyang University, Cheonan 31151, Korea;
| | - Sang-Kyu Lee
- BK21 Plus KNU Multi-Omics Based Creative Drug Research Team, College of Pharmacy, Kyungpook National University, Daegu 41566, Korea;
| | - Jong-Sil Lee
- Department of Pathology, Institute of Health Sciences, College of Medicine, Gyeongsang National University Hospital, Jinju 52727, Korea;
| | - Jung-Hwan Kim
- Department of Pharmacology, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju 52727, Korea
- Department of Convergence Medical Science, Gyeongsang National University, Jinju 52727, Korea
- Correspondence: (J.-H.K.); (H.-S.K.); Tel.: +82-55-772-8072 (J.-H.K.); +82-31-290-7789 (H.-S.K.)
| | - Hyung-Sik Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea; (K.-S.K.); (J.-S.L.); (J.-H.P.)
- Correspondence: (J.-H.K.); (H.-S.K.); Tel.: +82-55-772-8072 (J.-H.K.); +82-31-290-7789 (H.-S.K.)
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Přerovská T, Henke S, Bleha R, Spiwok V, Gillarová S, Yvin JC, Ferrières V, Nguema-Ona E, Lipovová P. Arabinogalactan-like Glycoproteins from Ulva lactuca (Chlorophyta) Show Unique Features Compared to Land Plants AGPs. JOURNAL OF PHYCOLOGY 2021; 57:619-635. [PMID: 33338254 DOI: 10.1111/jpy.13121] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 05/21/2023]
Abstract
Arabinogalactan proteins (AGPs) encompass a diverse group of plant cell wall proteoglycans, which play an essential role in plant development, signaling, plant-microbe interactions, and many others. Although they are widely distributed throughout the plant kingdom and extensively studied, they remain largely unexplored in the lower plants, especially in seaweeds. Ulva species have high economic potential since various applications were previously described including bioremediation, biofuel production, and as a source of bioactive compounds. This article presents the first experimental confirmation of AGP-like glycoproteins in Ulva species and provides a simple extraction protocol of Ulva lactuca AGP-like glycoproteins, their partial characterization and unique comparison to scarcely described Solanum lycopersicum AGPs. The reactivity with primary anti-AGP antibodies as well as Yariv reagent showed a great variety between Ulva lactuca and Solanum lycopersicum AGP-like glycoproteins. While the amino acid analysis of the AGP-like glycoproteins purified by the β-d-glucosyl Yariv reagent showed a similarity between algal and land plant AGP-like glycoproteins, neutral saccharide analysis revealed unique glycosylation of the Ulva lactuca AGP-like glycoproteins. Surprisingly, arabinose and galactose were not the most prevalent monosaccharides and the most outstanding was the presence of 3-O-methyl-hexose, which has never been described in the AGPs. The exceptional structure of the Ulva lactuca AGP-like glycoproteins implies a specialized adaptation to the marine environment and might bring new insight into the evolution of the plant cell wall.
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Affiliation(s)
- Tereza Přerovská
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 3, Prague, 16625, Czech Republic
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, Univ Rennes, 35000, Rennes, France
| | - Svatopluk Henke
- Department of Carbohydrates and Cerials, University of Chemistry and Technology Prague, Technická 3, Prague, 16625, Czech Republic
| | - Roman Bleha
- Department of Carbohydrates and Cerials, University of Chemistry and Technology Prague, Technická 3, Prague, 16625, Czech Republic
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 3, Prague, 16625, Czech Republic
| | - Simona Gillarová
- Department of Carbohydrates and Cerials, University of Chemistry and Technology Prague, Technická 3, Prague, 16625, Czech Republic
| | - Jean-Claude Yvin
- Centre Mondial de l'Innovation Roullier, Laboratoire de Nutrition Végétal, 18 Avenue Franklin Roosevelt, Saint-Malo, 35400, France
| | - Vincent Ferrières
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, Univ Rennes, 35000, Rennes, France
| | - Eric Nguema-Ona
- Centre Mondial de l'Innovation Roullier, Laboratoire de Nutrition Végétal, 18 Avenue Franklin Roosevelt, Saint-Malo, 35400, France
| | - Petra Lipovová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 3, Prague, 16625, Czech Republic
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Ahangarpour M, Kavianinia I, Harris PWR, Brimble MA. Photo-induced radical thiol-ene chemistry: a versatile toolbox for peptide-based drug design. Chem Soc Rev 2021; 50:898-944. [PMID: 33404559 DOI: 10.1039/d0cs00354a] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While the global market for peptide/protein-based therapeutics is witnessing significant growth, the development of peptide drugs remains challenging due to their low oral bioavailability, poor membrane permeability, and reduced metabolic stability. However, a toolbox of chemical approaches has been explored for peptide modification to overcome these obstacles. In recent years, there has been a revival of interest in photoinduced radical thiol-ene chemistry as a powerful tool for the construction of therapeutic peptides.
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Affiliation(s)
- Marzieh Ahangarpour
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand.
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Gana R, Vasudevan S. Ridge regression estimated linear probability model predictions of O-glycosylation in proteins with structural and sequence data. BMC Mol Cell Biol 2019; 20:21. [PMID: 31253080 PMCID: PMC6599295 DOI: 10.1186/s12860-019-0200-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/27/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND To-date, no claim regarding finding a consensus sequon for O-glycosylation has been made. Thus, predicting the likelihood of O-glycosylation with sequence and structural information using classical regression analysis is quite difficult. In particular, if a binary response is used to distinguish between O-glycosylated and non-O-glycosylated sequences, an appropriate set of non-O-glycosylatable sequences is hard to find. RESULTS Three sequences from similar post-translational modifications (PTMs) of proteins occurring at, or very near, the S/T-site are analyzed: N-glycosylation, O-mucin type (O-GalNAc) glycosylation, and phosphorylation. Results found include: 1) The consensus composite sequon for O-glycosylation is: ~(W-S/T-W), where "~" denotes the "not" operator. 2) The consensus sequon for phosphorylation is ~(W-S/T/Y/H-W); although W-S/T/Y/H-W is not an absolute inhibitor of phosphorylation. 3) For linear probability model (LPM) estimation, N-glycosylated sequences are good approximations to non-O-glycosylatable sequences; although N - ~P - S/T is not an absolute inhibitor of O-glycosylation. 4) The selective positioning of an amino acid along the sequence, differentiates the PTMs of proteins. 5) Some N-glycosylated sequences are also phosphorylated at the S/T-site in the N - ~P - S/T sequon. 6) ASA values for N-glycosylated sequences are stochastically larger than those for O-GlcNAc glycosylated sequences. 7) Structural attributes (beta turn II, II´, helix, beta bridges, beta hairpin, and the phi angle) are significant LPM predictors of O-GlcNAc glycosylation. The LPM with sequence and structural data as explanatory variables yields a Kolmogorov-Smirnov (KS) statistic of 99%. 8) With only sequence data, the KS statistic erodes to 80%, and 21% of out-of-sample O-GlcNAc glycosylated sequences are mispredicted as not being glycosylated. The 95% confidence interval around this mispredictions rate is 16% to 26%. CONCLUSIONS The data indicates the existence of a consensus sequon for O-glycosylation; and underscores the germaneness of structural information for predicting the likelihood of O-glycosylation.
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Affiliation(s)
- Rajaram Gana
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington D.C, USA.
| | - Sona Vasudevan
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington D.C, USA.
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7
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Ressler VT, Raines RT. Consequences of the Endogenous N-Glycosylation of Human Ribonuclease 1. Biochemistry 2019; 58:987-996. [PMID: 30633504 DOI: 10.1021/acs.biochem.8b01246] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribonuclease 1 (RNase 1) is the most prevalent human homologue of the archetypal enzyme RNase A. RNase 1 contains sequons for N-linked glycosylation at Asn34, Asn76, and Asn88 and is N-glycosylated at all three sites in vivo. The effect of N-glycosylation on the structure and function of RNase 1 is unknown. By using an engineered strain of the yeast Pichia pastoris, we installed a heptasaccharide (Man5GlcNAc2) on the side chain of Asn34, Asn76, and Asn88 to produce the authentic triglycosylated form of human RNase 1. As a glutamine residue is not a substrate for cellular oligosaccharyltransferase, we used strategic asparagine-to-glutamine substitutions to produce the three diglycosylated and three monoglycosylated forms of RNase 1. We found that the N-glycosylation of RNase 1 at any position attenuates its catalytic activity but enhances both its thermostability and its resistance to proteolysis. N-Glycosylation at Asn34 generates the most active and stable glycoforms, in accord with its sequon being highly conserved among vertebrate species. These data provide new insight on the biological role of the N-glycosylation of a human secretory enzyme.
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Affiliation(s)
- Valerie T Ressler
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Ronald T Raines
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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8
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Yang H, Yang C, Sun T. Characterization of glycopeptides using a stepped higher-energy C-trap dissociation approach on a hybrid quadrupole orbitrap. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1353-1362. [PMID: 29873418 DOI: 10.1002/rcm.8191] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/23/2018] [Accepted: 05/28/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Accurate characterization of glycopeptides without a prior glycan cleavage could provide valuable information on site-specific glycosylation, which is critical to reveal the biological functions of protein glycosylation. However, due to the distinct nature of oligosaccharides and ploypeptides, it is usually difficult to effectively fragment glycopeptides in mass spectrometry analysis. METHODS Here we applied a stepped normalized collisional energy (NCE) approach, which is able to combine fragment ions from three different collision energies, in a hybrid quadrupole orbitrap (Q Exactive Plus) to characterize glycopeptides. A systematic evaluation was firstly performed to find optimal NCE values for the fragmentation of glycan chains and peptide backbones from glycopeptides. Guided by the results of the systematic evaluation, the stepped NCE method was optimized and employed to analyze glycopeptides enriched from human serum. RESULTS The stepped NCE approach was found to effectively fragment both the glycan chains and peptide backbones from glycopeptides and record these fragments in a single MS/MS spectrum. In comparison with the regular HCD methods, the stepped NCE method identified more glycopeptides with higher scores from human serum samples. CONCLUSIONS Our studies demonstrate the capability of stepped NCE for the effective characterization of glycopeptides on a large scale.
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Affiliation(s)
- Hong Yang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China
| | - Chenxi Yang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, China
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9
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Saraswat M, Mäkitie A, Tohmola T, Dickinson A, Saraswat S, Joenväärä S, Renkonen S. Tongue Cancer Patients Can be Distinguished from Healthy Controls by Specific N-Glycopeptides Found in Serum. Proteomics Clin Appl 2018; 12:e1800061. [PMID: 29992770 DOI: 10.1002/prca.201800061] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/28/2018] [Indexed: 12/14/2022]
Abstract
PURPOSE There are no blood biomarkers to detect early-stage oral cavity squamous cell carcinoma (OSCC) prior to clinical signs. Most OSCC incidence is associated with significant morbidity and poor survival. The authors aimed to use mass-spectrometry (MS) technology to find specific N-glycopeptides potentially serving as serum biomarkers for preclinical OSCC screening. EXPERIMENTAL DESIGN Serum samples from 14 patients treated for OSCC (stage I or stage IV) with 12 age- and sex-matched controls are collected. Quantitative label-free N-glycoproteomics is performed, with MS/MS analysis of the statistically significantly different N-glycopeptides. RESULTS Combined with a database search using web-based software (GlycopeptideID), MS/MS provided detailed N-glycopeptide information, including glycosylation site, glycan composition, and proposed structures. Thirty-eight tryptic N-glycopeptides are identified, having 19 unique N-glycosylation sites representing 14 glycoproteins. OSCC patients, including stage I tumors, can be differentiated from healthy controls based on the expression levels of these glycoforms. N-glycopeptides of IgG1, IgG4, haptoglobin, and transferrin have statistically significant different abundances between cases and controls. CONCLUSIONS AND CLINICAL RELEVANCE The authors are the first to suggest specific N-glycopeptides to serve as potential serum biomarkers to detect preclinical OSCC in patients. These N-glycopeptides are the lead candidates for validation as future diagnostic modalities of OSCC as early as stage I.
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Affiliation(s)
- Mayank Saraswat
- Transplantation Laboratory, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, 00014, Helsinki, Finland.,Hospital District of Helsinki and Uusimaa Laboratory, Helsinki University Hospital, 00290, Helsinki, Finland
| | - Antti Mäkitie
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, 00130, Helsinki, Finland.,Division of Ear, Nose and Throat Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet and Karolinska Hospital, 11382, Stockholm, Sweden
| | - Tiialotta Tohmola
- Transplantation Laboratory, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, 00014, Helsinki, Finland.,Department of Biosciences, University of Helsinki, P.O. Box 65, 00014, Helsinki, Finland
| | - Amy Dickinson
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, 00130, Helsinki, Finland
| | - Shruti Saraswat
- Transplantation Laboratory, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, 00014, Helsinki, Finland
| | - Sakari Joenväärä
- Transplantation Laboratory, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, 00014, Helsinki, Finland.,Hospital District of Helsinki and Uusimaa Laboratory, Helsinki University Hospital, 00290, Helsinki, Finland
| | - Suvi Renkonen
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, 00130, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, 11382, Stockholm, Sweden
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Mookherjee A, Guttman M. Bridging the structural gap of glycoproteomics with ion mobility spectrometry. Curr Opin Chem Biol 2018; 42:86-92. [DOI: 10.1016/j.cbpa.2017.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/17/2017] [Accepted: 11/21/2017] [Indexed: 12/31/2022]
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11
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Adua E, Russell A, Roberts P, Wang Y, Song M, Wang W. Innovation Analysis on Postgenomic Biomarkers: Glycomics for Chronic Diseases. ACTA ACUST UNITED AC 2017; 21:183-196. [DOI: 10.1089/omi.2017.0035] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Eric Adua
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Alyce Russell
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Peter Roberts
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Manshu Song
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Wei Wang
- School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
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Chaffey PK, Guan X, Wang LX, Tan Z. Introduction: General Aspects of the Chemical Biology of Glycoproteins. CHEMICAL BIOLOGY OF GLYCOPROTEINS 2017. [DOI: 10.1039/9781782623823-00001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This chapter is meant to serve as an introduction to the remainder of the book by providing general background on the chemical biology of glycoproteins as well as a brief review of the chapters that follow. The purpose here is to introduce some basic concepts common to many forms of glycosylation for those readers who may be unfamiliar with the field. We begin with a discussion of the strategies and methods used to study protein glycosylation. During the overview, an effort is made to highlight a few relevant aspects of chemical glycobiology, including glycoprotein biosynthesis and a brief description of the synthesis and function of glycoproteins. Finally, we have a summary of the contributions from chemical biology over the years. It is our hope that, after reading this introductory chapter, the reader will have a broad view of the chemical glycobiology field as it currently stands and a deeper appreciation for some of the unique ideas that chemical biology brings to the field.
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Affiliation(s)
- Patrick K. Chaffey
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder CO 80303 USA
| | - Xiaoyang Guan
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder CO 80303 USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland College Park MD 20742 USA
| | - Zhongping Tan
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder CO 80303 USA
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13
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Strmečki S, Trefulka M, Zatloukalová P, Durech M, Vojtesek B, Paleček E. Immunoassays of chemically modified polysaccharides, glycans in glycoproteins and ribose in nucleic acids. Anal Chim Acta 2016; 955:108-115. [PMID: 28088277 DOI: 10.1016/j.aca.2016.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 12/08/2016] [Accepted: 12/16/2016] [Indexed: 01/23/2023]
Abstract
Glycosylation of proteins plays an important role in health and diseases. At present new simple and inexpensive methods of glycoprotein analysis are sought. We developed a monoclonal antibody Manost 2.1 in mice after immunization with the adduct of mannan with Os(VI)temed complex (temed is N,N,N',N'-tetramethylethylenediamine). The specificity of this antibody to different biomolecules treated with Os(VI)temed was tested using dot blot immunoassay. Manost 2.1 showed specificity toward Os(VI)temed-modified polysaccharides, glycoproteins and ribonucleotide at the 3'-end in DNA. The antibody recognized neither the unmodified compounds nor the non-glycosylated proteins treated with Os(VI)temed. We also performed western blotting and Coomassie silver blue staining of mixtures of biomacromolecules treated with Os(VI)temed and identified specifically the modified glycoproteins. The immunochemical method using Manost 2.1 was compared with electrochemical analyses based on redox signals of the Os(VI)temed adducts, with similar results in terms of sensitivity. This new antibody-based approach opens the door for rapid and inexpensive analysis of glycans and glycoproteins in various scientific and medical fields, including cancer research and the future application of glycoprotein detection in clinical practice.
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Affiliation(s)
- Slađana Strmečki
- Institute of Biophysics, Academy of the Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612 65 Brno, Czechia
| | - Mojmír Trefulka
- Institute of Biophysics, Academy of the Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612 65 Brno, Czechia
| | - Pavlína Zatloukalová
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Žluty kopec 7, 656 53 Brno, Czechia
| | - Michal Durech
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Žluty kopec 7, 656 53 Brno, Czechia
| | - Borivoj Vojtesek
- Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Žluty kopec 7, 656 53 Brno, Czechia
| | - Emil Paleček
- Institute of Biophysics, Academy of the Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612 65 Brno, Czechia; Masaryk Memorial Cancer Institute, Regional Centre for Applied Molecular Oncology, Žluty kopec 7, 656 53 Brno, Czechia.
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14
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Woo CM, Felix A, Zhang L, Elias JE, Bertozzi CR. Isotope-targeted glycoproteomics (IsoTaG) analysis of sialylated N- and O-glycopeptides on an Orbitrap Fusion Tribrid using azido and alkynyl sugars. Anal Bioanal Chem 2016; 409:579-588. [PMID: 27695962 DOI: 10.1007/s00216-016-9934-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/30/2016] [Accepted: 09/08/2016] [Indexed: 12/18/2022]
Abstract
Protein glycosylation is a post-translational modification (PTM) responsible for many aspects of proteomic diversity and biological regulation. Assignment of intact glycan structures to specific protein attachment sites is a critical step towards elucidating the function encoded in the glycome. Previously, we developed isotope-targeted glycoproteomics (IsoTaG) as a mass-independent mass spectrometry method to characterize azide-labeled intact glycopeptides from complex proteomes. Here, we extend the IsoTaG approach with the use of alkynyl sugars as metabolic labels and employ new probes in analysis of the sialylated glycoproteome from PC-3 cells. Using an Orbitrap Fusion Tribrid mass spectrometer, we identified 699 intact glycopeptides from 192 glycoproteins. These intact glycopeptides represent a total of eight sialylated glycan structures across 126 N- and 576 O-glycopeptides. IsoTaG is therefore an effective platform for identification of intact glycopeptides labeled by alkynyl or azido sugars and will facilitate further studies of the glycoproteome.
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Affiliation(s)
- Christina M Woo
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Alejandra Felix
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Lichao Zhang
- Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA
| | - Joshua E Elias
- Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA. .,Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA.
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15
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Abstract
Detailed structural elucidation of protein glycosylation is a tedious process often involving several techniques. Glycomics and glycoproteomics approaches with mass spectrometry offer a rapid platform for glycan profiling but are limited by the inability to resolve isobaric species such as linkage and positional isomers. Recently, ion mobility spectrometry (IMS) has been shown to effectively resolve isobaric oligosaccharides, but the utility of IMS to obtain glycan structural information on a site-specific level with proteomic analyses has yet to be investigated. Here, we report that the addition of IMS to conventional glycoproteomics platforms adds additional information regarding glycan structure and is particularly useful for differentiation of sialic acid linkage isomers on both N- and O-linked glycopeptides. With further development IMS may hold the potential for rapid and complete structural elucidation of glycan chains at a site-specific level.
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Affiliation(s)
- Miklos Guttman
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195, United States
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16
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Quality and Batch-to-Batch Consistency of Original and Biosimilar Epoetin Products. J Pharm Sci 2016; 105:542-550. [DOI: 10.1016/j.xphs.2015.10.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 09/24/2015] [Accepted: 10/09/2015] [Indexed: 12/19/2022]
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17
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Plasma Glycoproteomics Reveals Sepsis Outcomes Linked to Distinct Proteins in Common Pathways. Crit Care Med 2015; 43:2049-2058. [PMID: 26086942 DOI: 10.1097/ccm.0000000000001134] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Sepsis remains a predominant cause of mortality in the ICU, yet strategies to increase survival have proved largely unsuccessful. This study aimed to identify proteins linked to sepsis outcomes using a glycoproteomic approach to target extracellular proteins that trigger downstream pathways and direct patient outcomes. DESIGN Plasma was obtained from the Lactate Assessment in the Treatment of Early Sepsis cohort. N-linked plasma glycopeptides were quantified by solid-phase extraction coupled with mass spectrometry. Glycopeptides were assigned to proteins using RefSeq (National Center of Biotechnology Information, Bethesda, MD) and visualized in a heat map. Protein differences were validated by immunoblotting, and proteins were mapped for biological processes using Database for Annotation, Visualization and Integrated Discovery (National Institute of Allergy and Infectious Diseases, National Institutes of Health; Bethesda, MD) and for functional pathways using Kyoto Encyclopedia of Genes and Genomes (Kanehisa Laboratories, Kyoto, Japan) databases. SETTING Hospitalized care. PATIENTS Patients admitted to the emergency department were enrolled in the study when the diagnosis of sepsis was made, within 6 hours of presentation. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS A total of 501 glycopeptides corresponding to 234 proteins were identified. Of these, 66 glycopeptides were unique to the survivor group and corresponded to 54 proteins, 60 were unique to the nonsurvivor group and corresponded to 43 proteins, and 375 were common responses between groups and corresponded to 137 proteins. Immunoblotting showed that nonsurvivors had increased total kininogen; decreased total cathepsin-L1, vascular cell adhesion molecule, periostin, and neutrophil gelatinase-associated lipocalin; and a two-fold decrease in glycosylated clusterin (all p < 0.05). Kyoto Encyclopedia of Genes and Genomes analysis identified six enriched pathways. Interestingly, survivors relied on the extrinsic pathway of the complement and coagulation cascade, whereas nonsurvivors relied on the intrinsic pathway. CONCLUSION This study identifies proteins linked to patient outcomes and provides insight into unexplored mechanisms that can be investigated for the identification of novel therapeutic targets.
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18
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Pihíková D, Belicky Š, Kasák P, Bertok T, Tkac J. Sensitive detection and glycoprofiling of a prostate specific antigen using impedimetric assays. Analyst 2015; 141:1044-51. [PMID: 26647853 DOI: 10.1039/c5an02322j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This study presents a proof-of-concept for the development of an impedimetric biosensor for ultra-sensitive glycoprofiling of prostate specific antigen (PSA). The biosensor exhibits three unique characteristics: (1) analysis of PSA with limit of detection (LOD) down to 4 aM; (2) analysis of the glycan part of PSA with LOD down to 4 aM level and; (3) both assays (i.e., PSA quantification and PSA glycoprofiling) can be performed on the same interface due to label-free analysis.
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Affiliation(s)
- D Pihíková
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava, 845 38, Slovak Republic.
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19
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Daubenspeck JM, Jordan DS, Simmons W, Renfrow MB, Dybvig K. General N-and O-Linked Glycosylation of Lipoproteins in Mycoplasmas and Role of Exogenous Oligosaccharide. PLoS One 2015; 10:e0143362. [PMID: 26599081 PMCID: PMC4657876 DOI: 10.1371/journal.pone.0143362] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/03/2015] [Indexed: 12/21/2022] Open
Abstract
The lack of a cell wall, flagella, fimbria, and other extracellular appendages and the possession of only a single membrane render the mycoplasmas structurally simplistic and ideal model organisms for the study of glycoconjugates. Most species have genomes of about 800 kb and code for few proteins predicted to have a role in glycobiology. The murine pathogens Mycoplasma arthritidis and Mycoplasma pulmonis have only a single gene annotated as coding for a glycosyltransferase but synthesize glycolipid, polysaccharide and glycoproteins. Previously, it was shown that M. arthritidis glycosylated surface lipoproteins through O-linkage. In the current study, O-linked glycoproteins were similarly found in M. pulmonis and both species of mycoplasma were found to also possess N-linked glycans at residues of asparagine and glutamine. Protein glycosylation occurred at numerous sites on surface-exposed lipoproteins with no apparent amino acid sequence specificity. The lipoproteins of Mycoplasma pneumoniae also are glycosylated. Glycosylation was dependent on the glycosidic linkages from host oligosaccharides. As far as we are aware, N-linked glycoproteins have not been previously described in Gram-positive bacteria, the organisms to which the mycoplasmas are phylogenetically related. The findings indicate that the mycoplasma cell surface is heavily glycosylated with implications for the modulation of mycoplasma-host interactions.
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Affiliation(s)
- James M. Daubenspeck
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - David S. Jordan
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Warren Simmons
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Matthew B. Renfrow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Kevin Dybvig
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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20
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Agniel R, Vendrely C, Poulouin L, Bascetin R, Benachour H, Gallet O, Leroy-Dudal J. Lectins as probes for assessing the accessibility ofN-linked glycans in relation to the conformational changes of fibronectin. J Mol Recognit 2015; 28:731-41. [DOI: 10.1002/jmr.2487] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Rémy Agniel
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122); Université de Cergy-Pontoise, F-95000 Cergy-Pontoise; 2 Avenue Adolphe Chauvin Cergy-Pontoise Cedex 95302 France
| | - Charlotte Vendrely
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122); Université de Cergy-Pontoise, F-95000 Cergy-Pontoise; 2 Avenue Adolphe Chauvin Cergy-Pontoise Cedex 95302 France
| | - Laurent Poulouin
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122); Université de Cergy-Pontoise, F-95000 Cergy-Pontoise; 2 Avenue Adolphe Chauvin Cergy-Pontoise Cedex 95302 France
- Orange; Direction Nord de France; 2 rue Trémière Villeneuve d'Ascq F-59650 France
| | - Rümeyza Bascetin
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122); Université de Cergy-Pontoise, F-95000 Cergy-Pontoise; 2 Avenue Adolphe Chauvin Cergy-Pontoise Cedex 95302 France
| | - Hamanou Benachour
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122); Université de Cergy-Pontoise, F-95000 Cergy-Pontoise; 2 Avenue Adolphe Chauvin Cergy-Pontoise Cedex 95302 France
| | - Olivier Gallet
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122); Université de Cergy-Pontoise, F-95000 Cergy-Pontoise; 2 Avenue Adolphe Chauvin Cergy-Pontoise Cedex 95302 France
| | - Johanne Leroy-Dudal
- Equipe de Recherche sur les Relations Matrice Extracellulaire-Cellules, ERRMECe (EA1391), Institut des matériaux, I-MAT (FD4122); Université de Cergy-Pontoise, F-95000 Cergy-Pontoise; 2 Avenue Adolphe Chauvin Cergy-Pontoise Cedex 95302 France
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21
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2009-2010. MASS SPECTROMETRY REVIEWS 2015; 34:268-422. [PMID: 24863367 PMCID: PMC7168572 DOI: 10.1002/mas.21411] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 07/16/2013] [Accepted: 07/16/2013] [Indexed: 05/07/2023]
Abstract
This review is the sixth update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2010. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, arrays and fragmentation are covered in the first part of the review and applications to various structural typed constitutes the remainder. The main groups of compound that are discussed in this section are oligo and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Many of these applications are presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis.
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Affiliation(s)
- David J. Harvey
- Department of BiochemistryOxford Glycobiology InstituteUniversity of OxfordOxfordOX1 3QUUK
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22
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Paleček E, Tkáč J, Bartošík M, Bertók T, Ostatná V, Paleček J. Electrochemistry of nonconjugated proteins and glycoproteins. Toward sensors for biomedicine and glycomics. Chem Rev 2015; 115:2045-108. [PMID: 25659975 PMCID: PMC4360380 DOI: 10.1021/cr500279h] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Emil Paleček
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Tkáč
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Martin Bartošík
- Regional
Centre for Applied Molecular Oncology, Masaryk
Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Tomáš Bertók
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Veronika Ostatná
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Paleček
- Central
European Institute of Technology, Masaryk
University, Kamenice
5, 625 00 Brno, Czech Republic
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23
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Trefulka M, Paleček E. Direct chemical modification and voltammetric detection of glycans in glycoproteins. Electrochem commun 2014. [DOI: 10.1016/j.elecom.2014.08.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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24
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Alsenaidy MA, Jain NK, Kim JH, Middaugh CR, Volkin DB. Protein comparability assessments and potential applicability of high throughput biophysical methods and data visualization tools to compare physical stability profiles. Front Pharmacol 2014; 5:39. [PMID: 24659968 PMCID: PMC3950620 DOI: 10.3389/fphar.2014.00039] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/19/2014] [Indexed: 11/13/2022] Open
Abstract
In this review, some of the challenges and opportunities encountered during protein comparability assessments are summarized with an emphasis on developing new analytical approaches to better monitor higher-order protein structures. Several case studies are presented using high throughput biophysical methods to collect protein physical stability data as function of temperature, agitation, ionic strength and/or solution pH. These large data sets were then used to construct empirical phase diagrams (EPDs), radar charts, and comparative signature diagrams (CSDs) for data visualization and structural comparisons between the different proteins. Protein samples with different sizes, post-translational modifications, and inherent stability are presented: acidic fibroblast growth factor (FGF-1) mutants, different glycoforms of an IgG1 mAb prepared by deglycosylation, as well as comparisons of different formulations of an IgG1 mAb and granulocyte colony stimulating factor (GCSF). Using this approach, differences in structural integrity and conformational stability profiles were detected under stress conditions that could not be resolved by using the same techniques under ambient conditions (i.e., no stress). Thus, an evaluation of conformational stability differences may serve as an effective surrogate to monitor differences in higher-order structure between protein samples. These case studies are discussed in the context of potential utility in protein comparability studies.
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Affiliation(s)
- Mohammad A Alsenaidy
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas Lawrence, KS, USA
| | - Nishant K Jain
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas Lawrence, KS, USA
| | - Jae H Kim
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas Lawrence, KS, USA
| | - C Russell Middaugh
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas Lawrence, KS, USA
| | - David B Volkin
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas Lawrence, KS, USA
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25
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Bosch D, Schots A. Plant glycans: friend or foe in vaccine development? Expert Rev Vaccines 2014; 9:835-42. [DOI: 10.1586/erv.10.83] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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26
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Lei C, Qian K, Noonan O, Nouwens A, Yu C. Applications of nanomaterials in mass spectrometry analysis. NANOSCALE 2013; 5:12033-12042. [PMID: 24162102 DOI: 10.1039/c3nr04194h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Mass spectrometry (MS) based analyses have received intense research interest in a series of rapidly developing disciplines. Although current MS techniques have enjoyed great successes, several key challenges still remain in practical applications, especially for the detection of biomolecules in biological systems. The use of nanomaterials in MS based analysis provides a promising approach due to their unique physical and chemical properties. In this review, nanomaterials with different compositions and nanostructures employed in MS applications are summarised and classified by their functions. Such an integrated and wide reaching review will provide a comprehensive handbook to researchers with various backgrounds working in this exciting interdisciplinary area.
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Affiliation(s)
- Chang Lei
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.
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27
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Jordan DS, Daubenspeck JM, Laube AH, Renfrow MB, Dybvig K. O-linked protein glycosylation in Mycoplasma. Mol Microbiol 2013; 90:1046-53. [PMID: 24118505 DOI: 10.1111/mmi.12415] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2013] [Indexed: 01/06/2023]
Abstract
Although mycoplasmas have a paucity of glycosyltransferases and nucleotidyltransferases recognizable by bioinformatics, these bacteria are known to produce polysaccharides and glycolipids. We show here that mycoplasmas also produce glycoproteins and hence have glycomes more complex than previously realized. Proteins from several species of Mycoplasma reacted with a glycoprotein stain, and the murine pathogen Mycoplasma arthritidis was chosen for further study. The presence of M. arthritidis glycoproteins was confirmed by high-resolution mass spectrometry. O-linked glycosylation was clearly identified at both serine and threonine residues. No consensus amino acid sequence was evident for the glycosylation sites of the glycoproteins. A single hexose was identified as the O-linked modification, and glucose was inferred by (13) C-labelling to be the hexose at several of the glycosylation sites. This is the first study to conclusively identify sites of protein glycosylation in any of the mollicutes.
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Affiliation(s)
- David S Jordan
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
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28
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29
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Costa AR, Rodrigues ME, Henriques M, Oliveira R, Azeredo J. Glycosylation: impact, control and improvement during therapeutic protein production. Crit Rev Biotechnol 2013; 34:281-99. [PMID: 23919242 DOI: 10.3109/07388551.2013.793649] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The emergence of the biopharmaceutical industry represented a major revolution for modern medicine, through the development of recombinant therapeutic proteins that brought new hope for many patients with previously untreatable diseases. There is a ever-growing demand for these therapeutics that forces a constant technological evolution to increase product yields while simultaneously reducing costs. However, the process changes made for this purpose may also affect the quality of the product, a factor that was initially overlooked but which is now a major focus of concern. Of the many properties determining product quality, glycosylation is regarded as one of the most important, influencing, for example, the biological activity, serum half-life and immunogenicity of the protein. Consequently, monitoring and control of glycosylation is now critical in biopharmaceutical manufacturing and a requirement of regulatory agencies. A rapid evolution is being observed in this context, concerning the influence of glycosylation in the efficacy of different therapeutic proteins, the impact on glycosylation of a diversity of parameters/processes involved in therapeutic protein production, the analytical methodologies employed for glycosylation monitoring and control, as well as strategies that are being explored to use this property to improve therapeutic protein efficacy (glycoengineering). This work reviews the main findings on these subjects, providing an up-to-date source of information to support further studies.
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Affiliation(s)
- Ana Rita Costa
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar , Braga , Portugal
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30
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Lombardi A, Andreozzi C, Pavone V, Triglione V, Angiolini L, Caccia P. Evaluation of the oligosaccharide composition of commercial follicle stimulating hormone preparations. Electrophoresis 2013; 34:2394-406. [DOI: 10.1002/elps.201300045] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 04/30/2013] [Accepted: 04/30/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Angela Lombardi
- Department of Chemical Sciences; University “Federico II” of Naples; Naples; Italy
| | - Concetta Andreozzi
- Department of Chemical Sciences; University “Federico II” of Naples; Naples; Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences; University “Federico II” of Naples; Naples; Italy
| | - Valeria Triglione
- Biopharmaceutical Products Division; IBSA Institut Biochimique S.A; Pambio-Noranco; Switzerland
| | - Luca Angiolini
- Biopharmaceutical Products Division; IBSA Institut Biochimique S.A; Pambio-Noranco; Switzerland
| | - Paolo Caccia
- Biopharmaceutical Products Division; IBSA Institut Biochimique S.A; Pambio-Noranco; Switzerland
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31
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Li F, Wang X, Liu Y, Liu H, Li Z. Dephosphorylation of intact glycoprotein to greatly improve digestion efficiency coupled with matrix-assisted laser desorption/ionization–Fourier transform ion cyclotron resonance mass spectrometric analysis. Anal Chim Acta 2013; 787:140-7. [DOI: 10.1016/j.aca.2013.05.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/20/2013] [Accepted: 05/23/2013] [Indexed: 02/01/2023]
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32
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Guttman M, Weinkam P, Sali A, Lee KK. All-atom ensemble modeling to analyze small-angle x-ray scattering of glycosylated proteins. Structure 2013; 21:321-31. [PMID: 23473666 PMCID: PMC3840220 DOI: 10.1016/j.str.2013.02.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 01/22/2013] [Accepted: 02/11/2013] [Indexed: 10/27/2022]
Abstract
The flexible and heterogeneous nature of carbohydrate chains often renders glycoproteins refractory to traditional structure determination methods. Small-angle X-ray scattering (SAXS) can be a useful tool for obtaining structural information of these systems. All-atom modeling of glycoproteins with flexible glycan chains was applied to interpret the solution SAXS data for a set of glycoproteins. For simpler systems (single glycan, with a well-defined protein structure), all-atom modeling generates models in excellent agreement with the scattering pattern and reveals the approximate spatial occupancy of the glycan chain in solution. For more complex systems (several glycan chains, or unknown protein substructure), the approach can still provide insightful models, though the orientations of glycans become poorly determined. Ab initio shape reconstructions appear to capture the global morphology of glycoproteins but in most cases offer little information about glycan spatial occupancy. The all-atom modeling methodology is available as a web server at http://salilab.org/allosmod-foxs.
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Affiliation(s)
- Miklos Guttman
- Department of Medicinal Chemistry; University of Washington, Seattle, WA 98195
| | - Patrick Weinkam
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kelly K. Lee
- Department of Medicinal Chemistry; University of Washington, Seattle, WA 98195
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Go EP, Liao HX, Alam SM, Hua D, Haynes BF, Desaire H. Characterization of host-cell line specific glycosylation profiles of early transmitted/founder HIV-1 gp120 envelope proteins. J Proteome Res 2013; 12:1223-34. [PMID: 23339644 PMCID: PMC3674872 DOI: 10.1021/pr300870t] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Glycosylation plays an essential role in regulating protein function by modulating biological, structural, and therapeutic properties. However, due to its inherent heterogeneity and diversity, the comprehensive analysis of protein glycosylation remains a challenge. As part of our continuing effort in the analysis of glycosylation profiles of recombinant HIV-1 envelope-based immunogens, we evaluated and compared the host-cell specific glycosylation pattern of recombinant HIV-1 surface glycoprotein, gp120, derived from clade C transmitted/founder virus 1086.C expressed in Chinese hamster ovary (CHO) and human embryonic kidney containing T antigen (293T) cell lines. We used an integrated glycopeptide-based mass mapping workflow that includes a partial deglycosylation step described in our previous study with the inclusion of a fragmentation technique, electron transfer dissociation (ETD), to complement collision-induced dissociation. The inclusion of ETD facilitated the analysis by providing additional validation for glycopeptide identification and expanding the identified glycopeptides to include coverage of O-linked glycosylation. The site-specific glycosylation analysis shows that the transmitted/founder 1086.C gp120 expressed in CHO and 293T displayed distinct similarities and differences. For N-linked glycosylation, two sites (N386 and N392) in the V4 region were populated with high mannose glycans in the CHO cell-derived 1086.C gp120, while these sites had a mixture of high mannose and processed glycans in the 293T cell-derived 1086.C gp120. Compositional analysis of O-linked glycans revealed that 293T cell-derived 1086.C gp120 consisted of core 1, 2, and 4 type O-linked glycans, while CHO cell-derived 1086.C exclusively consisted of core 1 type O-linked glycans. Overall, glycosylation site occupancy of the CHO and 293T cell-derived 1086.C gp120 showed a high degree of similarity except for one site at N88 in the C1 region. This site was partially occupied in 293T-gp120 but fully occupied in CHO-gp120. Site-specific glycopeptide analysis of transmitted/founder 1086.C gp120 expressed in CHO cells revealed the presence of phosphorylated glycans, while 293T cell-produced 1086.C gp120 glycans were not phosphorylated. While the influence of phosphorylated glycans on immunogenicity is unclear, distinguishing host-cell specific variations in glycosylation profiles provide insights into the similarity (or difference) in recombinant vaccine products. While these differences had minimal effect on envelope antigenicity, they may be important in considering immunogenicity and functional capacities of recombinant envelope proteins produced in different expression systems.
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Affiliation(s)
- Eden P. Go
- Department of Chemistry, University of Kansas, Lawrence, KS
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, NC
| | - S. Munir Alam
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, NC
| | - David Hua
- Department of Chemistry, University of Kansas, Lawrence, KS
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, NC
- Department of Immunology, Duke University Medical Center, Durham, NC
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Kuzmanov U, Kosanam H, Diamandis EP. The sweet and sour of serological glycoprotein tumor biomarker quantification. BMC Med 2013; 11:31. [PMID: 23390961 PMCID: PMC3751898 DOI: 10.1186/1741-7015-11-31] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 02/07/2013] [Indexed: 12/25/2022] Open
Abstract
Aberrant and dysregulated protein glycosylation is a well-established event in the process of oncogenesis and cancer progression. Years of study on the glycobiology of cancer have been focused on the development of clinically viable diagnostic applications of this knowledge. However, for a number of reasons, there has been only sparse and varied success. The causes of this range from technical to biological issues that arise when studying protein glycosylation and attempting to apply it to practical applications. This review focuses on the pitfalls, advances, and future directions to be taken in the development of clinically applicable quantitative assays using glycan moieties from serum-based proteins as analytes. Topics covered include the development and progress of applications of lectins, mass spectrometry, and other technologies towards this purpose. Slowly but surely, novel applications of established and development of new technologies will eventually provide us with the tools to reach the ultimate goal of quantification of the full scope of heterogeneity associated with the glycosylation of biomarker candidate glycoproteins in a clinically applicable fashion.
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Affiliation(s)
- Uros Kuzmanov
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, 6th floor, 60 Murray Street, Box 32, Toronto, ON M5T 3L9, Canada
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Thuy TT, Tengstrand E, Åberg M, Thorsén G. Discrimination between glycosylation patterns of therapeutic antibodies using a microfluidic platform, MALDI-MS and multivariate statistics. J Pharm Biomed Anal 2012; 70:47-52. [DOI: 10.1016/j.jpba.2012.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/17/2012] [Accepted: 05/20/2012] [Indexed: 11/28/2022]
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Schulz BL, Cooper-White J, Punyadeera CK. Saliva proteome research: current status and future outlook. Crit Rev Biotechnol 2012; 33:246-59. [DOI: 10.3109/07388551.2012.687361] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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37
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Sánchez-Pomales G, Morris TA, Falabella JB, Tarlov MJ, Zangmeister RA. A lectin-based gold nanoparticle assay for probing glycosylation of glycoproteins. Biotechnol Bioeng 2012; 109:2240-9. [DOI: 10.1002/bit.24513] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 03/08/2012] [Accepted: 03/20/2012] [Indexed: 12/15/2022]
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Modification of an exposed loop in the C1 domain reduces immune responses to factor VIII in hemophilia A mice. Blood 2012; 119:5294-300. [PMID: 22498747 DOI: 10.1182/blood-2011-11-391680] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Development of neutralizing Abs to blood coagulation factor VIII (FVIII) provides a major complication in hemophilia care. In this study we explored whether modulation of the uptake of FVIII by APCs can reduce its intrinsic immunogenicity. Endocytosis of FVIII by professional APCs is significantly blocked by mAb KM33, directed toward the C1 domain of FVIII. We created a C1 domain variant (FVIII-R2090A/K2092A/F2093A), which showed only minimal binding to KM33 and retained its activity as measured by chromogenic assay. FVIII-R2090A/K2092A/F2093A displayed a strongly reduced internalization by human monocyte-derived dendritic cells and macrophages, as well as murine BM-derived dendritic cells. We subsequently investigated the ability of this variant to induce an immune response in FVIII-deficient mice. We show that mice treated with FVIII-R2090A/K2092A/F2093A have significantly lower anti-FVIII Ab titers and FVIII-specific CD4(+) T-cell responses compared with mice treated with wild-type FVIII. These data show that alanine substitutions at positions 2090, 2092, and 2093 reduce the immunogenicity of FVIII. According to our findings we hypothesize that FVIII variants displaying a reduced uptake by APCs provide a novel therapeutic approach to reduce inhibitor development in hemophilia A.
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Kaltashov IA, Bobst CE, Abzalimov RR, Wang G, Baykal B, Wang S. Advances and challenges in analytical characterization of biotechnology products: mass spectrometry-based approaches to study properties and behavior of protein therapeutics. Biotechnol Adv 2012; 30:210-22. [PMID: 21619926 PMCID: PMC3176981 DOI: 10.1016/j.biotechadv.2011.05.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 04/13/2011] [Accepted: 05/09/2011] [Indexed: 12/19/2022]
Abstract
Biopharmaceuticals are a unique class of medicines due to their extreme structural complexity. The structure of these therapeutic proteins is critically important for their efficacy and safety, and the ability to characterize it at various levels (from sequence to conformation) is critical not only at the quality control stage, but also throughout the discovery and design stages. Biological mass spectrometry (MS) offers a variety of approaches to study structure and behavior of complex protein drugs and has already become a default tool for characterizing the covalent structure of protein therapeutics, including sequence and post-translational modifications. Recently, MS-based methods have also begun enjoying a dramatic growth in popularity as a means to provide information on higher order structure and dynamics of biotechnology products. In particular, hydrogen/deuterium exchange MS and charge state distribution analysis of protein ions in electrospray ionization (ESI) MS offer a convenient way to assess the integrity of protein conformation. Native ESI MS also allows the interactions of protein drugs with their therapeutic targets and other physiological partners to be monitored using simple model systems. MS-based methods are also applied to study pharmacokinetics of biopharmaceutical products, where they begin to rival traditional immunoassays. MS already provides valuable support to all stages of development of biopharmaceuticals, from discovery to post-approval monitoring, and its impact on the field of biopharmaceutical analysis will undoubtedly continue to grow.
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Affiliation(s)
- Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA.
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40
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Guttman M, Scian M, Lee KK. Tracking hydrogen/deuterium exchange at glycan sites in glycoproteins by mass spectrometry. Anal Chem 2011; 83:7492-9. [PMID: 21863800 DOI: 10.1021/ac201729v] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hydrogen/deuterium exchange coupled to mass spectrometry (HDX-MS) has emerged as a technique for studying glycoproteins, which are often refractory to classical methods. Glycan chains are generally assumed to exchange protons very rapidly, making them invisible to this technique. Here, we show that under conditions commonly used for HDX-MS, acetamido groups within glycan chains retain a significant amount of deuterium. Using mono- and polysaccharide standards along with glycopeptides from a panel of glycoproteins, we demonstrate that N-acetyl hexosamines, along with modified Asn side chains, are responsible for this effect. Model compounds for sialic acid also displayed similar exchange kinetics, but terminal sialic acids in the context of an entire glycan chain did not contribute to deuterium retention. Furthermore, the presence of sialic acid appears to enhance the exchange rate of the nearby N-acetyl glucosamines. The ability to detect deuterium exchange at the glycan level opens the possibility of applying HDX-MS to monitor glycan interactions and dynamics.
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Affiliation(s)
- M Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, USA.
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Ponsel D, Neugebauer J, Ladetzki-Baehs K, Tissot K. High affinity, developability and functional size: the holy grail of combinatorial antibody library generation. Molecules 2011; 16:3675-700. [PMID: 21540796 PMCID: PMC6263270 DOI: 10.3390/molecules16053675] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 04/20/2011] [Accepted: 04/22/2011] [Indexed: 01/12/2023] Open
Abstract
Since the initial description of phage display technology for the generation of human antibodies, a variety of selection methods has been developed. The most critical parameter for all in vitro-based approaches is the quality of the antibody library. Concurrent evolution of the libraries has allowed display and selection technologies to reveal their full potential. They come in different flavors, from naïve to fully synthetic and differ in terms of size, quality, method of preparation, framework and CDR composition. Early on, the focus has mainly been on affinities and thus on library size and diversity. Subsequently, the increased awareness of developability and cost of goods as important success factors has spurred efforts to generate libraries with improved biophysical properties and favorable production characteristics. More recently a major focus on reduction of unwanted side effects through reduced immunogenicity and improved overall biophysical behavior has led to a re-evaluation of library design.
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Affiliation(s)
| | - Julia Neugebauer
- Author to whom correspondence should be addressed; ; Tel.: +49-89-89927-179; Fax: +49-89-89927-5179
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42
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Hu ZZ, Huang H, Wu CH, Jung M, Dritschilo A, Riegel AT, Wellstein A. Omics-based molecular target and biomarker identification. Methods Mol Biol 2011; 719:547-71. [PMID: 21370102 PMCID: PMC3742302 DOI: 10.1007/978-1-61779-027-0_26] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Genomic, proteomic, and other omic-based approaches are now broadly used in biomedical research to facilitate the understanding of disease mechanisms and identification of molecular targets and biomarkers for therapeutic and diagnostic development. While the Omics technologies and bioinformatics tools for analyzing Omics data are rapidly advancing, the functional analysis and interpretation of the data remain challenging due to the inherent nature of the generally long workflows of Omics experiments. We adopt a strategy that emphasizes the use of curated knowledge resources coupled with expert-guided examination and interpretation of Omics data for the selection of potential molecular targets. We describe a downstream workflow and procedures for functional analysis that focus on biological pathways, from which molecular targets can be derived and proposed for experimental validation.
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Affiliation(s)
- Zhang-Zhi Hu
- Lombardi Cancer Center, Georgetown University, Washington, DC, USA.
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43
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Sánchez-Pomales G, Zangmeister RA. Recent Advances in Electrochemical Glycobiosensing. INTERNATIONAL JOURNAL OF ELECTROCHEMISTRY 2011. [DOI: 10.4061/2011/825790] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Biosensors based on electrochemical transduction mechanisms have recently made advances into the field of glycan analysis. These glyco-biosensors offer simple, rapid, sensitive, and economical approaches to the measurement need for rapid glycan analysis for biomarker detection, cancer and disease diagnostics, and bioprocess monitoring of therapeutic glycoproteins. Although the prevalent methods of glycan analysis (high-performance liquid chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy) provide detailed identification and structural analysis of glycan species, there are significantly few low-cost, rapid glycan assays available for diagnostic and screening applications. Here we review instances in which glyco-biosensors have been used for glycan analysis using a variety of electrochemical transduction mechanisms (e.g., amperometric, potentiometric, impedimetric, and voltammetric), selective binding agents (e.g., lectins and antibodies), and redox species (e.g., enzyme substrates, inorganic, and nanomaterial).
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Affiliation(s)
- Germarie Sánchez-Pomales
- Bioprocess Measurements Group, Biochemical Science Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Rebecca A. Zangmeister
- Bioprocess Measurements Group, Biochemical Science Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
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Turtoi A, De Pauw E, Castronovo V. Innovative proteomics for the discovery of systemically accessible cancer biomarkers suitable for imaging and targeted therapies. THE AMERICAN JOURNAL OF PATHOLOGY 2010; 178:12-8. [PMID: 21224037 DOI: 10.1016/j.ajpath.2010.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 08/10/2010] [Accepted: 08/30/2010] [Indexed: 12/30/2022]
Abstract
The discovery of biomarkers that are readily accessible through the circulating blood and are selectively overexpressed in pathological tissues has become a major research objective, particularly in the field of oncology. Indisputably, this group of molecules has a high potential to serve as an innovative tool for effective imaging and targeted cancer therapy approaches. In this attractive therapeutic concept, specific cancer proteins are reached by intravenously administered ligands that are coupled to cytotoxic drugs. Such compounds are able to induce cancer destruction while sparing normal tissues. Owing to the performance of mass spectrometry technology, current high-throughput proteomic analysis allows for the identification of a high number of proteins that are differentially expressed in the cancerous tissues. However, such approaches provide no information regarding the effective accessibility of the >biomarkers and, therefore, the possibility for these discovered proteins to be targeted. To bypass this major limitation, which clearly slows the discovery of such biomarkers, innovative methodological strategies have been developed to enrich the clinical specimens before the mass spectrometry analysis. The focus is laid on the group of proteins that are necessarily located either at the exterior face of the plasma membrane or in the extracellular matrix. The present review addresses the current technologies meant for the discovery and analysis of accessible antigens from clinically relevant samples.
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Affiliation(s)
- Andrei Turtoi
- Metastasis Research Laboratory, GIGA-Cancer, University of Liège, Liège, Belgium
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Zhao J, Liu YH, Reichert P, Pflanz S, Pramanik B. Glycosylation analysis of interleukin-23 receptor: elucidation of glycosylation sites and characterization of attached glycan structures. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:1416-1425. [PMID: 21053369 DOI: 10.1002/jms.1858] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Interleukin-23 (IL-23) is a heterodimeric cytokine, a central factor in chronic/autoimmune inflammation. It signals through a heterodimeric receptor consisting of IL-23r, which is heavily glycosylated. The structural characterization of IL-23r has not been reported. In this work, glycosylation profiles of soluble recombinant human IL-23r (rhIL-23r) were established using mass spectrometry (MS), which included defining glycosylation sites, degree of glycosylation occupancy of each site and structure of attached oligosaccharides. Specifically, precursor ion scan of oxonium ion protonated N-acetylglucosamine (GlcNAc(+)) (m/z 204) was performed using a triple quadrupole MS instrument to locate the retention time of glycopeptides. Both the glycopeptides and their corresponding deglycosylated forms in each collected HPLC fraction were studied by liquid chromatography-tandem mass spectrometry (LC-MS/MS) (LTQ-Orbitrap) for glycosylation site profiling. The attached glycan structures were elucidated by collision-induced dissociation (CID) fragmentation of target glycopeptides in combination with accurate mass measurement. Eight glycosylation sites were identified on IL-23r (Asn24, Asn209, Asn239, Asn157, Asn118, Asn250, Asn58 and Asn6). Most of the glycosylation sites were > 95% occupied except Asn250 and Asn6. Those two sites were 88% and 45% occupied by estimation from trypsin digestion and were 55% and 42% occupied from LysC digestion. Multiple glycoforms were observed in IL-23r. Most of them were bi-, tri- or tetra-antennary complex type structures with fucose and sialic acid. High mannose and hybrid type glycans were only observed on Asn157. The structural characterization on IL-23r glycosylation provides useful information for better understanding of the biological function of IL-23r.
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Affiliation(s)
- Jia Zhao
- Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
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46
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Lazar IM, Lazar AC, Cortes DF, Kabulski JL. Recent advances in the MS analysis of glycoproteins: Theoretical considerations. Electrophoresis 2010; 32:3-13. [PMID: 21171109 DOI: 10.1002/elps.201000393] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/15/2010] [Accepted: 09/16/2010] [Indexed: 01/19/2023]
Abstract
Protein glycosylation is involved in a broad range of biological processes that regulate protein function and control cell fate. As aberrant glycosylation has been found to be implicated in numerous diseases, the study and large-scale characterization of protein glycosylation is of great interest not only to the biological and biomedical research community, but also to the pharmaceutical and biotechnology industry. Due to the complex chemical structure and differing chemical properties of the protein/peptide and glycan moieties, the analysis and structural characterization of glycoproteins has been proven to be a difficult task. Large-scale endeavors have been further limited by the dynamic outcome of the glycosylation process itself, and, occasionally, by the low abundance of glycoproteins in biological samples. Recent advances in MS instrumentation and progress in miniaturized technologies for sample handling, enrichment and separation, have resulted in robust and compelling analysis strategies that effectively address the challenges of the glycoproteome. This review summarizes the key steps that are involved in the development of efficient glycoproteomic analysis methods, and the latest innovations that led to successful strategies for the characterization of glycoproteins and their corresponding glycans. As a follow-up to this work, we review innovative capillary and microfluidic-MS workflows for the identification, sequencing and characterization of glycoconjugates.
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Affiliation(s)
- Iulia M Lazar
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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Abstract
PURPOSE To compare the quality of therapeutic erythropoietin (EPO) products, including two biosimilars, with respect to content, aggregation, isoform profile and potency. METHODS Two original products, Eprex (epoetin alpha) and Dynepo (epoetin delta), and two biosimilar products, Binocrit (epoetin alpha) and Retacrit (epoetin zeta), were compared using (1) high performance size exclusion chromatography, (2) ELISA, (3) SDS-PAGE, (4) capillary zone electrophoresis and (5) in-vivo potency. RESULTS Tested EPO products differed in content, isoform composition, and potency. CONCLUSION Of the tested products, the biosimilars have the same or even better quality as the originals. Especially, the potency of originals may significantly differ from the value on the label.
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49
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Fleron M, Greffe Y, Musmeci D, Massart AC, Hennequiere V, Mazzucchelli G, Waltregny D, De Pauw-Gillet MC, Castronovo V, De Pauw E, Turtoi A. Novel post-digest isotope coded protein labeling method for phospho- and glycoproteome analysis. J Proteomics 2010; 73:1986-2005. [PMID: 20601274 DOI: 10.1016/j.jprot.2010.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 06/02/2010] [Accepted: 06/03/2010] [Indexed: 11/19/2022]
Abstract
In the field of proteomics there is an apparent lack of reliable methodology for quantification of posttranslational modifications. Present study offers a novel post-digest ICPL quantification strategy directed towards characterization of phosphorylated and glycosylated proteins. The value of the method is demonstrated based on the comparison of two prostate related metastatic cell lines originating from two distinct metastasis sites (PC3 and LNCaP). The method consists of protein digestion, ICPL labeling, mixing of the samples, PTM enrichment and MS-analysis. Phosphorylated peptides were isolated using TiO(2), whereas the enrichment of glycosylated peptides was performed using hydrazide based chemistry. Isolated PTM peptides were analyzed along with non enriched sample using 2D-(SCX-RP)-Nano-HPLC-MS/MS instrumentation. Taken together the novel ICPL labeling method offered a significant improvement of the number of identified (∼600 individual proteins) and quantified proteins (>95%) in comparison to the classical ICPL method. The results were validated using alternative protein quantification strategies as well as label-free MS quantification method. On the biological level, the comparison of PC3 and LNCaP cells has shown specific modulation of proteins implicated in the fundamental process related to metastasis dissemination. Finally, a preliminary study involving clinically relevant autopsy cases reiterated the potential biological value of the discovered proteins.
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Affiliation(s)
- M Fleron
- Histology-Cytology Laboratory, Department of Biomedical and Preclinical Sciences, University of Liege, B-4000 Liege, Belgium
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50
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Katrlík J, Svitel J, Gemeiner P, Kozár T, Tkac J. Glycan and lectin microarrays for glycomics and medicinal applications. Med Res Rev 2010; 30:394-418. [PMID: 20099267 DOI: 10.1002/med.20195] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Three different array formats to study a challenging field of glycomics are presented here, based on the use of a panel of immobilized glycan or lectins, and on in silico computational approach. Glycan and lectin arrays are routinely used in combination with other analytical tools to decipher a complex nature of glycan-mediated recognition responsible for signal transduction of a broad range of biological processes. Fundamental aspects of the glycan and lectin array technology are discussed, with the focus on the choice and availability of the biorecognition elements, fabrication protocols, and detection platforms involved. Moreover, practical applications of both technologies especially in the field of clinical diagnostics are provided. The future potential of a complementary in silico array technology to reveal details of the protein-glycan-binding profiles is discussed here.
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Affiliation(s)
- Jaroslav Katrlík
- Department of Glycobiotechnology, Center for Glycomics, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
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