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Adams TM, Zhao P, Kong R, Wells L. ppmFixer: a mass error adjustment for pGlyco3.0 to correct near-isobaric mismatches. Glycobiology 2024; 34:cwae006. [PMID: 38263491 PMCID: PMC11005163 DOI: 10.1093/glycob/cwae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/25/2024] Open
Abstract
Modern glycoproteomics experiments require the use of search engines due to the generation of countless spectra. While these tools are valuable, manual validation of search engine results is often required for detailed analysis of glycopeptides as false-discovery rates are often not reliable for glycopeptide data. Near-isobaric mismatches are a common source of misidentifications for the popular glycopeptide-focused search engine pGlyco3.0, and in this technical note we share a strategy and script that improves the accuracy of the search utilizing two manually validated datasets of the glycoproteins CD16a and HIV-1 Env as proof-of-principle.
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Affiliation(s)
- Trevor M Adams
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens 30602, Georgia
| | - Peng Zhao
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens 30602, Georgia
| | - Rui Kong
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory University, 7 Frist Ave, Atlanta 30317, Georgia
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens 30602, Georgia
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2
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Cheng S, Xu M, Li M, Feng Y, He L, Liu T, Ma L, Li X. Improving Anti-HIV activity and pharmacokinetics of enfuvirtide (T20) by modification with oligomannose. Eur J Med Chem 2024; 269:116299. [PMID: 38479167 DOI: 10.1016/j.ejmech.2024.116299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/25/2024] [Accepted: 03/01/2024] [Indexed: 04/07/2024]
Abstract
Dendritic cells (DCs) play a pivotal role in controlling HIV-1 infections of CD4+ T cells. DC-SIGN, which is expressed on the surface of DCs, efficiently captures HIV-1 virions by binding to the highly mannosylated membrane protein, gp120, and then the DCs transport the virus to target T cells in lymphoid organs. This study explored the modification of T20, a peptide inhibitor of HIV-1 fusion, by conjugation of the N-terminus with varying sizes of oligomannose, which are DC-SIGN-specific carbohydrates, aiming to create dual-targeting HIV inhibitors. Mechanistic studies indicated the dual-target binding of the conjugates. Antiviral assays demonstrated that N-terminal mannosylation of T20 resulted in increased inhibition of the viral infection of TZM-b1 cells (EC50 = 0.3-0.8 vs. 1.4 nM). Pentamannosylated T20 (M5-T20) exhibited a stronger inhibitory effect on virus entry into DC-SIGN+ 293T cells compared with T20 (67% vs. 50% inhibition at 500 μM). M5-T20 displayed an extended half-life in rats relative to T20 (T1/2: 8.56 vs. 1.64 h, respectively). These conjugates represent a potential new treatment for HIV infections with improved antiviral activity and pharmacokinetics, and this strategy may prove useful in developing dual-target inhibitors for other pathogens that require DC-SIGN involvement for infection.
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Affiliation(s)
- Shuihong Cheng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou district, Beijing, 101408, China
| | - Mingyue Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou district, Beijing, 101408, China
| | - Mingli Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou district, Beijing, 101408, China
| | - Yong Feng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou district, Beijing, 101408, China
| | - Lin He
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Tong Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou district, Beijing, 101408, China
| | - Liying Ma
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Xuebing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou district, Beijing, 101408, China.
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3
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Mitsutake K, Shinya N, Seki M, Ohara T, Uemura K, Fukunaga M, Sakai J, Nagao M, Sata M, Hamada Y, Kawasuji H, Yamamoto Y, Nakamatsu M, Koizumi Y, Mikamo H, Ukimura A, Aoyagi T, Sawai T, Tanaka T, Izumikawa K, Takayama Y, Nakamura K, Kanemitsu K, Tokimatsu I, Nakajima K, Akine D. Antimicrobial therapy and outcome of methicillin-resistant Staphylococcus aureus endocarditis: A retrospective multicenter study in Japan. J Infect Chemother 2024:S1341-321X(24)00068-0. [PMID: 38432557 DOI: 10.1016/j.jiac.2024.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/08/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND MRSA (methicillin-resistant Staphylococcus aureus)-infective endocarditis (IE) is associated with high morbidity and mortality. This study aimed to assess data from patients with MRSA-IE across multiple facilities in Japan, with a specific focus on antimicrobial therapy and prognosis. METHODS This retrospective study enrolled patients with a confirmed diagnosis of IE attributed to MRSA, spanning the period from January 2015 to April 2019. RESULTS Sixty-four patients from 19 centers were included, with a median age of 67 years. The overall mortality rate was 28.1% at 30 days, with an in-hospital mortality of 45.3%. The most frequently chosen initial anti-MRSA agents were glycopeptide in 67.2% of cases. Daptomycin and linezolid were selected as initial therapy in 23.4% and 17.2% of cases, respectively. Approximately 40% of all patients underwent medication changes due to difficulty in controlling infection or drug-related side effects. Significant prognostic factors by multivariable analysis were DIC for 30-day mortality and surgical treatment for 30-day and in-hospital mortality. For vancomycin as initial monotherapy, there was a trend toward a worse prognosis for 30-day and in-hospital mortality (OR, 6.29; 95%CI, 1.00-39.65; p = 0.050, OR, 3.61; 95%CI, 0.93-14.00; p = 0.064). Regarding the choice of initial antibiotic therapy, statistical analysis did not show significant differences in prognosis. CONCLUSION Glycopeptide and daptomycin were the preferred antibiotics for the initial therapy of MRSA-IE. Antimicrobial regimens were changed for various reasons. Prognosis was not significantly affected by choice of antibiotic therapy (glycopeptide, daptomycin, linezolid), but further studies are needed to determine which antimicrobials are optimal as first-line agents.
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Affiliation(s)
- Kotaro Mitsutake
- Department of Infectious Diseases and Infection Control, Saitama International Medical Center, Saitama Medical University, 397-1, Hidaka, Saitama, 350-1298, Japan.
| | - Natsuki Shinya
- Department of Infectious Diseases and Infection Control, Saitama International Medical Center, Saitama Medical University, 397-1, Hidaka, Saitama, 350-1298, Japan
| | - Masafumi Seki
- Department of Infectious Diseases and Infection Control, Saitama International Medical Center, Saitama Medical University, 397-1, Hidaka, Saitama, 350-1298, Japan; Department of Infectious Diseases, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1 Fukumuro, Miyagino-ku, Sendai, Miyagi, 983-8536, Japan
| | - Takahiro Ohara
- Division of Geriatric and Community Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1 Fukumuro, Miyagino-ku, Sendai, Miyagi, 983-8536, Japan
| | - Kohei Uemura
- Department of Biostatistics and Bioinformatics, Interfaculty Initiative in Information Studies, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8655, Japan
| | - Masato Fukunaga
- Department of Cardiology, Kokura Memorial Hospital, 3-2-1 Asano, Kokurakita, Kitakyushu, Fukuoka, 802-8555, Japan
| | - Jun Sakai
- Department of Infectious Disease and Infection Control, Saitama Medical University Hospital, 1981 Kamoda, Kawagoe, Saitama, 350-8550, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto City, Kyoto, 606-8507, Japan
| | - Makoto Sata
- National Cerebral and Cardiovascular Center Division of Pulmonology and Infection Control, 6-1, Kishibe Shinmachi, Suita, Osaka, 564-8565, Japan
| | - Yohei Hamada
- Department of Infectious Disease and Hospital Epidemiology, Saga University Hospital, 5-1-1 Nabeshima, Saga, 849-0937, Japan
| | - Hitoshi Kawasuji
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, 2630 Sugitani, Toyama, Toyama, 930-0194, Japan
| | - Yoshihiro Yamamoto
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, 2630 Sugitani, Toyama, Toyama, 930-0194, Japan
| | - Masashi Nakamatsu
- Department of Infection Control, University of the Ryukyus Hospital, 207 Aza-Uehara, Nishihara, Nakagami-gun, Okinawa, 903-0215, Japan
| | - Yusuke Koizumi
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1 Iwasaku, Ganmata, Nagakute, Aichi, 480-1195, Japan
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1 Iwasaku, Ganmata, Nagakute, Aichi, 480-1195, Japan
| | - Akira Ukimura
- Infection Control Center, Osaka Medical and Pharmaceutical University Hospital, 2-7 Daigaku-cho, Takatsuki, Osaka, 569-0801, Japan
| | - Tetsuji Aoyagi
- Department of Clinical Microbiology and Infection, Tohoku University Graduate School of Medicine, Department of Comprehensive Infectious Diseases, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai, 980-8575, Japan
| | - Toyomitsu Sawai
- Nagasaki Harbor Medical Center, Department of Respiratory Medicine, 6-39 Shinchi-cho, Nagasaki City, Nagasaki, 850-0842, Japan
| | - Takeshi Tanaka
- Infection Control and Education Center, Nagasaki University Hospital, 1 Chome-7-1 Sakamoto, Nagasaki, 852-8501, Japan
| | - Koichi Izumikawa
- Infection Control and Education Center, Nagasaki University Hospital, 1 Chome-7-1 Sakamoto, Nagasaki, 852-8501, Japan
| | - Yoko Takayama
- Department of Infection Control and Infectious Diseases Research and Development Center for New Medical Frontiers Kitasato University School of Medicine, 1-15-1, Kitazato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan
| | - Kiwamu Nakamura
- Department of Infection Control, Fukushima Medical University, 1 Hikarigaoka, Fukushima-shi, Fukushima, 960-1295, Japan
| | - Keiji Kanemitsu
- Department of Infection Control, Fukushima Medical University, 1 Hikarigaoka, Fukushima-shi, Fukushima, 960-1295, Japan
| | - Issei Tokimatsu
- Department of Medicine, Division of Clinical Infectious Diseases, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8666, Japan
| | - Kazuhiko Nakajima
- Department of Infection Prevention and Control, Hyogo Medical University, 1-1, Mukogawa, Nishinomiya, Hyogo, 663-850, Japan
| | - Dai Akine
- Division of Clinical Infectious Diseases, School of Medicine, Jichi Medical University, 3311-1, Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
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Kokubu R, Ohno S, Manabe N, Yamaguchi Y. Molecular Dynamics Simulation and Docking of MUC1 O- Glycopeptide. Methods Mol Biol 2024; 2763:373-379. [PMID: 38347427 DOI: 10.1007/978-1-0716-3670-1_32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Advances in computer performance and computational simulations allow increasing sophistication in applications in biological systems. Molecular dynamics (MD) simulations are especially suitable for studying conformation, dynamics, and interaction of flexible biomolecules such as free glycans and glycopeptides. Computer simulations are best performed when the scope and limitations in performance have been thoroughly assessed. Proper outputs are obtained only under suitable parameter settings, and results need to be properly validated. In this chapter, we will introduce an example of molecular dynamics simulations of MUC1 O-glycopeptide and its docking to anti-MUC1 antibody Fv fragment.
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Affiliation(s)
- Ryoka Kokubu
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Shiho Ohno
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Noriyoshi Manabe
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Yoshiki Yamaguchi
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan.
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5
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Zhao J, Ye F, Huang P, Wang P. Recent advances in chemical synthesis of O-linked glycopeptides and glycoproteins: An advanced synthetic tool for exploring the biological realm. Curr Opin Chem Biol 2023; 77:102405. [PMID: 37897925 DOI: 10.1016/j.cbpa.2023.102405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/30/2023]
Abstract
Glycoproteins play crucial roles in various biological processes. To investigate the relationship between glycan structure and function, researchers have employed various chemical methods to precisely synthesize homogeneous O-glycoproteins. This review summarizes the recent progress of their synthetic strategies, highlighting the significant advancements in this area.
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Affiliation(s)
- Jie Zhao
- Center for Chemical Glycobiology, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China; Shenzhen Research Institute of Shanghai Jiao Tong University, Shenzhen, 518057, China
| | - Farong Ye
- Center for Chemical Glycobiology, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Huang
- Center for Chemical Glycobiology, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Ping Wang
- Center for Chemical Glycobiology, Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China; Shenzhen Research Institute of Shanghai Jiao Tong University, Shenzhen, 518057, China.
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6
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Tai J, Hu H, Cao X, Liang X, Lu Y, Zhang H. Identification of animal species of origin in meat based on glycopeptide analysis by UPLC-QTOF-MS. Anal Bioanal Chem 2023; 415:7235-7246. [PMID: 37957327 DOI: 10.1007/s00216-023-04992-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/31/2023] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Adulteration of meat and meat products causes a concerning threat for consumers. It is necessary to develop novel robust and sensitive methods which can authenticate the origin of meat species to compensate for the drawbacks of existing methods. In the present study, the sarcoplasmic proteins of six meat species, namely, pork, beef, mutton, chicken, duck and turkey, were analyzed by one-dimensional gel electrophoresis. It was found that enolase could be used as a potential biomarker protein to distinguish between livestock and poultry meats. The glycosylation sites and glycans of enolase were analyzed by UPLC-QTOF-MS and a total of 41 glycopeptides were identified, indicating that the enolase N-glycopeptide profiles of different meats were species-specific. The identification models of livestock meat, poultry and mixed animal were established based on the glycopeptide contents, and the explanation degree of the three models was higher than 90%. The model prediction performance and feasibility results showed that the average prediction accuracy of the three models was 75.43%, with the animal-derived meat identification model showing superiority in identifying more closely related species. The obtained results indicated that the developed strategy was promising for application in animal-derived meat species monitoring and the quality supervision of animal-derived food.
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Affiliation(s)
- Jingjing Tai
- School of Food and Bioengineering, Zhejiang Gongshang University, Hangzhou, 310018, Zhejiang, China
| | - Huang Hu
- School of Agriculture, JinHua Polytechnic, Jinhua, 321016, Zhejiang, China
| | - Xiaoji Cao
- Research Center of Analysis and Measurement, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Xinle Liang
- School of Food and Bioengineering, Zhejiang Gongshang University, Hangzhou, 310018, Zhejiang, China
| | - Yanbin Lu
- School of Food and Bioengineering, Zhejiang Gongshang University, Hangzhou, 310018, Zhejiang, China
| | - Hong Zhang
- School of Food and Bioengineering, Zhejiang Gongshang University, Hangzhou, 310018, Zhejiang, China.
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Huang J, Fu L, Zhang X, Huang S, Dong Y, Hu K, Han Y, Zhou K, Min C, Huang Y, Tang G. Noninvasive imaging of FAP expression using positron emission tomography: A comparative evaluation of a [ 18F]-labeled glycopeptide-containing FAPI with [ 18F]FAPI-42. Eur J Nucl Med Mol Imaging 2023; 50:3363-3374. [PMID: 37266596 DOI: 10.1007/s00259-023-06282-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/20/2023] [Indexed: 06/03/2023]
Abstract
PURPOSE Research on fibroblast activating protein (FAP)-targeting inhibitor (FAPI) has become an important focus for cancer imaging and radiotherapy. Quinoline-based tracers [68 Ga]FAPI-04 and [18F]FAPI-42 have been widely used for positron emission tomography (PET) imaging of most tumors. However, there exist some limitations of these tracers with high uptake in biliary duct system and unstable uptake in pancreas, unsuitable for abdominal tumors PET imaging. Here we developed a [18F]-labeled glycopeptide-containing FAPI tracer (named [18F]FAPT) for PET imaging of FAP in cancers. METHODS [18F]FAPT was synthesized manually and automatically. The competitive binding to FAP, cellular internalization, and efflux characteristics were examined in vitro using A549-FAP cells. Dynamic MicroPET and biodistribution studies of [18F]FAPT were then conducted in A549-FAP and U87MG xenograft tumor mouse models compared with [18F]FAPI-42. Five healthy volunteers and three patients with cancer underwent [18F]FAPT PET/CT. RESULTS Preclinical and clinical studies showed specific binding of [18F]FAPT to FAP and favorable pharmacokinetic properties with better hydrophilicity, lower uptake in biliary duct system, higher tumor uptake and longer tumor retention compared with [18F]FAPI-42. The biodistribution of [18F]FAPT in healthy volunteers and patients with cancer displayed low uptake in most normal tissues except for pancreas, thyroid and salivary gland, which could contribute to high tumor-to-background ratios in most cancers. CONCLUSION [18F]FAPT is better PET tracer than [18F]FAPI-42 for imaging of biliary duct system cancer, potentially providing a tool to examine FAP expression in most cancers with high tumor-to-background ratios.
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Affiliation(s)
- Jiawen Huang
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, PET Center and Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - LiLan Fu
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, PET Center and Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - XiaoJun Zhang
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, PET Center and Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Shun Huang
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, PET Center and Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Ye Dong
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, PET Center and Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Kongzhen Hu
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, PET Center and Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - YanJiang Han
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, PET Center and Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Kemin Zhou
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, PET Center and Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Cao Min
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, PET Center and Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - YanChao Huang
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, PET Center and Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Ganghua Tang
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, PET Center and Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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8
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Mamahit YP, Maki Y, Okamoto R, Kajihara Y. Semisynthesis of homogeneous misfolded glycoprotein interleukin-8. Carbohydr Res 2023; 531:108847. [PMID: 37354703 DOI: 10.1016/j.carres.2023.108847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 06/26/2023]
Abstract
To uncover how cells distinguish between misfolded and correctly-folded glycoproteins, homogeneous misfolded glycoproteins are needed as a probe for analysis of their structure and chemical characteristic nature. In this study, we have synthesized misfolded glycosyl interleukin-8 (IL-8) by combining E. coli expression and chemical synthesis to improve the synthetic efficiency. In order to prepare N-terminal peptide-thioester segment (1-33), we prepared an E. coli expressed peptide and then activated the C-terminal Cys by using an intramolecular N-to-S acyl shift reaction, followed by trans-thioesterification of the Cys-thioester with an external bis(2-sulfanylethyl)amine (SEA). The glycopeptide segment (34-49) was prepared by solid phase peptide synthesis and the C-terminal peptide (50-72) was prepared in E. coli. These peptide and glycopeptide segments were successfully coupled by sequential native chemical ligation. To obtain homogeneous misfolded glycoproteins by shuffling the disulfide bond pattern, folding conditions were optimized to maximize the yield of individual homogeneous misfolded glycoproteins.
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Affiliation(s)
- Yugoviandi P Mamahit
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yuta Maki
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan; Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Ryo Okamoto
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan; Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yasuhiro Kajihara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan; Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.
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9
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Liu Y, Nomura K, Abe J, Kajihara Y. Recent advances on the synthesis of N-linked glycoprotein for the elucidation of glycan functions. Curr Opin Chem Biol 2023; 73:102263. [PMID: 36746076 DOI: 10.1016/j.cbpa.2023.102263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/05/2022] [Accepted: 12/30/2022] [Indexed: 02/05/2023]
Abstract
Glycoproteins play roles in many biological events, while, the glycan structure-function relationship has remained to be studied. In order to understand glycan function, homogeneous glycoproteins have been synthesized. This review introduced recent progress of their synthetic approaches.
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Affiliation(s)
- Yanbo Liu
- Department of Chemistry Osaka University, 1-1 Machikaneyama, Toyonaka, 560-0043 Japan
| | - Kota Nomura
- Department of Chemistry Osaka University, 1-1 Machikaneyama, Toyonaka, 560-0043 Japan
| | - Junpei Abe
- Department of Chemistry Osaka University, 1-1 Machikaneyama, Toyonaka, 560-0043 Japan
| | - Yasuhiro Kajihara
- Department of Chemistry Osaka University, 1-1 Machikaneyama, Toyonaka, 560-0043 Japan.
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10
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Chau TH, Chernykh A, Ugonotti J, Parker BL, Kawahara R, Thaysen-Andersen M. Glycomics-Assisted Glycoproteomics Enables Deep and Unbiased N-Glycoproteome Profiling of Complex Biological Specimens. Methods Mol Biol 2023; 2628:235-263. [PMID: 36781790 DOI: 10.1007/978-1-0716-2978-9_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Mass spectrometry-driven glycomics and glycoproteomics, the system-wide profiling of detached glycans and intact glycopeptides from biological samples, respectively, are powerful approaches to interrogate the heterogenous glycoproteome. Efforts to develop integrated workflows employing both glycomics and glycoproteomics have been invested since the concerted application of these complementary approaches enables a deeper exploration of the glycoproteome. This protocol paper outlines, step-by-step, an integrated -omics technology, the "glycomics-assisted glycoproteomics" method, that first establishes the N-glycan fine structures and their quantitative distribution pattern of protein extracts via porous graphitized carbon-LC-MS/MS. The N-glycome information is then used to augment and guide the challenging reversed-phase LC-MS/MS-based profiling of intact N-glycopeptides from the same protein samples. Experimental details and considerations relating to the sample preparation and the N-glycomics and N-glycoproteomics data collection, analysis, and integration are discussed. Benefits of the glycomics-assisted glycoproteomics method, which can be readily applied to both simple and complex biological specimens such as protein extracts from cells, tissues, and bodily fluids (e.g., serum), include quantitative information of the protein carriers and site(s) of glycosylation, site occupancy, and the site-specific glycan structures directly from biological samples. The glycomics-assisted glycoproteomics method therefore facilitates a comprehensive view of the complexity and dynamics of the heterogenous glycoproteome.
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Affiliation(s)
- The Huong Chau
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Anastasia Chernykh
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Julian Ugonotti
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Benjamin L Parker
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Rebeca Kawahara
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia.
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW, Australia.
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Aichi, Japan.
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11
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Harvey EJ, Ashiru-Oredope D, Hill LF, Demirjian A; United Kingdom Health Security Agency Staphylococcus capitis Incident Management Team. Need for standardized vancomycin dosing for coagulase-negative staphylococci in hospitalized infants. Clin Microbiol Infect 2023; 29:10-2. [PMID: 36195185 DOI: 10.1016/j.cmi.2022.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/01/2022] [Accepted: 09/19/2022] [Indexed: 01/26/2023]
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12
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Ramarajan MG, Saraswat M, Budhraja R, Garapati K, Raymond K, Pandey A. Mass spectrometric analysis of chondroitin sulfate-linked peptides. J Proteins Proteom 2022; 13:187-203. [PMID: 36213313 PMCID: PMC9526814 DOI: 10.1007/s42485-022-00092-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 11/26/2022]
Abstract
Chondroitin sulfate proteoglycans (CSPGs) are extracellular matrix components composed of linear glycosaminoglycan (GAG) side chains attached to a core protein. CSPGs play a vital role in neurodevelopment, signal transduction, cellular proliferation and differentiation and tumor metastasis through interaction with growth factors and signaling proteins. These pleiotropic functions of proteoglycans are regulated spatiotemporally by the GAG chains attached to the core protein. There are over 70 chondroitin sulfate-linked proteoglycans reported in cells, cerebrospinal fluid and urine. A core glycan linker of 3-6 monosaccharides attached to specific serine residues can be extended by 20-200 disaccharide repeating units making intact CSPGs very large and impractical to analyze. The current paradigm of CSPG analysis involves digesting the GAG chains by chondroitinase enzymes and analyzing either the protein part, the disaccharide repeats, or both by mass spectrometry. This method, however, provides no information about the site of attachment or the composition of linker oligosaccharides and the degree of sulfation and/or phosphorylation. Further, the analysis by mass spectrometry and subsequent identification of novel CSPGs is hampered by technical challenges in their isolation, less optimal ionization and data analysis. Unknown identity of the linker oligosaccharide also makes it more difficult to identify the glycan composition using database searching approaches. Following chondroitinase digestion of long GAG chains linked to tryptic peptides, we identified intact GAG-linked peptides in clinically relevant samples including plasma, urine and dermal fibroblasts. These intact glycopeptides including their core linker glycans were identified by mass spectrometry using optimized stepped higher energy collision dissociation and electron-transfer/higher energy collision dissociation combined with hybrid database search/de novo glycan composition search. We identified 25 CSPGs including three novel CSPGs that have not been described earlier. Our findings demonstrate the utility of combining enrichment strategies and optimized high-resolution mass spectrometry analysis including alternative fragmentation methods for the characterization of CSPGs. Supplementary Information The online version contains supplementary material available at 10.1007/s42485-022-00092-3.
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Affiliation(s)
- Madan Gopal Ramarajan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905 USA
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
- Manipal Academy of Higher Education (MAHE), Manipal, 576104 Karnataka India
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560 029 India
| | - Mayank Saraswat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905 USA
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
- Manipal Academy of Higher Education (MAHE), Manipal, 576104 Karnataka India
| | - Rohit Budhraja
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905 USA
| | - Kishore Garapati
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905 USA
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India
- Manipal Academy of Higher Education (MAHE), Manipal, 576104 Karnataka India
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560 029 India
| | - Kimiyo Raymond
- Biochemical Genetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905 USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905 USA
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13
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Xin M, You S, Wu J, Xu Y, Li C, Zhu B, Shen J, Chen Z, Dang L, Dan W, Zhang X, Sun S. Evaluation of absorbent cotton for glycopeptide enrichment. Anal Bioanal Chem 2022; 414:8245-8253. [PMID: 36181511 DOI: 10.1007/s00216-022-04353-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 11/30/2022]
Abstract
Selecting proper and efficient glycopeptide enrichment approaches are essential for mass spectrometry-based glycoproteomics since glycopeptides are usually with microheterogeneity and low abundance in most biological samples. Herein, we introduced a cotton hydrophilic interaction liquid chromatography (HILIC) approach for large-scale glycopeptide enrichment with 80% acetonitrile/1% trifluoroacetic acid as the optimal sample loading buffer. The comparison of cotton HILIC with Venusil HILIC and mixed anion-exchange (MAX) approaches indicated that cotton HILIC was superior in overall glycopeptide enrichment, whereas Venusil HILIC preferred in complex glycan structures and MAX performed better with high mannose glycans. Exploration of capacity and recovery rate of cotton HILIC illustrated that 5mg cotton packed in a 200μL tip achieved a reasonable glycopeptide enrichment performance (~6% recovery) from ~0.5mg peptides. In conclusion, cotton HILIC can be used as an optional glycopeptide enrichment approach in glycosylation analysis with its specific merit.
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Affiliation(s)
- Miaomiao Xin
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China.,South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Research Institute of Fish Culture and Hydrobiology, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, 38925, Vodnany, Czech Republic
| | - Shanshan You
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Jingyu Wu
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Yintai Xu
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Cheng Li
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Bojing Zhu
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Jiechen Shen
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Zexuan Chen
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Liuyi Dang
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Wei Dan
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Xinwen Zhang
- Department of Medical Genetics, Xi'an Fourth Hospital, Xi'an, Shaanxi Province, 710004, People's Republic of China
| | - Shisheng Sun
- College of Life Science, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China.
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Zhi Y, Jia L, Shen J, Li J, Chen Z, Zhu B, Hao Z, Xu Y, Sun S. Formylation: an undesirable modification on glycopeptides and glycans during storage in formic acid solution. Anal Bioanal Chem 2022; 414:3311-3317. [PMID: 35229171 DOI: 10.1007/s00216-022-03989-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 11/30/2022]
Abstract
In glycomic and glycoproteomic studies, solutions containing diluted organic acids such as formic acid (FA) have been widely used for dissolving intact glycopeptide and glycan samples prior to mass spectrometry analysis. Here, we show that an undesirable + 28 Da modification occurred in a time-dependent manner when the glycan and glycopeptide samples were stored in FA solution at - 20 °C. We confirmed that this unexpected modification was caused by formylation between the hydroxyl groups of glycans and FA with a relatively low reaction rate. As this incomplete modification affected the glycan and glycopeptide identification and quantification in glycomic and glycoproteomic studies, the storage at - 20 °C should be avoided once the glycan and glycopeptide samples have been dissolved in FA solution.
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Affiliation(s)
- Yuan Zhi
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Li Jia
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Jiechen Shen
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Jun Li
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Zexuan Chen
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Bojing Zhu
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Zhifang Hao
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Yintai Xu
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China
| | - Shisheng Sun
- College of Life Sciences, Northwest University, Xi'an, Shaanxi Province, 710069, People's Republic of China.
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15
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Angata K, Wagatsuma T, Togayachi A, Sato T, Sogabe M, Tajiri K, Ozawa T, Nagashima I, Shimizu H, Iijima S, Korenaga M, Kuno A, Kaji H, Mizokami M, Narimatsu H. O-glycosylated HBsAg peptide can induce specific antibody neutralizing HBV infection. Biochim Biophys Acta Gen Subj 2022; 1866:130020. [PMID: 34582939 DOI: 10.1016/j.bbagen.2021.130020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/31/2021] [Accepted: 09/23/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Hepatitis B virus (HBV), which causes hepatitis, liver cirrhosis, and hepatocellular carcinoma, is a global human health problem. HBV contains three envelope proteins, S-, M-, and L-hepatitis B surface antigen (HBsAg). We recently found that O-glycosylated M-HBsAg, reactive with jacalin lectin, is one of the primary components of HBV DNA-containing virus particles. Thus, we aimed to analyze and target the glycosylation of HBsAg. METHODS HBsAg prepared from the serum of Japanese patients with HBV were analyzed using mass spectrometry. The glycopeptide modified with O-glycan was generated and used for immunization. The specificity of the generated antibody and the HBV infection inhibition activity was examined. RESULTS Mass spectrometry analysis revealed that T37 and/or T38 on M-HBsAg of genotype C were modulated by ±NeuAc(α2,3)Gal(β1,3)GalNAc. Chemically and enzymatically synthesized O-glycosylated peptide (Glyco-PS2) induced antibodies that recognize mainly PreS2 in M-HBsAg not in L-HBsAg, whereas the non-glycosylated peptide (PS2) induced antisera recognizing L-HBsAg but not O-glycosylated M-HBsAg. The removal of O-glycan from M-HBsAg partly decreased the reactivity of the Glyco-PS2 antibody, suggesting that peptide part was also recognized by the antibody. The antibody further demonstrated the inhibition of HBV infection in human hepatic cells in vitro. CONCLUSIONS Glycosylation of HBsAg occurs differently in different HBsAgs in a site-specific manner. The new Glyco-PS2 antibody, recognizing O-glycosylated M-HBsAg of genotype C, could inhibit HBV infection. GENERAL SIGNIFICANCE The detailed analysis of HBsAg identified different glycosylations of HBV surface. The glycosylated peptide based on mass spectrometry analysis showed higher potential to induce functional antibody against HBV.
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Affiliation(s)
- Kiyohiko Angata
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Takanori Wagatsuma
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan; Genome Medical Sciences Project, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
| | - Akira Togayachi
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Takashi Sato
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Maki Sogabe
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Kazuto Tajiri
- Graduate School of Medicine and Pharmaceutical Science, Faculty of Medicine, University of Toyama, Toyama, Toyama, Japan
| | - Tatsuhiko Ozawa
- Graduate School of Medicine and Pharmaceutical Science, Faculty of Medicine, University of Toyama, Toyama, Toyama, Japan
| | - Izuru Nagashima
- Multicellular System Regulation Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Hiroki Shimizu
- Multicellular System Regulation Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Sayuki Iijima
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
| | - Masaaki Korenaga
- Hepatitis Information Centre, Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
| | - Atsushi Kuno
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Hiroyuki Kaji
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Masashi Mizokami
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
| | - Hisashi Narimatsu
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan.
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16
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Li K, Li R, Zou P, Li L, Wang H, Kong D, Zheng G, Li LL. Glycopeptide-nanotransforrs eyedrops with enhanced permeability and retention for preventing fundus neovascularization. Biomaterials 2022; 281:121361. [PMID: 34991034 DOI: 10.1016/j.biomaterials.2021.121361] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/19/2021] [Accepted: 12/29/2021] [Indexed: 02/06/2023]
Abstract
Efficient and non-invasive drug delivery to the fundus has always been a medical difficulty. Here, a co-assembled glycopeptide nanotransforrs (GPNTs) named MRP@DOX as a drug delivery system is reported. The MRP@DOX co-assemble nanoparticles consisting of glycopeptide, cationic peptide, and doxorubicin (DOX). The nanoparticles are positively charged with the nano-size, which can be induced transformation by legumain cleavage. Once administrate to the eyes, MRP@DOX has a high penetration through the ocular surface to specifically targets M2 macrophages in the fundus. Then, the mannose receptor mediates phagocytosis and intracellular highly expressed legumain induces its nanofibrous transformation, which contributes to a 44.7% DOX retention in cells at 24 h than that of the non-transformed controls (MAP@DOX: 5.1%). The nanofiber transformation provides an inhibition of exocytosis, which explains the higher retention of the delivered drug. In the mouse OIR model, MRP@DOX completely restores the physiological angiogenesis and reduces pathological neovascularization. Pathological neovascularization branches and cell nuclei that break through the inner limiting membrane are reduced by 55% and 72%, respectively, which are 25% and 20% less than those in the non-transformed controls. In addition, MRP@DOX also has good histocompatibility, which provides a possible strategy for non-invasive treatment of fundus diseases in the future.
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Affiliation(s)
- Ke Li
- The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Hennan, 450052, China; Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Hennan, 450052, China
| | - Ruxiang Li
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No.11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Pengfei Zou
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No.11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Li Li
- The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Hennan, 450052, China
| | - Huajun Wang
- The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Hennan, 450052, China
| | - Deqian Kong
- The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Hennan, 450052, China; Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Hennan, 450052, China
| | - Guangying Zheng
- The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Hennan, 450052, China.
| | - Li-Li Li
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No.11 Beiyitiao, Zhongguancun, Beijing, 100190, China.
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17
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Nakakita SI, Nakakita Y, Kurihara R, Hirabayashi J. Preparation of Glycan Arrays Using Glycopeptides Derived From Biomaterials. Methods Mol Biol 2022; 2556:45-58. [PMID: 36175626 DOI: 10.1007/978-1-0716-2635-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In general, viruses recognize host cell surface glycans, but the measurement of virus-host cell glycan interaction is not widely operated. This is not only because commercially available, structure-defined glycans are limited, but also because such interactions, if any, between viruses and isolated glycans are relatively weak, and thus, difficult to detect by conventional methods, e.g., enzyme-linked immune-sorbent assay. We describe a practical method to detect virus binding to glycans; for this, preparation of glycan arrays using glycopeptides derived from biomaterials is necessary. In this context, neoglycoprotein is produced using bovine serum albumin (BSA) and commercially available glycopeptides, with which influenza viruses are detected using an evanescent-field-activated fluorescence scanner. It is clearly shown that H1N1 strains of influenza virus recognize BSA, to which DiNeuα2-6bianntena-peptide (SGP) is covalently linked, while on the other hand H5N1 strains recognize BSA linked to DiNeuα2-3bianntena-peptide (α2,3SGP).
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Affiliation(s)
- Shin-Ichi Nakakita
- Department of Functional Glycomics, Life Science Research Center, Kagawa University, Kagawa, Japan.
| | - Yukari Nakakita
- Department of Functional Glycomics, Life Science Research Center, Kagawa University, Kagawa, Japan
| | - Ryohsuke Kurihara
- Department of Chemistry for Medicine, Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Jun Hirabayashi
- Department of Functional Glycomics, Life Science Research Center, Kagawa University, Kagawa, Japan
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18
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Go EP, Zhang S, Ding H, Kappes JC, Sodroski J, Desaire H. The opportunity cost of automated glycopeptide analysis: case study profiling the SARS-CoV-2 S glycoprotein. Anal Bioanal Chem 2021; 413:7215-7227. [PMID: 34448030 PMCID: PMC8390178 DOI: 10.1007/s00216-021-03621-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/29/2021] [Accepted: 08/16/2021] [Indexed: 11/29/2022]
Abstract
Glycosylation analysis of viral glycoproteins contributes significantly to vaccine design and development. Among other benefits, glycosylation analysis allows vaccine developers to assess the impact of construct design or producer cell line choices for vaccine production, and it is a key measure by which glycoproteins that are produced for use in vaccination can be compared to their native viral forms. Because many viral glycoproteins are multiply glycosylated, glycopeptide analysis is a preferrable approach for mapping the glycans, yet the analysis of glycopeptide data can be cumbersome and requires the expertise of an experienced analyst. In recent years, a commercial software product, Byonic, has been implemented in several instances to facilitate glycopeptide analysis on viral glycoproteins and other glycoproteomics data sets, and the purpose of the study herein is to determine the strengths and limitations of using this software, particularly in cases relevant to vaccine development. The glycopeptides from a recombinantly expressed trimeric S glycoprotein of the SARS-CoV-2 virus were first analyzed using an expert-based analysis strategy; subsequently, analysis of the same data set was completed using Byonic. Careful assessment of instances where the two methods produced different results revealed that the glycopeptide assignments from Byonic contained more false positives than true positives, even when the data were assessed using a 1% false discovery rate. The work herein provides a roadmap for removing the spurious assignments that Byonic generates, and it provides an assessment of the opportunity cost for relying on automated assignments for glycopeptide data sets from viral glycoproteins.
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Affiliation(s)
- Eden P Go
- Department of Chemistry, University of Kansas, Lawrence, KS, 66049, USA
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, 02215, USA
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - John C Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, AL, 35233, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, 02215, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS, 66049, USA.
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19
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Sturm S, Dowle A, Audsley N, Isaac RE. Mass spectrometric characterisation of the major peptides of the male ejaculatory duct, including a glycopeptide with an unusual zwitterionic glycosylation. J Proteomics 2021; 246:104307. [PMID: 34174476 DOI: 10.1016/j.jprot.2021.104307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 11/25/2022]
Abstract
Peptides present in the seminal fluid of Drosophila melanogaster can function as antimicrobial agents, enzyme inhibitors and as pheromones that elicit physiological and behavioural responses in the post-mated female. Understanding the molecular interactions by which these peptides influence reproduction requires detailed knowledge of their molecular structures. However, this information is often lacking and cannot be gleaned from just gene sequences and standard proteomic data. We now report the native structures of four seminal fluid peptides (andropin, CG42782, Met75C and Acp54A1) from the ejaculatory duct of male D. melanogaster. The mature CG42782, Met75C and Acp54A1 peptides each have a cyclic structure formed by a disulfide bond, which will reduce conformational freedom and enhance metabolic stability. In addition, the presence of a penultimate Pro in CG42782 and Met75C will help prevent degradation by carboxypeptidases. Met75C has undergone more extensive post-translational modifications with the formation of an N-terminal pyroglutamyl residue and the attachment of a mucin-like O-glycan to the side chain of Thr4. Both of these modifications are expected to further enhance the stability of the secreted peptide. The glycan has a rare zwitterionic structure comprising an O-linked N-acetyl hexosamine, a hexose and, unusually, phosphoethanolamine. A survey of various genomes showed that andropin, CG42782, and Acp54A1 are relatively recent genes and are restricted to the melanogaster subgroup. Met75C, however, was also found in members of the obscura species groups and in Scaptodrosophila lebanonensis. Andropin is related to the cecropin gene family and probably arose by tandem gene duplication, whereas CG42782, Met75C and Acp54A1 possibly emerged de novo. We speculate that the post-translational modifications that we report for these gene products will be important not only for a biological function, but also for metabolic stability and might also facilitate transport across tissue barriers, such as the blood-brain barrier of the female insect. BIOLOGICAL SIGNIFICANCE: Seminal fluid peptides of D. melanogaster function as antimicrobials, enzyme inhibitors and as pheromones, eliciting physiological and behavioural responses in the post-mated female. A fuller understanding of how these peptides influence reproduction requires knowledge not only of their primary structure, but also of their post-translational modification. However, this information is often lacking and difficult to glean from standard proteomic data. The reported modifications, including the unusual glycosylation, adds much to our knowledge of this important class of peptides in this model organism, par excellence.
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Affiliation(s)
| | - Adam Dowle
- Bioscience Technology Facility, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Neil Audsley
- Institute for Agri-Food Research and Innovation, Newcastle University, Newcastle Upon-Tyne NE1 7RU, UK.
| | - R Elwyn Isaac
- School of Biology, University of Leeds, Leeds LS2 9JT, UK.
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20
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Lee MW, Yeon SH, Heo BY, Kwon J, Ryu H, Lee HJ, Yun HJ, Jo DY, Song IC. Impact of pre-transplant use of antibiotics on the graft-versus-host disease in adult patients with hematological malignancies. ACTA ACUST UNITED AC 2021; 26:96-102. [PMID: 33459581 DOI: 10.1080/16078454.2021.1872957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Changes in fecal microbiota affect the incidence and extent of graft-versus-host disease (GVHD) after allogeneic hematopoietic stem cell transplantation (HSCT). Most patients with hematological malignancies receive antibiotics for the treatment of febrile neutropenia prior to allogeneic HSCT, and pre-transplant use of antibiotics may influence the fecal microbiota and GVHD. METHODS We retrospectively analysed consecutive adult patients with hematological malignancies who received allogeneic HSCT at Chungnam National University Hospital between 2007 and 2018. Pre-transplant use of antibiotics was defined as the use of antibiotics before conditioning chemotherapy. RESULTS This study included 131 patients with a median age of 46 (range, 18-71) years: 76 (58%) patients were AML, 28 (21.4%) with ALL, 23 (17.6%) with MDS, and 4 (3.1%) with CML. All patients received calcineurin inhibitors with short-course methotrexate for GVHD prophylaxis. A total of 31 (23.7%) patients received anti-thymocyte globulin. All patients received antibiotics prior to HSCT: 70 (53.4%) patients received glycopeptide, 114 (87.0%) received cefepime, 87 (66.4%) received piperacillin/tazobactam, and 51 (38.9%) received carbapenem. Patients who received glycopeptide had more frequently extensive chronic GVHD (cGVHD) than those who did not (51.1% vs. 28.1% at 5 years) and had more frequently cGVHD of the lung (34.8% vs. 15.8% at 5 years). Pre-transplant use of glycopeptide did not affect the overall survival (OS) or GVHD- and relapse-free survival (GRFS) (median OS; 49 months in glycopeptide group vs. not reached in non-glycopeptide group, p=0.475; median GRFS; 9 months in glycopeptide group vs. 16 months in non-glycopeptide group, p=0.092). CONCLUSION Pre-transplant use of glycopeptide tends to increase the incidence of extensive cGVHD.
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Affiliation(s)
- Myung-Won Lee
- Department of Internal Medicine and Center of Hematopoietic stem cell transplantation, Chungnam National University Hospital, Daejeon, South Korea.,Center of Hematopoietic stem cell transplantation, Chungnam National University Hospital, Daejeon, South Korea
| | - Sang-Hoon Yeon
- Department of Internal Medicine and Center of Hematopoietic stem cell transplantation, Chungnam National University Hospital, Daejeon, South Korea
| | - Bu-Yeon Heo
- Department of Infection Biology, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Jaeyul Kwon
- Department of Infection Biology, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Hyewon Ryu
- Department of Internal Medicine and Center of Hematopoietic stem cell transplantation, Chungnam National University Hospital, Daejeon, South Korea
| | - Hyo-Jin Lee
- Department of Internal Medicine and Center of Hematopoietic stem cell transplantation, Chungnam National University Hospital, Daejeon, South Korea
| | - Hwan-Jung Yun
- Department of Internal Medicine and Center of Hematopoietic stem cell transplantation, Chungnam National University Hospital, Daejeon, South Korea
| | - Deog-Yeon Jo
- Department of Internal Medicine and Center of Hematopoietic stem cell transplantation, Chungnam National University Hospital, Daejeon, South Korea.,Center of Hematopoietic stem cell transplantation, Chungnam National University Hospital, Daejeon, South Korea
| | - Ik-Chan Song
- Department of Internal Medicine and Center of Hematopoietic stem cell transplantation, Chungnam National University Hospital, Daejeon, South Korea.,Center of Hematopoietic stem cell transplantation, Chungnam National University Hospital, Daejeon, South Korea
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21
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Wang C, Gao W, Yan S, Zhu XQ, Suo X, Liu X, Gupta N, Hu M. N-glycome and N-glycoproteome of a hematophagous parasitic nematode Haemonchus. Comput Struct Biotechnol J 2021; 19:2486-2496. [PMID: 34025939 PMCID: PMC8113779 DOI: 10.1016/j.csbj.2021.04.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 12/24/2022] Open
Abstract
N-glycosylation is a physiologically vital post-translational modification of proteins in eukaryotic organisms. Initial work on Haemonchus contortus - a blood-sucking nematode of ruminants with a broad geographical distribution - has shown that this parasite harbors N-glycans with exclusive chitobiose modifications. Besides, several immunogenic proteins (e.g., amino- and metallo-peptidases) are known to be N-glycosylated in adult worms. However, an informative atlas of N-glycosylation in H. contortus is not yet available. Herein, we report 291 N-glycosylated proteins with a total of 425 modification sites in the parasite. Among them, many peptidase families (e.g., peptidase C1 and M1) including potential vaccine targets were enriched. Notably, the glycan-rich conjugates are distributed primarily in the intestine and gonads of adult worms, and consequently hidden from the host's immune system. Collectively, these data provide a comprehensive atlas of N-glycosylation in a prevalent parasitic nematode while underlining its significance for infection, immunity and prevention.
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Key Words
- Con A, concanavalin A
- Fuc, fucose
- Gal, galactose
- Gal-Fuc, galactosylated fucose
- GalNAc, N-acetylgalactosamine
- GlcNAc, N-acetylglucosamine
- Glycopeptide
- HILIC, hydrophilic interaction chromatography
- Haemonchus contortus
- LC-MS/MS, liquid chromatography-tandem mass spectrometry
- MALDI-ToF MS, matrix-assisted laser desorption ionization-time of flight mass spectrometry
- Man, mannose
- Mass spectrometry
- N-glycan
- N-glycosylation
- OST, oligosaccharyltransferase
- PNGase A/F, peptide-N-glycosidase A/F
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Affiliation(s)
- Chunqun Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Wenjie Gao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China,College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Shi Yan
- Institut für Parasitologie, Veterinärmedizinische Universität, Wien, Austria
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xun Suo
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
| | - Xin Liu
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Nishith Gupta
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Department of Molecular Parasitology, Faculty of Life Sciences, Humboldt University, Berlin, Germany,Department of Biological Sciences, Birla Institute of Technology and Science Pilani (BITS-P), Hyderabad, India
| | - Min Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Corresponding author at: College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan St., Wuhan, Hubei Province 430070, China.
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22
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Saadé J, Biacchi M, Giorgetti J, Lechner A, Beck A, Leize-Wagner E, François YN. Analysis of Monoclonal Antibody Glycopeptides by Capillary Electrophoresis-Mass Spectrometry Coupling (CE-MS). Methods Mol Biol 2021; 2271:97-106. [PMID: 33908002 DOI: 10.1007/978-1-0716-1241-5_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Glycosylation is a crucial posttranslational modification (PTM) that might affect the safety and efficacy of monoclonal antibodies (mAbs). Capillary electrophoresis-mass spectrometry (CE-MS) enables the characterization of the primary structure of mAbs. A bottom-up proteomic workflow is designed to provide detailed information about the glycosylation. In this chapter, we describe the validated experimental protocol applied for the characterization and relative quantification of mAbs N-glycosylation at the glycopeptide level.
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Affiliation(s)
- Josiane Saadé
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg, France
| | - Michael Biacchi
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg, France
| | - Jérémie Giorgetti
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg, France
| | - Antony Lechner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg, France
| | - Alain Beck
- Centre d'Immunologie Pierre Fabre, Saint-Julien-en-Genevois, France
| | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg, France
| | - Yannis-Nicolas François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, Strasbourg, France.
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23
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Ogasawara S, Suzuki K, Naruchi K, Nakamura S, Shimabukuro J, Tsukahara N, Kaneko MK, Kato Y, Murata T. Crystal structure of an anti-podoplanin antibody bound to a disialylated O-linked glycopeptide. Biochem Biophys Res Commun 2020; 533:57-63. [PMID: 32921414 DOI: 10.1016/j.bbrc.2020.08.103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 12/18/2022]
Abstract
Podoplanin (PDPN) is a highly O-glycosylated glycoprotein that is utilized as a specific lymphatic endothelial marker under pathophysiological conditions. We previously developed an anti-human PDPN (hPDPN) monoclonal antibody (mAb), clone LpMab-3, which recognizes the epitope, including both the peptides and the attached disialy-core-l (NeuAcα2-3Galβl-3 [NeuAcα2-6]GalNAcαl-O-Thr) structure at the Thr76 residue in hPDPN. However, it is unclear if the mAb binds directly to both the peptides and glycans. In this study, we synthesized the binding epitope region of LpMab-3 that includes the peptide (-67LVATSVNSV-T-GIRIEDLP84-) possessing a disialyl-core-1 O-glycan at Thr76, and we determined the crystal structure of the LpMab-3 Fab fragment that was bound to the synthesized glycopeptide at a 2.8 Å resolution. The six amino acid residues and two sialic acid residues are directly associated with four complementarity-determining regions (CDRs; H1, H2, H3, and L3) and four CDRs (H2, H3, L1, and L3), respectively. These results suggest that IgG is advantageous for generating binders against spacious epitopes such as glycoconjugates.
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Affiliation(s)
- Satoshi Ogasawara
- Graduate School of Science, Chiba University, Chiba, Japan; Molecular Chirality Research Center, Chiba University, Chiba, Japan.
| | - Kano Suzuki
- Graduate School of Science, Chiba University, Chiba, Japan
| | - Kentaro Naruchi
- Medicinal Chemistry Pharmaceuticals, Co., Ltd., Sapporo, Japan
| | - Seiwa Nakamura
- Graduate School of Science, Chiba University, Chiba, Japan
| | | | | | - Mika K Kaneko
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yukinari Kato
- Tohoku University Graduate School of Medicine, Sendai, Japan; New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
| | - Takeshi Murata
- Graduate School of Science, Chiba University, Chiba, Japan; Molecular Chirality Research Center, Chiba University, Chiba, Japan.
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24
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Apostol CR, Hay M, Polt R. Glycopeptide drugs: A pharmacological dimension between "Small Molecules" and "Biologics". Peptides 2020; 131:170369. [PMID: 32673700 PMCID: PMC7448947 DOI: 10.1016/j.peptides.2020.170369] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/12/2020] [Accepted: 07/06/2020] [Indexed: 12/16/2022]
Abstract
Peptides are an important class of molecules with diverse biological activities. Many endogenous peptides, especially neuropeptides and peptide hormones, play critical roles in development and regulating homeostasis. Furthermore, as drug candidates their high receptor selectivity and potent binding leads to reduced off-target interactions and potential negative side effects. However, the therapeutic potential of peptides is severely hampered by their poor stability in vivo and low permeability across biological membranes. Several strategies have been successfully employed over the decades to address these concerns, and one of the most promising strategies is glycosylation. It has been demonstrated in numerous cases that glycosylation is an effective synthetic approach to improve the pharmacokinetic profiles and membrane permeability of peptides. The effects of glycosylation on peptide stability and peptide-membrane interactions in the context of blood-brain barrier penetration will be explored. Numerous examples of glycosylated analogues of endogenous peptides targeting class A and B G-protein coupled receptors (GPCRs) with an emphasis on O-linked glycopeptides will be reviewed. Notable examples of N-, S-, and C-linked glycopeptides will also be discussed. A small section is devoted to synthetic methods for the preparation of glycopeptides and requisite amino acid glycoside building blocks.
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Affiliation(s)
- Christopher R Apostol
- Dept. of Chemistry & Biochemistry, BIO5, The University of Arizona, Tucson, AZ 85721, USA.
| | - Meredith Hay
- Evelyn F. McKnight Brain Institute, Dept. of Physiology, The University of Arizona, Tucson, AZ 85724, USA
| | - Robin Polt
- Dept. of Chemistry & Biochemistry, BIO5, The University of Arizona, Tucson, AZ 85721, USA
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25
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Zhao G, Xu Y, Ouyang H, Luo Y, Sun S, Wang Z, Yang J, Jin C. Protein O-mannosylation affects protein secretion, cell wall integrity and morphogenesis in Trichoderma reesei. Fungal Genet Biol 2020; 144:103440. [PMID: 32758529 DOI: 10.1016/j.fgb.2020.103440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 07/23/2020] [Accepted: 07/29/2020] [Indexed: 10/23/2022]
Abstract
Protein O-mannosyltransferases (PMTs) initiate O-mannosylation of proteins in the ER. Trichoderma reesei strains displayed a single representative of each PMT subfamily, Trpmt1, Trpmt2 and Trpmt4. In this work, two knockout strains ΔTrpmt1and ΔTrpmt4were obtained. Both mutants showed retarded growth, defective cell walls, reduced conidiation and decreased protein secretion. Additionally, the ΔTrpmt1strain displayed a thermosensitive growth phenotype, while the ΔTrpmt4 strain showed abnormal polarity. Meanwhile, OETrpmt2 strain, in which the Trpmt2 was over-expressed, exhibited increased conidiation, enhanced protein secretion and abnormal polarity. Using a lectin enrichment method and MS/MS analysis, 173 O-glycoproteins, 295 O-glycopeptides and 649 O-mannosylation sites were identified as the targets of PMTs in T. reesei. These identified O-mannoproteins are involved in various physiological processes such as protein folding, sorting, transport, quality control and secretion, as well as cell wall integrity and polarity. By comparing proteins identified in the mutants and its parent strain, the potential specific protein substrates of PMTs were identified. Based on our results, TrPMT1 is specifically involved inO-mannosylation of intracellular soluble proteins and secreted proteins, specially glycosidases. TrPMT2 is involved inO-mannosylation of secreted proteins and GPI-anchor proteins, and TrPMT4 mainly modifies multiple transmembrane proteins. The TrPMT1-TrPMT4 complex is responsible for O-mannosylation of proteins involved in cell wall integrity. Overexpression of TrPMT2 enhances protein secretion, which might be a new strategy to improve expression efficiency in T. reesei.
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Affiliation(s)
- Guangya Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yueqiang Xu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China
| | - Haomiao Ouyang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanming Luo
- Public Technology Service Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shutao Sun
- Public Technology Service Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhongfu Wang
- College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Jinghua Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Cheng Jin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China; National Engineering Research Center for Non-food Bio-refinery, Guangxi Academy of Sciences, Nanning 530007, Guangxi, China.
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26
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Stevenson GW, Giuvelis D, Cormier J, Cone K, Atherton P, Krivitsky R, Warner E, St Laurent B, Dutra J, Bidlack JM, Szabò L, Polt R, Bilsky EJ. Behavioral pharmacology of the mixed-action delta-selective opioid receptor agonist BBI-11008: studies on acute, inflammatory and neuropathic pain, respiration, and drug self-administration. Psychopharmacology (Berl) 2020; 237:1195-1208. [PMID: 31912192 PMCID: PMC8106974 DOI: 10.1007/s00213-019-05449-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/27/2019] [Indexed: 01/23/2023]
Abstract
RATIONALE AND OBJECTIVES The present study characterized the behavioral pharmacology of a novel, mixed-action delta-selective (78:1) opioid receptor agonist, BBI-11008. This glycopeptide drug candidate was tested in assays assessing antinociception (acute, inflammatory, and neuropathic pain-like conditions) and side-effect endpoints (respiratory depression and drug self-administration). RESULTS BBI-11008 had a 78-fold greater affinity for the delta opioid receptor than the mu receptor, and there was no binding to the kappa opioid receptor. BBI-11008 (3.2-100; 10-32 mg kg-1, i.v.) and morphine (1-10; 1-3.2 mg kg-1, i.v.) produced antinociceptive and anti-allodynic effects in assays of acute thermal nociception and complete Freund's adjuvant (CFA)-induced inflammatory pain, with BBI-11008 being less potent than morphine in both assays. BBI-11008 (1-18 mg kg-1, i.v.) had similar efficacy to gabapentin (10-56 mg kg-1, i.v.) in a spinal nerve ligation (SNL) model of neuropathic pain. In the respiration assay, with increasing %CO2 exposure, BBI-11008 produced an initial increase (32 mg kg-1, s.c.) and then decrease (56 mg kg-1, s.c.) in minute volume (MV) whereas morphine (3.2-32 mg kg-1, s.c.) produced dose-dependent decreases in MV. In the drug self-administration procedure, BBI-11008 did not maintain self-administration at any dose tested. CONCLUSIONS These results suggest that the glycopeptide drug candidate possesses broad-spectrum antinociceptive and anti-allodynic activity across a range of pain-like conditions. Relative to morphine or fentanyl, the profile for BBI-11008 in the respiration and drug self-administration assays suggests that BBI-11008 may have less pronounced deleterious side effects. Continued assessment of this compound is warranted.
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MESH Headings
- Analgesics, Opioid/administration & dosage
- Analgesics, Opioid/chemistry
- Animals
- CHO Cells
- Cricetinae
- Cricetulus
- Dose-Response Relationship, Drug
- Humans
- Inflammation/drug therapy
- Inflammation/metabolism
- Inflammation/psychology
- Male
- Mice
- Morphine/administration & dosage
- Neuralgia/drug therapy
- Neuralgia/metabolism
- Neuralgia/psychology
- Pain Measurement/drug effects
- Pain Measurement/psychology
- Rats
- Rats, Sprague-Dawley
- Receptors, Opioid, delta/agonists
- Receptors, Opioid, delta/metabolism
- Receptors, Opioid, kappa/agonists
- Receptors, Opioid, kappa/metabolism
- Receptors, Opioid, mu/agonists
- Receptors, Opioid, mu/metabolism
- Respiratory Mechanics/drug effects
- Respiratory Mechanics/physiology
- Self Administration
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Affiliation(s)
- Glenn W Stevenson
- Department of Psychology, University of New England, Biddeford, ME, 04005, USA.
- Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, USA.
| | - Denise Giuvelis
- Department of Biomedical Sciences, University of New England College of Osteopathic Medicine, Biddeford, ME, 04005, USA
| | - James Cormier
- Department of Biomedical Sciences, University of New England College of Osteopathic Medicine, Biddeford, ME, 04005, USA
| | - Katherine Cone
- Department of Psychology, University of New England, Biddeford, ME, 04005, USA
| | - Phillip Atherton
- Department of Psychology, University of New England, Biddeford, ME, 04005, USA
| | - Rebecca Krivitsky
- Department of Psychology, University of New England, Biddeford, ME, 04005, USA
| | - Emily Warner
- Department of Psychology, University of New England, Biddeford, ME, 04005, USA
| | - Brooke St Laurent
- Department of Psychology, University of New England, Biddeford, ME, 04005, USA
| | - Julio Dutra
- Department of Psychology, University of New England, Biddeford, ME, 04005, USA
| | - Jean M Bidlack
- Department of Pharmacology and Physiology, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Lajos Szabò
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Robin Polt
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Edward J Bilsky
- Center for Excellence in the Neurosciences, University of New England, Biddeford, ME, USA
- Department of Biomedical Sciences, University of New England College of Osteopathic Medicine, Biddeford, ME, 04005, USA
- Department of Biomedical Sciences College of Osteopathic Medicine, Pacific Northwest University of Health Sciences, Yakima, WA, 98901, USA
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27
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Canassa-DeLeo T, Campo VL, Rodrigues LC, Marchiori MF, Fuzo C, Brigido MM, Sandomenico A, Ruvo M, Maranhão AQ, Dias-Baruffi M. Multifaceted antibodies development against synthetic α-dystroglycan mucin glycopeptide as promising tools for dystroglycanopathies diagnostic. Glycoconj J 2019; 37:77-93. [PMID: 31823246 DOI: 10.1007/s10719-019-09893-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/23/2019] [Accepted: 10/31/2019] [Indexed: 01/19/2023]
Abstract
Dystroglycanopathies are diseases characterized by progressive muscular degeneration and impairment of patient's quality of life. They are associated with altered glycosylation of the dystrophin-glycoprotein (DGC) complex components, such as α-dystroglycan (α-DG), fundamental in the structural and functional stability of the muscle fiber. The diagnosis of dystroglycanopathies is currently based on the observation of clinical manifestations, muscle biopsies and enzymatic measures, and the available monoclonal antibodies are not specific for the dystrophic hypoglycosylated muscle condition. Thus, modified α-DG mucins have been considered potential targets for the development of new diagnostic strategies toward these diseases. In this context, this work describes the synthesis of the hypoglycosylated α-DG mimetic glycopeptide NHAc-Gly-Pro-Thr-Val-Thr[αMan]-Ile-Arg-Gly-BSA (1) as a potential tool for the development of novel antibodies applicable to dystroglycanopathies diagnosis. Glycopeptide 1 was used for the development of polyclonal antibodies and recombinant monoclonal antibodies by Phage Display technology. Accordingly, polyclonal antibodies were reactive to glycopeptide 1, which enables the application of anti-glycopeptide 1 antibodies in immune reactive assays targeting hypoglycosylated α-DG. Regarding monoclonal antibodies, for the first time variable heavy (VH) and variable light (VL) immunoglobulin domains were selected by Phage Display, identified by NGS and described by in silico analysis. The best-characterized VH and VL domains were cloned, expressed in E. coli Shuffle T7 cells, and used to construct a single chain fragment variable that recognized the Glycopeptide 1 (GpαDG1 scFv). Molecular modelling of glycopeptide 1 and GpαDG1 scFv suggested that their interaction occurs through hydrogen bonds and hydrophobic contacts involving amino acids from scFv (I51, Y33, S229, Y235, and P233) and R8 and α-mannose from Glycopeptide 1.
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Affiliation(s)
- Thais Canassa-DeLeo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Vanessa Leiria Campo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil.,Centro Universitário Barão de Mauá, Rua Ramos de Azevedo 423, Jardim Paulista, CEP, Ribeirão Preto, 14090-180, SP, Brazil
| | - Lílian Cataldi Rodrigues
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Marcelo Fiori Marchiori
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Carlos Fuzo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Marcelo Macedo Brigido
- Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília, DF, CEP 70910-900, Brazil
| | - Annamaria Sandomenico
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone, 16, 80134, Naples, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone, 16, 80134, Naples, Italy
| | - Andrea Queiroz Maranhão
- Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília, DF, CEP 70910-900, Brazil
| | - Marcelo Dias-Baruffi
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, Ribeirão Preto, SP, 14040-903, Brazil.
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Zhang S, Cao X, Liu C, Li W, Zeng W, Li B, Chi H, Liu M, Qin X, Tang L, Yan G, Ge Z, Liu Y, Gao Q, Lu H. N- glycopeptide Signatures of IgA 2 in Serum from Patients with Hepatitis B Virus-related Liver Diseases. Mol Cell Proteomics 2019; 18:2262-2272. [PMID: 31501225 PMCID: PMC6823847 DOI: 10.1074/mcp.ra119.001722] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Indexed: 12/11/2022] Open
Abstract
N-glycosylation alteration has been reported in liver diseases. Characterizing N-glycopeptides that correspond to N-glycan structure with specific site information enables better understanding of the molecular pathogenesis of liver damage and cancer. Here, unbiased quantification of N-glycopeptides of a cluster of serum glycoproteins with 40-55 kDa molecular weight (40-kDa band) was investigated in hepatitis B virus (HBV)-related liver diseases. We used an N-glycopeptide method based on 18O/16O C-terminal labeling to obtain 82 comparisons of serum from patients with HBV-related hepatocellular carcinoma (HCC) and liver cirrhosis (LC). Then, multiple reaction monitoring (MRM) was performed to quantify N-glycopeptide relative to the protein content, especially in the healthy donor-HBV-LC-HCC cascade. TPLTAN205ITK (H5N5S1F1) and (H5N4S2F1) corresponding to the glycopeptides of IgA2 were significantly elevated in serum from patients with HBV infection and even higher in HBV-related LC patients, as compared with healthy donor. In contrast, the two glycopeptides of IgA2 fell back down in HBV-related HCC patients. In addition, the variation in the abundance of two glycopeptides was not caused by its protein concentration. The altered N-glycopeptides might be part of a unique glycan signature indicating an IgA-mediated mechanism and providing potential diagnostic clues in HBV-related liver diseases.
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Affiliation(s)
- Shu Zhang
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Xinyi Cao
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Chao Liu
- Beijing Advanced Innovation Center for Precision Medicine, Beihang University, Beijing 100083, China
| | - Wei Li
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Wenfeng Zeng
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190, China
| | - Baiwen Li
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiaotong University, Shanghai 201620, China
| | - Hao Chi
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing 100190, China
| | - Mingqi Liu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xue Qin
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Lingyi Tang
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Guoquan Yan
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Zefan Ge
- State Key Laboratory for Novel Software Technology, Nanjing University, Nanjing 210046, China
| | - Yinkun Liu
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Qiang Gao
- Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China.
| | - Haojie Lu
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Chemistry, Fudan University, Shanghai 200433, China; NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China.
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Abstract
Glycosylation is one of the most ubiquitous and complex post-translational modifications (PTMs). It plays pivotal roles in various biological processes. Studies at the glycopeptide level are typically considered as a downstream work resulting from enzymatic digested glycoproteins. Less attention has been focused on glycosylated endogenous signaling peptides due to their low abundance, structural heterogeneity and the lack of enabling analytical tools. Here, protocols are presented to isolate and characterize glycosylated neuropeptides utilizing nanoflow liquid chromatography coupled with mass spectrometry (LC-MS). We first demonstrate how to extract neuropeptides from raw tissues and perform further separation/cleanup before MS analysis. Then we describe hybrid MS methods for glycosylated neuropeptide profiling and site-specific analysis. We also include recommendations for data analysis to identify glycosylated neuropeptides in crustaceans where a complete neuropeptide database is still lacking. Other strategies and future directions are discussed to provide readers with alternative approaches and further unravel biological complexity rendered by glycosylation.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Qinjingwen Cao
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, United States; School of Pharmacy, University of Wisconsin-Madison, Madison, WI, United States.
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Park H, You S, Kim J, Kim W, Do J, Jang Y, Kim D, Lee J, Ha J, Oh DB, Kim JI, Kim HH. Seventeen O-acetylated N-glycans and six O-acetylation sites of Myozyme identified using liquid chromatography-tandem mass spectrometry. J Pharm Biomed Anal 2019; 169:188-95. [PMID: 30877930 DOI: 10.1016/j.jpba.2019.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/06/2019] [Accepted: 03/06/2019] [Indexed: 12/24/2022]
Abstract
O-acetylated sialic acid (SA) attached to the N-glycans of therapeutic glycoproteins reportedly inhibit sialidase activity, increase protein half-life, decrease protein antigenicity, and stabilize protein conformation. Recombinant human acid α-glucosidase (Myozyme) is the only drug approved by the United States Food and Drug Administration for the treatment of Pompe disease. In this study, unreported N-glycans containing O-acetylated SA in Myozyme and the relative quantities of total glycans were investigated using liquid chromatography (LC)-electrospray ionization (ESI)-high-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS). The 17 N-glycans (6.4% of total glycans) containing mono-, di-, mono/di-, and di/di-O-acetylated N-acetylneuraminic acid (Neu5Ac) were identified with mass accuracy, glycan-generated fragment ions, and the retention time on an LC column. The analysis of peptides containing mono- and/or di-O-acetylated Neu5Ac ions sorted from all peptides using nano-LC-ESI-HCD-MS/MS confirmed six O-acetylation sites (Asn 140, Asn 233, Asn 390, Asn 470, Asn 652, and Asn 882), at least five of which (Asn 140, Asn 233, Asn 390, Asn 470, and Asn 652) could contribute to the drug efficacy or cellular uptake of Myozyme. This is the first study to identify N-glycans containing O-acetylated Neu5Ac and O-acetylation sites in Myozyme.
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Gao W, Li H, Liu L, Huang P, Wang Z, Chen W, Ye M, Yu X, Tian R. An integrated strategy for high-sensitive and multi-level glycoproteome analysis from low micrograms of protein samples. J Chromatogr A 2019; 1600:46-54. [PMID: 31036360 DOI: 10.1016/j.chroma.2019.04.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/26/2019] [Accepted: 04/15/2019] [Indexed: 01/09/2023]
Abstract
Glycosylation, as a biologically important protein post-translational modification, often alters on both glycosites and glycans, simultaneously. However, most of current approaches focused on biased profiling of either glycosites or glycans, and limited by time-consuming process and milligrams of starting protein material. We describe here a simple and integrated spintip-based glycoproteomics technology (termed Glyco-SISPROT) for achieving a comprehensive view of glycoproteome with shorter sample processing time and low microgram starting material. By carefully integrating and optimizing SCX, C18 and Concanavalin A (Con A) packing material and their combination in spintip format, both predigested peptides and protein lysates could be processed by Glyco-SISPROT with high efficiency. More importantly, deglycopeptide, intact glycopeptide and glycans released by multiple glycosidases could be readily collected from the same Glyco-SISPROT workflow for LC-MS analysis. In total, above 1850 glycosites in ˜1770 unique deglycopeptides were characterized from mouse liver by using either 100 μg of predigested peptides or directly using 100 μg of protein lysates, in which about 30% of glycosites were released by both PNGase F and Endos. To the best of our knowledge, this approach should be one of the most comprehensive glycoproteomic approaches by using limited protein starting material. One significant benefit of Glyco-SISPROT is that whole processing time is dramatically reduced from a few days to less than 6 h with good reproducibility when protein lysates were directly processed by Glyco-SISPROT. We expect that this method will be suitable for multi-level glycoproteome analysis of rare biological samples with high sensitivity.
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Affiliation(s)
- Weina Gao
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150080, China; Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, 518055, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Hongjie Li
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150080, China; Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Liping Liu
- Shenzhen People's Hospital, The First affiliated Hospital of Southern University of Science and Technology, Shenzhen, 518020, China
| | - Peiwu Huang
- Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, 518055, China; State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong Special Administrative Region, China
| | - Zhikun Wang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150080, China; Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wendong Chen
- Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xiaofang Yu
- Shenzhen People's Hospital, The First affiliated Hospital of Southern University of Science and Technology, Shenzhen, 518020, China
| | - Ruijun Tian
- Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen, 518055, China.
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Marchiori MF, Iossi GP, Bortot LO, Dias-Baruffi M, Campo VL. Synthesis of novel triazole-derived glycopeptides as analogs of α-dystroglycan mucins. Carbohydr Res 2019; 472:23-32. [PMID: 30453095 DOI: 10.1016/j.carres.2018.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/05/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022]
Abstract
α-Dystroglycan (α-DG) mucins are essential for maintenance of the structural and functional stability of the muscle fiber and, when hypoglycosylated, they are directly involved in pathological processes such as dystroglycanopathies. Thus, this work reports the synthesis of the novel 1,2,3-triazole-derived glycosyl amino acids αGlcNAc-1-O-triazol-2Manα-ThrOH (1) and Gal-β1,4-αGlcNAc-1-O-triazol-2Manα-ThrOH (2), followed by solid-phase assembly to get the corresponding glycopeptides NHAcThrVal[αGlcNAc-1-triazol-2Manα]ThrIleArgGlyOH (3) and NHAcThrVal[Gal-β1,4-αGlcNAc-1-triazol-2Manα]ThrIleArgGlyOH (4) as analogs of α-DG mucins. The glycosyl amino acids 1 (72%) and 2 (35%) were synthesized by Cu(I)-assisted 1,3-dipolar azide-alkyne cycloaddition reactions (CuAAC) between the azide-glycosyl amino acid αManN3-FmocThrOBn (5) and the corresponding alkyne-functionalyzed sugars 2'-propynyl-αGlcNAc (6) and 2'-propynyl-Gal-β1,4-αGlcNAc (7), followed by hydrogenation reactions. Subsequently, glycopeptides 3 (23%) and 4 (12%) were obtained by solid phase synthesis, involving sequential couplings of Fmoc-protected amino acids or the glycosyl amino acids 1 and 2, followed by cleavage from resin, N-acetylation and O-deacetylation (NaOMe) reactions. Lastly, enzymatic galactosylation of glycopeptide 3 with bovine β-1,4-GalT showed that it was not a substrate for this enzyme, which could be better elucidated by docking simulations with β-1,4-GalT.
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Affiliation(s)
- Marcelo Fiori Marchiori
- Faculty of Pharmaceutical Sciences of Ribeirão Preto - USP, Av. do Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
| | - Giulia Pompolo Iossi
- Faculty of Pharmaceutical Sciences of Ribeirão Preto - USP, Av. do Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
| | - Leandro Oliveira Bortot
- Faculty of Pharmaceutical Sciences of Ribeirão Preto - USP, Av. do Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
| | - Marcelo Dias-Baruffi
- Faculty of Pharmaceutical Sciences of Ribeirão Preto - USP, Av. do Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil
| | - Vanessa Leiria Campo
- Faculty of Pharmaceutical Sciences of Ribeirão Preto - USP, Av. do Café S/N, CEP 14040-903, Ribeirão Preto, SP, Brazil; Barão de Mauá University Centre, 423 Ramos de Azevedo Street, Jardim Paulista, CEP 14090-180, Ribeirão Preto, SP, Brazil.
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Lee YD, Jeon YH, Kim YH, Ha KY, Hur JW, Ryu KS, Kim JS, Kim YJ. Clinical Characteristics and Outcomes of Patients with Culture-Negative Pyogenic Spondylitis according to Empiric Glycopeptide Use. Infect Chemother 2019; 51:274-283. [PMID: 31583861 PMCID: PMC6779574 DOI: 10.3947/ic.2019.51.3.274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/02/2019] [Indexed: 12/14/2022] Open
Abstract
Background The optimal choice of antibiotics is challenging in culture-negative pyogenic spondylitis (PS). The empiric use of glycopeptides is suggested depending on various risk factors, although clinical data are sparse. This study aimed to analyze the clinical characteristics and outcomes of patients with culture-negative PS and evaluate the effect of empiric glycopeptide use on clinical outcomes in these patients. Materials and Methods Data on the characteristics, treatment, and outcomes of 175 patients diagnosed with PS were retrospectively obtained from the electronic database of a tertiary referral hospital from 2009 to 2016. Patients with negative culture results were grouped by the duration of glycopeptide treatment: glycopeptide therapy <28 days (Group A) and glycopeptide therapy ≥28 days (Group B). Results Of 89 patients with negative culture results, 78 were included in the analysis (Group A, n = 66; Group B, n = 12). The mean age of patients with negative culture results was 65.5 years, and 52.6% were male. The median follow-up duration was 573 (interquartile range [IQR], 83 – 1,037) days. The duration of intravenous glycopeptide therapy was 0.0 (IQR, 0.0 – 0.0) days and 55.5 (IQR, 37.0 – 75.7) days for Groups A and B, respectively. Patients who used glycopeptide longer empirically (Group B) had more commonly undergone a previous spinal procedure, including surgery (P = 0.024). The length of hospitalization, erythrocyte sedimentation rate, and C-reactive protein level were significantly higher in Group B compared with those in Group A (P <0.001, P <0.001, and P = 0.006, respectively). Regarding treatment modalities, patients in Group B underwent surgery more frequently (P = 0.017). The duration of parenteral antibiotic treatment was longer in Group B (P <0.001). Recurrence was noted in 7 patients (9.0%), and the recurrence rate was not significantly different between the 2 groups (Group A, 5/66 [7.6%]; Group B, 2/12 [16.7%]; P = 0.293). Conclusion The recurrence rate among patients with culture-negative PS was not different based on the duration of empiric glycopeptide use. However, considering the small sample size and heterogeneity of our study population, we suggest that it is reasonable to administer glycopeptide antibiotics in these patients depending on clinical risk factors. Further large-scale prospective studies are needed to obtain more evidence for appropriate antibiotic treatment.
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Affiliation(s)
- Yong Dae Lee
- Division of Infectious Disease, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| | - Yoon Hee Jeon
- Division of Infectious Disease, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Young Hoon Kim
- Department of Orthopedic Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kee Yong Ha
- Department of Orthopedic Surgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung Woo Hur
- Department of Neurosurgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyeong Sik Ryu
- Department of Neurosurgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jin Sung Kim
- Department of Neurosurgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Youn Jeong Kim
- Division of Infectious Disease, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Slack TJ, Li W, Shi D, McArthur JB, Zhao G, Li Y, Xiao A, Khedri Z, Yu H, Liu Y, Chen X. Triazole-linked transition state analogs as selective inhibitors against V. cholerae sialidase. Bioorg Med Chem 2018; 26:5751-5757. [PMID: 30389408 PMCID: PMC6326775 DOI: 10.1016/j.bmc.2018.10.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/15/2018] [Accepted: 10/26/2018] [Indexed: 01/07/2023]
Abstract
Sialidases or neuraminidases are enzymes that catalyze the cleavage of terminal sialic acids from oligosaccharides and glycoconjugates. They play important roles in bacterial and viral infection and have been attractive targets for drug development. Structure-based drug design has led to potent inhibitors against neuraminidases of influenza A viruses that have been used successfully as approved therapeutics. However, selective and effective inhibitors against bacterial and human sialidases are still being actively pursued. Guided by crystal structural analysis, several derivatives of 2-deoxy-2,3-didehydro-N-acetylneuraminic acid (Neu5Ac2en or DANA) were designed and synthesized as triazole-linked transition state analogs. Inhibition studies revealed that glycopeptide analog E-(TriazoleNeu5Ac2en)-AKE and compound (TriazoleNeu5Ac2en)-A were selective inhibitors against Vibrio cholerae sialidase, while glycopeptide analog (TriazoleNeu5Ac2en)-AdE selectively inhibited Vibrio cholerae and A. ureafaciens sialidases.
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Affiliation(s)
- Teri J. Slack
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA,These authors contributed equality to this work
| | - Wanqing Li
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA,These authors contributed equality to this work
| | - Dashuang Shi
- Center for Genetic Medicine Research, Children’s National Medical Center, 111 Michigan Ave, NW, Washington DC 20012, USA
| | - John B. McArthur
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Gengxiang Zhao
- Center for Genetic Medicine Research, Children’s National Medical Center, 111 Michigan Ave, NW, Washington DC 20012, USA
| | - Yanhong Li
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
| | - An Xiao
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Zahra Khedri
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Hai Yu
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Yang Liu
- Center for Genetic Medicine Research, Children’s National Medical Center, 111 Michigan Ave, NW, Washington DC 20012, USA
| | - Xi Chen
- Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA,Corresponding author. Tel: +1 530 754 6037; fax: +1 530 752 8995. (X. Chen)
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Santos-Beneit F. Genome sequencing analysis of Streptomyces coelicolor mutants that overcome the phosphate-depending vancomycin lethal effect. BMC Genomics 2018; 19:457. [PMID: 29898657 PMCID: PMC6001138 DOI: 10.1186/s12864-018-4838-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/29/2018] [Indexed: 11/10/2022] Open
Abstract
Background Glycopeptide antibiotics inhibit bacterial cell-wall synthesis, and are important for the treatment of infections caused by multi drug-resistant strains of enterococci, streptococci and staphylococci. The main mechanism by which bacteria resist the action of glycopeptides is by producing a modified cell-wall in which the dipeptide D-Alanine-D-Alanine is substituted by D-Alanine-D-Lactate or D-Alanine-D-Serine. Recently, it has been shown that inorganic phosphate (Pi) induces hypersensitivity to vancomycin in Streptomyces coelicolor (which is highly resistant to the antibiotic in low-Pi media). This finding was surprising because the bacterium possesses the entire set of genes responsible for vancomycin resistance (VR); including those coding for the histidine kinase/response regulator pair VanS/VanR that activates the system. Results This work shows that high Pi amounts in the medium hamper the activation of the van promoters and consequently inhibit VR in S. coelicolor; i.e. the repression effect being stronger when basic or acidic forms of the nutrient are used. In addition, this work shows that lysozyme resistance is also highly regulated by the Pi concentration in the medium. At least five different mutations contribute to the overcoming of this repression effect over VR (but not over lysozyme resistance). Therefore, the interconnection of VR and lysozyme resistance mechanisms might be inexistent or complex. In particular, two kinds of mutant in which Pi control of VR has been lost (one class expresses the van genes in a constitutive manner; the other retains inducibility by vancomycin) have been isolated and further characterized in this study. Sequencing revealed that the first class of mutation conferred a single amino acid substitution in the second transmembrane helix of the VanS protein; whereas the other class hampered the expression or activity of a putative homolog (SCO1213) to the staphylococcal GatD protein. Complementation, phenotypic and bioinformatics analyses identified SCO1213, and its upstream gene (i.e. murT), as relevant genetic determinants involved with VR in S. coelicolor. Conclusion The genomic approach of this study together with other genetic and phenotypic analyses has allowed the identification of the uncharacterized murT-gatD Streptomyces genes and the characterization of their involvement with the Pi control of VR in S. coelicolor. Electronic supplementary material The online version of this article (10.1186/s12864-018-4838-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fernando Santos-Beneit
- Centre for Bacterial Cell Biology, Medical School, Newcastle University, Newcastle Upon Tyne, UK. .,Present address: Área de Microbiología, Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain.
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Wang H, Wang X, Xie C, Zhang M, Ruan H, Wang S, Jiang K, Wang F, Zhan C, Lu W, Wang H. Nanodisk-based glioma-targeted drug delivery enabled by a stable glycopeptide. J Control Release 2018; 284:26-38. [PMID: 29885416 DOI: 10.1016/j.jconrel.2018.06.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/16/2018] [Accepted: 06/04/2018] [Indexed: 01/06/2023]
Abstract
Heptapeptide ATWLPPR (A7R) binds specifically to vascular endothelial growth factor receptor 2 (VEGFR2) and neuropilin-1 (NRP-1) overexpressed in glioma cells, exhibiting high potential to achieve glioma targeted drug delivery. However, in vivo application of A7R peptide remains challenging due to the poor proteolytic stability and inaccessibility of A7R to the brain. To tackle these problems, we identified a glycosylated A7R derivative to enhance in vivo stability and brain transport efficacy. Our results showed that glycosylation of peptide could efficiently improve stability in serum, traverse the blood-brain barrier (BBB) and be uptaken by glioma cells. Furthermore, a novel glioma-targeted drug delivery system was constructed successfully employing glycopeptide as the targeting moiety and nanodisk as the carrier of paclitaxel (PTX). Physicochemical characterization showed that the nanodisk presented suitable size of 50 nm and adequate loading capacity of PTX. Compared to non-glycosylated nanodisk, glycopeptide modification could significantly enhance the uptake of disks by brain capillary endothelial cells through glucose transporter 1 (GLUT1). In vivo imaging and glioma fluorescence section results also indicated that nanodisks modified with glycopeptide showed a higher accumulation in glioma. The glycopeptide-enabled PTX delivery system exhibited superior anti-glioma efficacy in intracranial glioma xenograft model. These results suggested that glycosylation of peptides provided an efficient pathway to design multifunctional and stable brain targeting ligands.
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Togayachi A, Tomioka A, Fujita M, Sukegawa M, Noro E, Takakura D, Miyazaki M, Shikanai T, Narimatsu H, Kaji H. Identification of Poly-N-Acetyllactosamine-Carrying Glycoproteins from HL-60 Human Promyelocytic Leukemia Cells Using a Site-Specific Glycome Analysis Method, Glyco-RIDGE. J Am Soc Mass Spectrom 2018; 29:1138-1152. [PMID: 29675740 PMCID: PMC6004004 DOI: 10.1007/s13361-018-1938-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 05/15/2023]
Abstract
To elucidate the relationship between the protein function and the diversity and heterogeneity of glycans conjugated to the protein, glycosylation sites, glycan variation, and glycan proportions at each site of the glycoprotein must be analyzed. Glycopeptide-based structural analysis technology using mass spectrometry has been developed; however, complicated analyses of complex spectra obtained by multistage fragmentation are necessary, and sensitivity and throughput of the analyses are low. Therefore, we developed a liquid chromatography/mass spectrometry (MS)-based glycopeptide analysis method to reveal the site-specific glycome (Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile, Glyco-RIDGE). This method used accurate masses and retention times of glycopeptides, without requiring MS2, and could be applied to complex mixtures. To increase the number of identified peptide, fractionation of sample glycopeptides for reduction of sample complexity is required. Therefore, in this study, glycopeptides were fractionated into four fractions by hydrophilic interaction chromatography, and each fraction was analyzed using the Glyco-RIDGE method. As a result, many glycopeptides having long glycans were enriched in the highest hydrophilic fraction. Based on the monosaccharide composition, these glycans were thought to be poly-N-acetyllactosamine (polylactosamine [pLN]), and 31 pLN-carrier proteins were identified in HL-60 cells. Gene ontology enrichment analysis revealed that pLN carriers included many molecules related to signal transduction, receptors, and cell adhesion. Thus, these findings provided important insights into the analysis of the glycoproteome using our novel Glyco-RIDGE method. Graphical Abstract ᅟ.
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Affiliation(s)
- Akira Togayachi
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Azusa Tomioka
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Mika Fujita
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Masako Sukegawa
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Erika Noro
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Daisuke Takakura
- Project for utilizing glycans in the development of innovative drug discovery technologies, Japan Bioindustry Association (JBA), Hatchobori, Chuo-ku, Tokyo, 104-0032, Japan
| | - Michiyo Miyazaki
- Project for utilizing glycans in the development of innovative drug discovery technologies, Japan Bioindustry Association (JBA), Hatchobori, Chuo-ku, Tokyo, 104-0032, Japan
| | - Toshihide Shikanai
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan
| | - Hisashi Narimatsu
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan.
| | - Hiroyuki Kaji
- Glycoscience & Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science & Technology, Tsukuba, Ibaraki, 305-8568, Japan.
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Phillips-Jones MK, Harding SE. Antimicrobial resistance (AMR) nanomachines-mechanisms for fluoroquinolone and glycopeptide recognition, efflux and/or deactivation. Biophys Rev 2018; 10:347-362. [PMID: 29525835 PMCID: PMC5899746 DOI: 10.1007/s12551-018-0404-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 02/05/2018] [Indexed: 12/11/2022] Open
Abstract
In this review, we discuss mechanisms of resistance identified in bacterial agents Staphylococcus aureus and the enterococci towards two priority classes of antibiotics-the fluoroquinolones and the glycopeptides. Members of both classes interact with a number of components in the cells of these bacteria, so the cellular targets are also considered. Fluoroquinolone resistance mechanisms include efflux pumps (MepA, NorA, NorB, NorC, MdeA, LmrS or SdrM in S. aureus and EfmA or EfrAB in the enterococci) for removal of fluoroquinolone from the intracellular environment of bacterial cells and/or protection of the gyrase and topoisomerase IV target sites in Enterococcus faecalis by Qnr-like proteins. Expression of efflux systems is regulated by GntR-like (S. aureus NorG), MarR-like (MgrA, MepR) regulators or a two-component signal transduction system (TCS) (S. aureus ArlSR). Resistance to the glycopeptide antibiotic teicoplanin occurs via efflux regulated by the TcaR regulator in S. aureus. Resistance to vancomycin occurs through modification of the D-Ala-D-Ala target in the cell wall peptidoglycan and removal of high affinity precursors, or by target protection via cell wall thickening. Of the six Van resistance types (VanA-E, VanG), the VanA resistance type is considered in this review, including its regulation by the VanSR TCS. We describe the recent application of biophysical approaches such as the hydrodynamic technique of analytical ultracentrifugation and circular dichroism spectroscopy to identify the possible molecular effector of the VanS receptor that activates expression of the Van resistance genes; both approaches demonstrated that vancomycin interacts with VanS, suggesting that vancomycin itself (or vancomycin with an accessory factor) may be an effector of vancomycin resistance. With 16 and 19 proteins or protein complexes involved in fluoroquinolone and glycopeptide resistances, respectively, and the complexities of bacterial sensing mechanisms that trigger and regulate a wide variety of possible resistance mechanisms, we propose that these antimicrobial resistance mechanisms might be considered complex 'nanomachines' that drive survival of bacterial cells in antibiotic environments.
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Affiliation(s)
- Mary K Phillips-Jones
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, Loughborough, Leicestershire, UK.
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, Loughborough, Leicestershire, UK
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Xie Y, Liu Q, Li Y, Deng C. Core-shell structured magnetic metal-organic framework composites for highly selective detection of N- glycopeptides based on boronic acid affinity chromatography. J Chromatogr A 2018; 1540:87-93. [PMID: 29429745 DOI: 10.1016/j.chroma.2018.02.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 02/02/2018] [Accepted: 02/05/2018] [Indexed: 01/17/2023]
Abstract
Boronic acid affinity chromatography (BAAC) is one of the most significant methods in glycoproteomics research due to its low bias towards glycopeptides and easy enrichment process. In this work, core-shell structured magnetic metal-organic framework (MOF) composites with abundant boronic acid groups were designed and synthesized for selective glycopeptide enrichment based on BAAC. The as-prepared core-shell structured magnetic MOF composites (denoted as Fe3O4@PVP/PEI@MOF (B)) inherited strong magnetic responsiveness from the Fe3O4 core as well as ultrahigh surface area and abundant boronic acid sites from the MOF shell. The affinity between boronic acid and cis-diols groups endowed the composites with improved sensitivity (0.5 fmol/μL) and selectivity (1:100) towards glycopeptides, achieving remarkable results in glycopeptides detection from standard glycoprotein digests as well as complex bio-samples. As a result, a total of 209 N-glycosylation peptides from 89 different glycoproteins were identified from human serum digests, indicating its broad prospect in glycoproteome study.
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Affiliation(s)
- Yiqin Xie
- The Fifth People's Hospital of Shanghai, Department of Chemistry, Institutes of Biomedical Sciences, and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200433, China
| | - Qianjing Liu
- The Fifth People's Hospital of Shanghai, Department of Chemistry, Institutes of Biomedical Sciences, and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200433, China
| | - Yan Li
- Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai, 201206, China.
| | - Chunhui Deng
- The Fifth People's Hospital of Shanghai, Department of Chemistry, Institutes of Biomedical Sciences, and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200433, China.
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Baker MR, Ching T, Tabb DL, Li QX. Characterization of Plant Glycoproteins: Analysis of Plant Glycopeptide Mass Spectrometry Data with plantGlycoMS, a Package in the R Statistical Computing Environment. Methods Mol Biol 2018; 1789:205-220. [PMID: 29916082 DOI: 10.1007/978-1-4939-7856-4_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
plantGlycoMS is a set of tools, implemented in R, which is used to assess and validate glycopeptide spectrum matches (gPSMs). Validity of gPSMs is based on characteristic fragmentation patterns of glycopeptides (gPSMvalidator), adherence of the glycan moiety to the known N-glycan biosynthesis pathway in plants (pGlycoFilter), and elution of the glycopeptide within the observed retention time window of other glycopeptides sharing the same peptide backbone (rt.Restrict). plantGlycoMS also contains a tool for relative quantitation of glycoforms based on selected ion chromatograms of glycopeptide ion precursors in the mass spectrometry level 1 data (glycoRQ). This protocol walks the user through this workflow with example mass spectrometry data obtained for a plant glycoprotein.
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Affiliation(s)
- Margaret R Baker
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Travers Ching
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - David L Tabb
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical TB Research, Stellenbosch University, Cape Town, South Africa
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA.
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41
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Lee J, Hua S, Lee SH, Oh MJ, Yun J, Kim JY, Kim JH, Kim JH, An HJ. Designation of fingerprint glycopeptides for targeted glycoproteomic analysis of serum haptoglobin: insights into gastric cancer biomarker discovery. Anal Bioanal Chem 2017; 410:1617-1629. [PMID: 29285644 DOI: 10.1007/s00216-017-0811-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/14/2017] [Accepted: 12/06/2017] [Indexed: 02/06/2023]
Abstract
Gastric cancer (GC) is one of the leading causes of cancer-related death worldwide, largely because of difficulties in early diagnosis. Despite accumulating evidence indicating that aberrant glycosylation is associated with GC, site-specific localization of the glycosylation to increase specificity and sensitivity for clinical use is still an analytical challenge. Here, we created an analytical platform with a targeted glycoproteomic approach for GC biomarker discovery. Unlike the conventional glycomic approach with untargeted mass spectrometric profiling of released glycan, our platform is characterized by three key features: it is a target-protein-specific, glycosylation-site-specific, and structure-specific platform with a one-shot enzyme reaction. Serum haptoglobin enriched by immunoaffinity chromatography was subjected to multispecific proteolysis to generate site-specific glycopeptides and to investigate the macroheterogeneity and microheterogeneity. Glycopeptides were identified and quantified by nano liquid chromatography-mass spectrometry and nano liquid chromatography-tandem mass spectrometry. Ninety-six glycopeptides, each corresponding to a unique glycan/glycosite pairing, were tracked across all cancer and control samples. Differences in abundance between the two groups were marked by particularly high magnitudes. Three glycopeptides exhibited exceptionally high control-to-cancer fold changes along with receiver operating characteristic curve areas of 1.0, indicating perfect discrimination between the two groups. From the results taken together, our platform, which provides biological information as well as high sensitivity and reproducibility, may be useful for GC biomarker discovery. Graphical abstract ᅟ.
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Affiliation(s)
- Jua Lee
- Asia Glycomics Reference Site, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764, Republic of Korea.,Graduate School of Analytical Science and Technology, #455 College of Engineering II, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764, Republic of Korea
| | - Serenus Hua
- Asia Glycomics Reference Site, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764, Republic of Korea.,Graduate School of Analytical Science and Technology, #455 College of Engineering II, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764, Republic of Korea
| | - Sung Hyeon Lee
- GLYCAN Co. Ltd., Healthcare Innovation Park, 172 Dolma-ro, Bundang-gu, Seongnam, 13605, Republic of Korea
| | - Myung Jin Oh
- Asia Glycomics Reference Site, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764, Republic of Korea.,Graduate School of Analytical Science and Technology, #455 College of Engineering II, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764, Republic of Korea
| | - Jaekyung Yun
- Asia Glycomics Reference Site, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764, Republic of Korea.,Graduate School of Analytical Science and Technology, #455 College of Engineering II, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764, Republic of Korea
| | - Jin Young Kim
- Department of Mass Spectrometry, Korea Basic Science Institute, Ochang, 863-883, Republic of Korea
| | - Jae-Han Kim
- Department of Food and Nutrition, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764, Republic of Korea
| | - Jung Hoe Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Joo An
- Asia Glycomics Reference Site, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764, Republic of Korea. .,Graduate School of Analytical Science and Technology, #455 College of Engineering II, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764, Republic of Korea.
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Hui K, Upjohn L, Nalder M, Buising K, Pedagogos E, Nelson C, Kirkpatrick CMJ, Kong DCM. Vancomycin dosing in chronic high-flux haemodialysis: a systematic review. Int J Antimicrob Agents 2018; 51:678-86. [PMID: 29284156 DOI: 10.1016/j.ijantimicag.2017.12.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/04/2017] [Accepted: 12/16/2017] [Indexed: 11/23/2022]
Abstract
The aim of this study was to systematically evaluate whether non-weight-based dosing (non-WBD) or weight-based dosing (WBD) of vancomycin leads to a higher proportion of patients achieving the pharmacokinetic/pharmacodynamic target. Studies from January 1985 to February 2017 were identified through Cochrane, MEDLINE and Embase databases. Those conducted in adults with end-stage renal disease receiving high-flux haemodialysis (HD) and intravenous vancomycin were included. The primary outcome was the proportion of patients with a pre-HD vancomycin concentration of 15-20 mg/L and/or an area under the concentration-time curve/minimum inhibitory concentration (AUC/MIC) ratio ≥400. Of the 3948 studies screened, 5 met the inclusion criteria. The proportion of patients with pre-HD concentrations between 15-20 mg/L were 35% (non-WBD) and 13% (WBD) post-loading dose. During maintenance dosing, the proportion of patients with pre-HD concentrations between 15-20 mg/L were 37% (non-WBD) and 50-67% (WBD). The proportion of pre-HD concentrations <15 mg/L was greater in the non-WBD group post-loading dose but was similar between the non-WBD and WBD group during maintenance dosing. One study reported that all patients had an AUC/MIC ≥ 400 for micro-organisms with an MIC ≤ 1 mg/L for weight-based maintenance dosing. The limited data suggest that WBD may be preferential as there was a smaller proportion of pre-HD concentrations falling below 15 mg/L. However, larger well-designed studies of higher quality are required to provide guidance for vancomycin dosing in the high-flux HD setting. Future research should focus on reporting AUC/MIC ratios and exploring clinical outcomes in this patient population.
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Lin CH, Krisp C, Packer NH, Molloy MP. Development of a data independent acquisition mass spectrometry workflow to enable glycopeptide analysis without predefined glycan compositional knowledge. J Proteomics 2017; 172:68-75. [PMID: 29069609 DOI: 10.1016/j.jprot.2017.10.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 10/16/2017] [Accepted: 10/20/2017] [Indexed: 01/16/2023]
Abstract
Glycoproteomics investigates glycan moieties in a site specific manner to reveal the functional roles of protein glycosylation. Identification of glycopeptides from data-dependent acquisition (DDA) relies on high quality MS/MS spectra of glycopeptide precursors and often requires manual validation to ensure confident assignments. In this study, we investigated pseudo-MRM (MRM-HR) and data-independent acquisition (DIA) as alternative acquisition strategies for glycopeptide analysis. These approaches allow data acquisition over the full MS/MS scan range allowing data re-analysis post-acquisition, without data re-acquisition. The advantage of MRM-HR over DDA for N-glycopeptide detection was demonstrated from targeted analysis of bovine fetuin where all three N-glycosylation sites were detected, which was not the case with DDA. To overcome the duty cycle limitation of MRM-HR acquisition needed for analysis of complex samples such as plasma we trialed DIA. This allowed development of a targeted DIA method to identify N-glycopeptides without pre-defined knowledge of the glycan composition, thus providing the potential to identify N-glycopeptides with unexpected structures. This workflow was demonstrated by detection of 59 N-glycosylation sites from 41 glycoproteins from a HILIC enriched human plasma tryptic digest. 21 glycoforms of IgG1 glycopeptides were identified including two truncated structures that are rarely reported. SIGNIFICANCE We developed a data-independent mass spectrometry workflow to identify specific glycopeptides from complex biological mixtures. The novelty is that this approach does not require glycan composition to be pre-defined, thereby allowing glycopeptides carrying unexpected glycans to be identified. This is demonstrated through the analysis of immunoglobulins in human plasma where we detected two IgG1 glycoforms that are rarely observed.
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Affiliation(s)
- Chi-Hung Lin
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney 2109, Australia; Australian Proteome Analysis Facility, Macquarie University, Sydney 2109, Australia
| | - Christoph Krisp
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney 2109, Australia; Australian Proteome Analysis Facility, Macquarie University, Sydney 2109, Australia
| | - Nicolle H Packer
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney 2109, Australia
| | - Mark P Molloy
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney 2109, Australia; Australian Proteome Analysis Facility, Macquarie University, Sydney 2109, Australia.
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Giorgetti J, D'Atri V, Canonge J, Lechner A, Guillarme D, Colas O, Wagner-Rousset E, Beck A, Leize-Wagner E, François YN. Monoclonal antibody N-glycosylation profiling using capillary electrophoresis - Mass spectrometry: Assessment and method validation. Talanta 2017; 178:530-537. [PMID: 29136858 DOI: 10.1016/j.talanta.2017.09.083] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/20/2017] [Accepted: 09/28/2017] [Indexed: 01/08/2023]
Abstract
Characterization of therapeutic proteins represents a major challenge for analytical sciences due to their heterogeneity caused by post-translational modifications (PTM). Among these PTM, glycosylation which is possibly the most prominent, require comprehensive identification because of their major influence on protein structure and effector functions of monoclonal antibodies (mAbs). As a consequence, glycosylation profiling must be deeply characterized. For this application, several analytical methods such as separation-based or MS-based methods, were evaluated. However, no CE-ESI-MS approach has been assessed and validated. Here, we illustrate how the use of CE-ESI-MS method permits the comprehensive characterization of mAbs N-glycosylation at the glycopeptide level to perform relative quantitation of N-glycan species. Validation of the CE-ESI-MS method in terms of robustness and reproducibility was demonstrated through the relative quantitation of glycosylation profiles for ten different mAbs produced in different cell lines. Glycosylation patterns obtained for each mAbs were compared to Hydrophilic Interaction Chromatography of 2-aminobenzamide labelled glycans with fluorescence detector (HILIC-FD) analysis considered as a reference method. Very similar glycoprofiling were obtained with the CE-ESI-MS and HILIC-FD demonstrating the attractiveness of CE-ESI-MS method to characterize and quantify the glycosylation heterogeneity of a wide range of therapeutic mAbs with high accuracy and precision.
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Affiliation(s)
- Jérémie Giorgetti
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, France
| | - Valentina D'Atri
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Centre Médical Universitaire (CMU), Rue Michel-Servet 1, 1206 Geneva, Switzerland
| | - Julie Canonge
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, France
| | - Antony Lechner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, France
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Centre Médical Universitaire (CMU), Rue Michel-Servet 1, 1206 Geneva, Switzerland
| | - Olivier Colas
- Centre d'immunologie Pierre Fabre, Saint-Julien-en-Genevois, France
| | | | - Alain Beck
- Centre d'immunologie Pierre Fabre, Saint-Julien-en-Genevois, France
| | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, France
| | - Yannis-Nicolas François
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS), UMR 7140 (Unistra-CNRS), Université de Strasbourg, France.
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Yu Q, Wang B, Chen Z, Urabe G, Glover MS, Shi X, Guo LW, Kent KC, Li L. Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)-Enabled Intact Glycopeptide/Glycoproteome Characterization. J Am Soc Mass Spectrom 2017; 28:1751-1764. [PMID: 28695533 PMCID: PMC5711575 DOI: 10.1007/s13361-017-1701-4] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/28/2017] [Accepted: 04/29/2017] [Indexed: 05/04/2023]
Abstract
Protein glycosylation, one of the most heterogeneous post-translational modifications, can play a major role in cellular signal transduction and disease progression. Traditional mass spectrometry (MS)-based large-scale glycoprotein sequencing studies heavily rely on identifying enzymatically released glycans and their original peptide backbone separately, as there is no efficient fragmentation method to produce unbiased glycan and peptide product ions simultaneously in a single spectrum, and that can be conveniently applied to high throughput glycoproteome characterization, especially for N-glycopeptides, which can have much more branched glycan side chains than relatively less complex O-linked glycans. In this study, a redefined electron-transfer/higher-energy collision dissociation (EThcD) fragmentation scheme is applied to incorporate both glycan and peptide fragments in one single spectrum, enabling complete information to be gathered and great microheterogeneity details to be revealed. Fetuin was first utilized to prove the applicability with 19 glycopeptides and corresponding five glycosylation sites identified. Subsequent experiments tested its utility for human plasma N-glycoproteins. Large-scale studies explored N-glycoproteomics in rat carotid arteries over the course of restenosis progression to investigate the potential role of glycosylation. The integrated fragmentation scheme provides a powerful tool for the analysis of intact N-glycopeptides and N-glycoproteomics. We also anticipate this approach can be readily applied to large-scale O-glycoproteome characterization. Graphical Abstract ᅟ.
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Affiliation(s)
- Qing Yu
- School of Pharmacy, University of Wisconsin, Madison, WI, 53705, USA
| | - Bowen Wang
- Department of Surgery, Wisconsin Institutes for Medical Research, Madison, WI, 53705, USA
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Go Urabe
- Department of Surgery, Wisconsin Institutes for Medical Research, Madison, WI, 53705, USA
| | - Matthew S Glover
- School of Pharmacy, University of Wisconsin, Madison, WI, 53705, USA
- Cardiovascular Research Center Training Program in Translational Cardiovascular Science, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Xudong Shi
- Department of Surgery, Wisconsin Institutes for Medical Research, Madison, WI, 53705, USA
| | - Lian-Wang Guo
- Department of Surgery, Wisconsin Institutes for Medical Research, Madison, WI, 53705, USA
| | - K Craig Kent
- The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, Madison, WI, 53705, USA.
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA.
- Cardiovascular Research Center Training Program in Translational Cardiovascular Science, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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Abstract
The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.
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Affiliation(s)
- Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Christian Heiss
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.
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Shajahan A, Heiss C, Ishihara M, Azadi P. Glycomic and glycoproteomic analysis of glycoproteins-a tutorial. Anal Bioanal Chem 2017; 409:4483-4505. [PMID: 28585084 PMCID: PMC5498624 DOI: 10.1007/s00216-017-0406-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/27/2017] [Accepted: 05/10/2017] [Indexed: 01/18/2023]
Abstract
The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.
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Affiliation(s)
- Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Christian Heiss
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Mayumi Ishihara
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA.
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48
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Xie Y, Deng C, Li Y. Designed synthesis of ultra-hydrophilic sulfo-functionalized metal-organic frameworks with a magnetic core for highly efficient enrichment of the N-linked glycopeptides. J Chromatogr A 2017; 1508:1-6. [PMID: 28602507 DOI: 10.1016/j.chroma.2017.05.055] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 05/22/2017] [Accepted: 05/24/2017] [Indexed: 10/19/2022]
Abstract
Highly efficient extraction and enrichment of the N-linked glycopeptides from complex biological samples before mass spectrometry analysis remains important but challenging, due to the low abundance and suppression by proteins and salts. Herein, a facile route to an ultra-hydrophilic metal-organic frameworks (MOFs)-functionalized magnetic nanoparticle (Fe3O4@PDA@Zr-SO3H) was proposed. The as-prepared MOFs was endowed with excellent and unique properties, such as excellent hydrophilicity, ultrahigh surface area, and strong magnetic responsiveness. By virtue of these properties and based on hydrophilic interaction, Fe3O4@PDA@Zr-SO3H exhibited outstanding sensitivity and selectivity, remarkable recyclability and stability towards N-linked glycopeptide enrichment. In deep, a total of 177 N-linked glycopeptides, assigned to 85 different glycoproteins, were identified from the healthy human serum after treated with the Fe3O4@PDA@Zr-SO3H. These results confirmed that our strategy offered a promising platform for preparing hydrophilic metal-organic framework-functionalized magnetic nanoparticles for glycosylation analysis by mass spectrometry analysis.
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Affiliation(s)
- Yiqin Xie
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200433, China.
| | - Yan Li
- Pharmaceutical Analysis Department, School of Pharmacy, Fudan University, Shanghai 201203, China.
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Montero-Morales L, Maresch D, Castilho A, Turupcu A, Ilieva KM, Crescioli S, Karagiannis SN, Lupinek C, Oostenbrink C, Altmann F, Steinkellner H. Recombinant plant-derived human IgE glycoproteomics. J Proteomics 2017; 161:81-87. [PMID: 28400175 DOI: 10.1016/j.jprot.2017.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/20/2017] [Accepted: 04/04/2017] [Indexed: 10/19/2022]
Abstract
The increasing biotechnological interest in human IgE antibodies demands advanced systems which allow their proper expression. However, this is still a challenge due to the complexity of the molecule, particularly regarding the diverse N-glycosylation pattern. Here, we present the expression of recombinant IgE in wild type and glycan-engineered Nicotiana benthamiana plants and in-depth N-glycosylation analyses. Mass spectrometric profiling revealed that plant IgE has a site occupancy rate that ranges from non-occupied at glycosite 6 (GS6) to 100% occupancy at GS1 and 2. Similarly to human cell-derived IgE, plant versions carry complex N-glycans at GS1-5 and oligomannosidic structures at GS7. Computational modelling suggests that spatial position (or orientation) of glycans can impair processing or site occupancy on adjacent glycosites. IgE expressed in glycoengineered and wild type plants carry, respectively, GnGn and plant-typical GnGnXF structures at large homogeneity. This contrasts with the glycan diversity of HEK cell-derived IgE, carrying at least 20 different glycoforms. Importantly, IgE glycoengineering allows the control of its glycosylation, a so far unmet need when using well-established expression systems. This enables the elucidation of possible carbohydrate-dependent IgE functions. SIGNIFICANCE Targeted glycosylation of recombinant proteins may provide an advantage in therapeutic applications. Despite increasing biotechnological interest in IgE antibodies, knowledge and impact of glycosylation on this antibody class are scarce. With the ability to glyco-engineer recombinant IgE, we provide an important step towards the generation of IgE with other targeted N-glycans. This will facilitate detailed structure-function studies and may lead to the production of IgE with optimized activities.
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Affiliation(s)
- Laura Montero-Morales
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Daniel Maresch
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Alexandra Castilho
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Aysegül Turupcu
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Kristina M Ilieva
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences and Medicine, King's College London, Guy's Hospital, London, UK; Breast Cancer Now Research Unit, Research Oncology, Division of Cancer Studies, Faculty of Life Sciences and Medicine, King's College London, Guy's Hospital, London, UK
| | - Silvia Crescioli
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences and Medicine, King's College London, Guy's Hospital, London, UK
| | - Sophia N Karagiannis
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine, Faculty of Life Sciences and Medicine, King's College London, Guy's Hospital, London, UK; Breast Cancer Now Research Unit, Research Oncology, Division of Cancer Studies, Faculty of Life Sciences and Medicine, King's College London, Guy's Hospital, London, UK
| | - Christian Lupinek
- Dept. of Pathophysiology and Allergy Research, Medical University of Vienna, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Friedrich Altmann
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Herta Steinkellner
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
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Kemna MJ, Plomp R, van Paassen P, Koeleman CAM, Jansen BC, Damoiseaux JGMC, Cohen Tervaert JW, Wuhrer M. Galactosylation and Sialylation Levels of IgG Predict Relapse in Patients With PR3-ANCA Associated Vasculitis. EBioMedicine 2017; 17:108-118. [PMID: 28169190 PMCID: PMC5360573 DOI: 10.1016/j.ebiom.2017.01.033] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 01/18/2017] [Accepted: 01/23/2017] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVE The objective of our study is to investigate the Fc glycosylation profiles of both antigen-specific IgG targeted against proteinase 3 (PR3-ANCA) and total IgG as prognostic markers of relapse in patients with Granulomatosis with Polyangiitis (GPA). METHODS Seventy-five patients with GPA and a PR3-ANCA rise during follow-up were included, of whom 43 patients relapsed within a median period of 8 (2-16) months. The N-glycan at Asn297 of affinity-purified and denatured total IgG and PR3-ANCA was determined by mass spectrometry of glycopeptides in samples obtained at the time of the PR3-ANCA rise and at the time of the relapse or time-matched during remission. RESULTS Patients with total IgG1 exhibiting low galactosylation or low sialylation were highly prone to relapse after an ANCA rise (HR 3.46 [95%-CI 1.73-6.96], p<0.0001 and HR 3.22 [95%-CI 1.52-6.83], p=0.002, respectively). In relapsing patients, total IgG1 galactosylation, sialylation and bisection significantly decreased and fucosylation significantly increased from the time of the PR3-ANCA rise to the relapse (p<0.0001, p=0.0087, p<0.0001 and p=0.0025), while the glycosylation profile remained similar in non-relapsing patients. PR3-ANCA IgG1 galactosylation, sialylation and fucosylation of PR3-ANCA IgG1 decreased in relapsing patients (p=0.0073, p=0.0049 and p=0.0205), but also in non-relapsing patients (p=0.0007, p=0.0114 and p=0.0002), while bisection increased only in non-relapsing patients (p<0.0001). CONCLUSION While Fc glycosylation profiles have been associated with clinically manifest autoimmune diseases, in the present study we show that low galactosylation and sialyation in total IgG1 but not PR3-ANCA IgG1 predicts disease reactivation in patients with GPA who experience an ANCA rise during follow-up. We postulate that glycosylation profiles may be useful in pre-emptive therapy studies using ANCA rises as guideline.
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Affiliation(s)
- Michael J Kemna
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands; Department of Internal Medicine, Division of Nephrology and Clinical Immunology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Rosina Plomp
- Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Pieter van Paassen
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands; Department of Internal Medicine, Division of Nephrology and Clinical Immunology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Carolien A M Koeleman
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Bas C Jansen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan G M C Damoiseaux
- Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jan Willem Cohen Tervaert
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands.
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
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