1
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Zhang X, Su Z, Zhao Y, Wu D, Wu Y, Li G. Recent advances of nanopore technique in single cell analysis. Analyst 2024; 149:1350-1363. [PMID: 38312056 DOI: 10.1039/d3an01973j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Single cells and their dynamic behavior are closely related to biological research. Monitoring their dynamic behavior is of great significance for disease prevention. How to achieve rapid and non-destructive monitoring of single cells is a major issue that needs to be solved urgently. As an emerging technology, nanopores have been proven to enable non-destructive and label-free detection of single cells. The structural properties of nanopores enable a high degree of sensitivity and accuracy during analysis. In this article, we summarize and classify the different types of solid-state nanopores that can be used for single-cell detection and illustrate their specific applications depending on the size of the analyte. In addition, their research progress in material transport and microenvironment monitoring is also highlighted. Finally, a brief summary of existing research challenges and future trends in nanopore single-cell analysis is tentatively provided.
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Affiliation(s)
- Xue Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Zhuoqun Su
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Yan Zhao
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Yongning Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Guoliang Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
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2
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Schnider B, Escudero FL, Imberty A, Lisacek F. BiotechLec: an interactive guide of commercial lectins for glycobiology and biomedical research applications. Glycobiology 2023; 33:684-686. [PMID: 37083961 PMCID: PMC10627245 DOI: 10.1093/glycob/cwad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/14/2023] [Indexed: 04/22/2023] Open
Abstract
For decades, lectins have been used as probes in glycobiology and this usage has gradually spread to other domains of Life Science. Nowadays, researchers investigate glycan recognition with lectins in diverse biotechnology and clinical applications, addressing key questions regarding binding specificity. The latter is documented in scattered and heterogeneous sources, and this situation calls for a centralized and easy-access reference. To address this need, an on-line solution called BiotechLec (https://www.unilectin.eu/biotechlec) is proposed in a new section of UniLectin, a platform dedicated to lectin molecular knowledge.
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Affiliation(s)
- Boris Schnider
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, route de Drize 7, Geneva CH-1227, Switzerland
- Computer Science Department, University of Geneva, route de Drize 7, Geneva CH-1227, Switzerland
| | - Francisco L Escudero
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, route de Drize 7, Geneva CH-1227, Switzerland
| | - Anne Imberty
- University Grenoble Alpes, CNRS, CERMAV, 601 rue de la chimie, Grenoble 38000, France
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, route de Drize 7, Geneva CH-1227, Switzerland
- Computer Science Department, University of Geneva, route de Drize 7, Geneva CH-1227, Switzerland
- Section of Biology, University of Geneva, route de Drize 7, Geneva CH-1227, Switzerland
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3
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Yu W, Zhao X, Jalloh AS, Li Y, Zhao Y, Dinner B, Yang Y, Ouyang S, Tian T, Zhao Z, Yang R, Chen M, Lauvau G, Guo Z, Wu P, Li JP. Chemoenzymatic Measurement of LacNAc in Single-Cell Multiomics Reveals It as a Cell-Surface Indicator of Glycolytic Activity of CD8 + T Cells. J Am Chem Soc 2023; 145:12701-12716. [PMID: 37276352 PMCID: PMC10733619 DOI: 10.1021/jacs.3c02602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Despite the rich information about the physiological state of a cell encoded in the dynamic changes of cell-surface glycans, chemical methods to capture specific glycan epitopes at the single-cell level are quite limited. Here, we report a chemoenzymatic method for the single-cell detection of N-acetyllactosamine (LacNAc) by labeling LacNAc with a specific DNA barcode. The chemoenzymatic labeling does not alter the transcriptional status of immune cells and is compatible with multiple scRNA-seq platforms. Integrated analysis of LacNAc and the transcriptome of T cells at the single-cell level reveals that the amount of cell-surface LacNAc is significantly upregulated in activated CD8+ T cells but maintained at basal levels in resting CD8+ T cells (i.e., naive and central memory T cells). Further analysis confirms that LacNAc levels are positively correlated with the glycolytic activity of CD8+ T cells during differentiation. Taken together, our study demonstrates the feasibility of the chemoenzymatic detection of cell-surface glycan in single-cell RNA sequencing-based multiomics with TCR sequence and cell-surface epitope information (i.e., scTCR and CITE-seq), and provides a new way to characterize the biological role of glycan in diverse physiological states.
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Affiliation(s)
- Wenhao Yu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xinlu Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Abubakar S Jalloh
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1301 Morris Park Avenue, Bronx, New York 10461, United States
| | - Yachao Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yingying Zhao
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Brandon Dinner
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Yang Yang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shian Ouyang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Tian Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zihan Zhao
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing 210008, China
| | - Rong Yang
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing 210008, China
| | - Mingkuan Chen
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Gregoire Lauvau
- Department of Microbiology & Immunology, Albert Einstein College of Medicine of Yeshiva University, 1301 Morris Park Avenue, Bronx, New York 10461, United States
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Peng Wu
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1301 Morris Park Avenue, Bronx, New York 10461, United States
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jie P Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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4
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Wang D, Zhao Z, Xue X, Shi J, Shi W. Glycans in spent embryo culture medium are related to the implantation ability of blastocysts. Heliyon 2023; 9:e16255. [PMID: 37229168 PMCID: PMC10205493 DOI: 10.1016/j.heliyon.2023.e16255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 04/26/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
Research question Does glycan profile in spent blastocyst culture medium have the potential to be used as a biomarker to predict implantation outcome. Design A nested case-control study was conducted in Northwest women's and children's Hospital, Xi'an, China. The patients underwent fresh IVF/ICSI cycles with single blastocyst transfer were included. Total 78 cases were included and separated into groups according to success (n = 39) and failure (n = 39) implantation outcomes. The glycosylation patterns in spent blastocyst culture medium were detected by lectin microarray containing 37 lectins using pooled samples and confirmed by reversed lectin microarray using individual sample. Results Binding signals of 10 lectins were found to be different between samples from successful and failed implantation. And 8 of them were confirmed that glycans binding to lectin NPA, UEA-I, MAL-I, LCA and GNA were significantly increased while DBA and BPL were decreased in the successful implantation compared to failed implantation. The glycan binding to lectin PHA-E + L had no difference between two groups. No significant differences in the glycan profile were found in spent culture medium of embryos with different morphological grades except the glycan binding to UEA-I between blastocysts of Poor and blastocysts of Medium. Conclusion Detection of glycan profile in spent culture medium may lead to a novel non-invasive assessment assay of embryo viability. In addition, these results may be helpful to further understanding molecular mechanisms in embryo implantation.
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Affiliation(s)
- Dongyang Wang
- Translational Medicine Center, Northwest Women and Children’s Hospital, No.1616 Yanxiang Road, Xi’an, Shaanxi, 710061, People’s Republic of China
- Assisted Reproduction Center, Northwest Women and Children’s Hospital, No.73 Houzaimen, Xi’an, Shaanxi, 710003, People’s Republic of China
| | - Zhenghao Zhao
- Assisted Reproduction Center, Northwest Women and Children’s Hospital, No.73 Houzaimen, Xi’an, Shaanxi, 710003, People’s Republic of China
| | - Xia Xue
- Assisted Reproduction Center, Northwest Women and Children’s Hospital, No.73 Houzaimen, Xi’an, Shaanxi, 710003, People’s Republic of China
| | - Juanzi Shi
- Translational Medicine Center, Northwest Women and Children’s Hospital, No.1616 Yanxiang Road, Xi’an, Shaanxi, 710061, People’s Republic of China
- Assisted Reproduction Center, Northwest Women and Children’s Hospital, No.73 Houzaimen, Xi’an, Shaanxi, 710003, People’s Republic of China
| | - Wenhao Shi
- Translational Medicine Center, Northwest Women and Children’s Hospital, No.1616 Yanxiang Road, Xi’an, Shaanxi, 710061, People’s Republic of China
- Assisted Reproduction Center, Northwest Women and Children’s Hospital, No.73 Houzaimen, Xi’an, Shaanxi, 710003, People’s Republic of China
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5
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Simplifying the detection and monitoring of protein glycosylation during in vitro glycoengineering. Sci Rep 2023; 13:567. [PMID: 36631484 PMCID: PMC9834283 DOI: 10.1038/s41598-023-27634-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/03/2023] [Indexed: 01/13/2023] Open
Abstract
The majority of mammalian proteins are glycosylated, with the glycans serving to modulate a wide range of biological activities. Variations in protein glycosylation can have dramatic effects on protein stability, immunogenicity, antibody effector function, pharmacological safety and potency, as well as serum half-life. The glycosylation of therapeutic biologicals is a critical quality attribute (CQA) that must be carefully monitored to ensure batch-to-batch consistency. Notably, many factors can affect the composition of the glycans during glycoprotein production, and variations in glycosylation are among the leading causes of pharmaceutical batch rejection. Currently, the characterization of protein glycosylation relies heavily on methods that employ chromatography and/or mass spectrometry, which require a high level of expertise, are time-consuming and costly and, because they are challenging to implement during in-process biologics production or during in vitro glycan modification, are generally performed only post-production. Here we report a simplified approach to assist in monitoring glycosylation features during glycoprotein engineering, that employs flow cytometry using fluorescent microspheres chemically coupled to high-specificity glycan binding reagents. In our GlycoSense method, a range of carbohydrate-sensing microspheres with distinct optical properties may be combined into a multiplex suspension array capable of detecting multiple orthogonal glycosylation features simultaneously, using commonplace instrumentation, without the need for glycan release. The GlycoSense method is not intended to replace more detailed post-production glycan profiling, but instead, to complement them by potentially providing a cost-effective, rapid, yet robust method for use at-line as a process analytic technology (PAT) in a biopharmaceutical workflow or at the research bench. The growing interest in using in vitro glycoengineering to generate glycoproteins with well-defined glycosylation, provides motivation to demonstrate the capabilities of the GlycoSense method, which we apply here to monitor changes in the protein glycosylation pattern (GlycoPrint) during the in vitro enzymatic modification of the glycans in model glycoproteins.
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6
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Meyer CF, Seath CP, Knutson SD, Lu W, Rabinowitz JD, MacMillan DWC. Photoproximity Labeling of Sialylated Glycoproteins (GlycoMap) Reveals Sialylation-Dependent Regulation of Ion Transport. J Am Chem Soc 2022; 144:23633-23641. [PMID: 36525649 PMCID: PMC10782853 DOI: 10.1021/jacs.2c11094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Sialylation, the addition of sialic acid to glycans, is a crucial post-translational modification of proteins, contributing to neurodevelopment, oncogenesis, and immune response. In cancer, sialylation is dramatically upregulated. Yet, the functional biochemical consequences of sialylation remain mysterious. Here, we establish a μMap proximity labeling platform that utilizes metabolically inserted azidosialic acid to introduce iridium-based photocatalysts on sialylated cell-surface glycoproteins as a means to profile local microenvironments across the sialylated proteome. In comparative experiments between primary cervical cells and a cancerous cell line (HeLa), we identify key differences in both the global sialome and proximal proteins, including solute carrier proteins that regulate metabolite and ion transport. In particular, we show that cell-surface interactions between receptors trafficking ethanolamine and zinc are sialylation-dependent and impact intracellular metabolite levels. These results establish a μMap method for interrogating proteoglycan function and support a role for sialylated glycoproteins in regulating cell-surface transporters.
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Affiliation(s)
- Claudio F. Meyer
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Ciaran P. Seath
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Steve D. Knutson
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Wenyun Lu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Joshua D. Rabinowitz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Ludwig Institute for Cancer Research, Princeton University, Princeton, New Jersey, 08544, United States
| | - David W. C. MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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7
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Bojar D, Meche L, Meng G, Eng W, Smith DF, Cummings RD, Mahal LK. A Useful Guide to Lectin Binding: Machine-Learning Directed Annotation of 57 Unique Lectin Specificities. ACS Chem Biol 2022; 17:2993-3012. [PMID: 35084820 PMCID: PMC9679999 DOI: 10.1021/acschembio.1c00689] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glycans are critical to every facet of biology and medicine, from viral infections to embryogenesis. Tools to study glycans are rapidly evolving; however, the majority of our knowledge is deeply dependent on binding by glycan binding proteins (e.g., lectins). The specificities of lectins, which are often naturally isolated proteins, have not been well-defined, making it difficult to leverage their full potential for glycan analysis. Herein, we use a combination of machine learning algorithms and expert annotation to define lectin specificity for this important probe set. Our analysis uses comprehensive glycan microarray analysis of commercially available lectins we obtained using version 5.0 of the Consortium for Functional Glycomics glycan microarray (CFGv5). This data set was made public in 2011. We report the creation of this data set and its use in large-scale evaluation of lectin-glycan binding behaviors. Our motif analysis was performed by integrating 68 manually defined glycan features with systematic probing of computational rules for significant binding motifs using mono- and disaccharides and linkages. Combining machine learning with manual annotation, we create a detailed interpretation of glycan-binding specificity for 57 unique lectins, categorized by their major binding motifs: mannose, complex-type N-glycan, O-glycan, fucose, sialic acid and sulfate, GlcNAc and chitin, Gal and LacNAc, and GalNAc. Our work provides fresh insights into the complex binding features of commercially available lectins in current use, providing a critical guide to these important reagents.
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Affiliation(s)
- Daniel Bojar
- Department
of Chemistry and Molecular Biology and Wallenberg Centre for Molecular
and Translational Medicine, University of
Gothenburg, Gothenburg, Sweden 405 30
| | - Lawrence Meche
- Biomedical
Chemistry Institute, Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New
York, New York 10003, United States
| | - Guanmin Meng
- Department
of Chemistry, University of Alberta, Edmonton, Canada, T6G 2G2
| | - William Eng
- Biomedical
Chemistry Institute, Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New
York, New York 10003, United States
| | - David F. Smith
- Department
of Biochemistry, Glycomics Center, School of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - Richard D. Cummings
- Department
of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Lara K. Mahal
- Biomedical
Chemistry Institute, Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New
York, New York 10003, United States,Department
of Chemistry, University of Alberta, Edmonton, Canada, T6G 2G2,E-mail:
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8
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Oinam L, Hayashi R, Hiemori K, Kiyoi K, Sage-Ono K, Miura K, Ono M, Tateno H. Quantitative evaluation of glycan-binding specificity of recombinant concanavalin A produced in lettuce (Lactuca sativa). Biotechnol Bioeng 2022; 119:1781-1791. [PMID: 35394653 DOI: 10.1002/bit.28099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 02/25/2022] [Accepted: 03/31/2022] [Indexed: 11/10/2022]
Abstract
Concanavalin A (ConA), a mannose (Man)-specific leguminous lectin isolated from the jack bean (Canavalia ensiformis) seed extracts, was discovered over a century ago. Although ConA has been extensively applied in various life science research, recombinant mature ConA expression has not been fully established. Here, we aimed to produce recombinant ConA (rConA) in lettuce (Lactuca sativa) using an Agrobacterium tumefaciens-mediated transient expression system. rConA could be produced as a fully active form from soluble fractions of lettuce leaves and purified by affinity chromatography. From 12 g wet weight of lettuce leaves, 0.9 mg rConA could be purified. The glycan-binding properties of rConA were then compared with that of the native ConA isolated from jack bean using glycoconjugate microarray and frontal affinity chromatography. rConA demonstrated a glycan-binding specificity similar to nConA. Both molecules bound to N-glycans containing a terminal Man residue. Consistent with previous reports, terminal Manα1-6Man was found to be an essential unit for the high-affinity binding of rConA and nConA, while bisecting GlcNAc diminished the binding of rConA and nConA to Manα1-6Man-terminated N-glycans. These results demonstrate that the fully active rConA could be produced using the A. tumefaciens-mediated transient expression system and used as a recombinant substitute for nConA.
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Affiliation(s)
- Lalhaba Oinam
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Ryoma Hayashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Keiko Hiemori
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Kayo Kiyoi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Kimiyo Sage-Ono
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Michiyuki Ono
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hiroaki Tateno
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
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9
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Cao X, Wang S, Gadi MR, Liu D, Wang PG, Wan XF, Zhang J, Chen X, Pepi LE, Azadi P, Li L. Systematic synthesis of bisected N-glycans and unique recognitions by glycan-binding proteins. Chem Sci 2022; 13:7644-7656. [PMID: 35872821 PMCID: PMC9241959 DOI: 10.1039/d1sc05435j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 05/29/2022] [Indexed: 12/13/2022] Open
Abstract
Bisected N-glycans represent a unique class of protein N-glycans that play critical roles in many biological processes. Herein, we describe the systematic synthesis of these structures. A bisected N-glycan hexasaccharide was chemically assembled with two orthogonal protecting groups attached at the C2 of the branching mannose residues, followed by sequential installation of GlcNAc and LacNAc building blocks to afford two asymmetric bisecting "cores". Subsequent enzymatic modular extension of the "cores" yielded a comprehensive library of biantennary N-glycans containing the bisecting GlcNAc and presenting 6 common glycan determinants in a combinatorial fashion. These bisected N-glycans and their non-bisected counterparts were used to construct a distinctive glycan microarray to study their recognition by a wide variety of glycan-binding proteins (GBPs), including plant lectins, animal lectins, and influenza A virus hemagglutinins. Significantly, the bisecting GlcNAc could bestow (PHA-L, rDCIR2), enhance (PHA-E), or abolish (ConA, GNL, anti-CD15s antibody, etc.) N-glycan recognition of specific GBPs, and is tolerated by many others. In summary, synthesized compounds and the unique glycan microarray provide ideal standards and tools for glycoanalysis and functional glycomic studies. The microarray data provide new information regarding the fine details of N-glycan recognition by GBPs, and in turn improve their applications.
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Affiliation(s)
- Xuefeng Cao
- Department of Chemistry, Georgia State UniversityAtlantaGAUSA
| | - Shuaishuai Wang
- Department of Chemistry, Georgia State UniversityAtlantaGAUSA
| | | | - Ding Liu
- Department of Chemistry, Georgia State UniversityAtlantaGAUSA
| | - Peng G. Wang
- Department of Chemistry, Georgia State UniversityAtlantaGAUSA
| | - Xiu-Feng Wan
- MU Center for Research on Influenza Systems Biology (CRISB), University of MissouriColumbiaMOUSA,Department of Molecular Microbiology and Immunology, School of Medicine, University of MissouriColumbiaMOUSA,Bond Life Sciences Center, University of MissouriColumbiaMOUSA,Department of Electrical Engineering & Computer Science, College of Engineering, University of MissouriColumbiaMOUSA
| | | | - Xi Chen
- Department of Chemistry, University of CaliforniaOne Shields AvenueDavisCAUSA
| | - Lauren E. Pepi
- Complex Carbohydrate Research Center, University of GeorgiaAthensGAUSA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of GeorgiaAthensGAUSA
| | - Lei Li
- Department of Chemistry, Georgia State UniversityAtlantaGAUSA
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10
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Oinam L, Tateno H. Glycan Profiling by Sequencing to Uncover Multicellular Communication: Launching Glycobiology in Single Cells and Microbiomes. Front Cell Dev Biol 2022; 10:919168. [PMID: 35712658 PMCID: PMC9197256 DOI: 10.3389/fcell.2022.919168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Glycans are essential building blocks of life that are located at the outermost surface of all cells from mammals to bacteria and even viruses. Cell surface glycans mediate multicellular communication in diverse biological processes and are useful as “surface markers” to identify cells. Various single-cell sequencing technologies have already emerged that enable the high-throughput analysis of omics information, such as transcriptome and genome profiling on a cell-by-cell basis, which has advanced our understanding of complex multicellular interactions. However, there has been no robust technology to analyze the glycome in single cells, mainly because glycans with branched and heterogeneous structures cannot be readily amplified by polymerase chain reactions like nucleic acids. We hypothesized that the generation of lectins conjugated with DNA barcodes (DNA-barcoded lectins) would enable the conversion of glycan information to gene information, which may be amplified and measured using DNA sequencers. This technology will enable the simultaneous analysis of glycan and RNA in single cells. Based on this concept, we developed a technology to analyze glycans and RNA in single cells, which was referred to as scGR-seq. Using scGR-seq, we acquired glycan and gene expression profiles of individual cells constituting heterogeneous cell populations, such as tissues. We further extended Glycan-seq to the profiling of the surface glycans of bacteria and even gut microbiota. Glycan-seq and scGR-seq are new technologies that enable us to elucidate the function of glycans in cell–cell and cell–microorganism communication, which extends glycobiology to the level of single cells and microbiomes.
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Affiliation(s)
- Lalhaba Oinam
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Hiroaki Tateno
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
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11
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Thomès L, Burkholz R, Bojar D. Glycowork: A Python package for glycan data science and machine learning. Glycobiology 2021; 31:1240-1244. [PMID: 34192308 PMCID: PMC8600276 DOI: 10.1093/glycob/cwab067] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/02/2021] [Accepted: 06/25/2021] [Indexed: 12/14/2022] Open
Abstract
While glycans are crucial for biological processes, existing analysis modalities make it difficult for researchers with limited computational background to include these diverse carbohydrates into workflows. Here, we present glycowork, an open-source Python package designed for glycan-related data science and machine learning by end users. Glycowork includes functions to, for instance, automatically annotate glycan motifs and analyze their distributions via heatmaps and statistical enrichment. We also provide visualization methods, routines to interact with stored databases, trained machine learning models and learned glycan representations. We envision that glycowork can extract further insights from glycan datasets and demonstrate this with workflows that analyze glycan motifs in various biological contexts. Glycowork can be freely accessed at https://github.com/BojarLab/glycowork/.
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Affiliation(s)
- Luc Thomès
- Department of Chemistry and Molecular Biology and Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Rebekka Burkholz
- Department of Biostatistics, Harvard School of Public Health, Boston, 02115 MA, USA
| | - Daniel Bojar
- Department of Chemistry and Molecular Biology and Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 41390 Gothenburg, Sweden
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12
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Zheng M, Zheng M, Epstein S, Harnagel AP, Kim H, Lupoli TJ. Chemical Biology Tools for Modulating and Visualizing Gram-Negative Bacterial Surface Polysaccharides. ACS Chem Biol 2021; 16:1841-1865. [PMID: 34569792 DOI: 10.1021/acschembio.1c00341] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial cells present a wide diversity of saccharides that decorate the cell surface and help mediate interactions with the environment. Many Gram-negative cells express O-antigens, which are long sugar polymers that makeup the distal portion of lipopolysaccharide (LPS) that constitutes the surface of the outer membrane. This review highlights chemical biology tools that have been developed in recent years to facilitate the modulation of O-antigen synthesis and composition, as well as related bacterial polysaccharide pathways, and the detection of unique glycan sequences. Advances in the biochemistry and structural biology of O-antigen biosynthetic machinery are also described, which provide guidance for the design of novel chemical and biomolecular probes. Many of the tools noted here have not yet been utilized in biological systems and offer researchers the opportunity to investigate the complex sugar architecture of Gram-negative cells.
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Affiliation(s)
- Meng Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Maggie Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Samuel Epstein
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Alexa P. Harnagel
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Hanee Kim
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Tania J. Lupoli
- Department of Chemistry, New York University, New York, 10003 New York, United States
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13
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Minoshima F, Ozaki H, Odaka H, Tateno H. Integrated analysis of glycan and RNA in single cells. iScience 2021; 24:102882. [PMID: 34401666 PMCID: PMC8349903 DOI: 10.1016/j.isci.2021.102882] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/13/2021] [Accepted: 07/15/2021] [Indexed: 12/03/2022] Open
Abstract
Single-cell sequencing has emerged as an indispensable technology to dissect cellular heterogeneity but never been applied to the simultaneous analysis of glycan and RNA. Using oligonucleotide-labeled lectins, we first established lectin-based glycan profiling of single cells by sequencing (scGlycan-seq). We then combined the scGlycan-seq with single-cell transcriptome profiling for joint analysis of glycan and RNA in single cells (scGR-seq). Using scGR-seq, we analyzed the two modalities in human induced pluripotent stem cells (hiPSCs) before and after differentiation into neural progenitor cells at the single-cell resolution. The combination of RNA and glycan separated the two cell types clearer than either one of them. Furthermore, integrative analysis of glycan and RNA modalities in single cells found known and unknown lectins that were specific to hiPSCs and coordinated with neural differentiation. Taken together, we demonstrate that scGR-seq can reveal the cellular heterogeneity and biological roles of glycans across multicellular systems.
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Affiliation(s)
- Fumi Minoshima
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Haruka Ozaki
- Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
- Center for Artificial Intelligence Research, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Haruki Odaka
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Hiroaki Tateno
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
- JST PRESTO, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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14
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Comprehensive analysis of glycosphingolipid glycans by lectin microarrays and MALDI-TOF mass spectrometry. Nat Protoc 2021; 16:3470-3491. [PMID: 34099941 DOI: 10.1038/s41596-021-00544-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 03/25/2021] [Indexed: 12/15/2022]
Abstract
Glycosphingolipids (GSLs) are ubiquitous glycoconjugates present on the cell membrane; they play significant roles in many bioprocesses such as cell adhesion, embryonic development, signal transduction and carcinogenesis. Analyzing such amphiphilic molecules is a major challenge in the field of glycosphingolipidomics. We provide a step-by-step protocol that uses a lectin microarray to analyze GSL glycans from cultured cells. The procedure describes (i) extraction of GSLs from cell pellets, (ii) N-monodeacylation using sphingolipid ceramide N-deacylase digestion to form lyso-GSLs, (iii) fluorescence labeling at the newly exposed amine group, (iv) preparation of a lectin microarray, (v) GSL-glycan analysis by a lectin microarray, (vi) complementary mass spectrometry analysis and (vii) data acquisition and analysis. This method is high-throughput, low cost and easy to conduct, and it provides detailed information about glycan linkages. This protocol takes ~10 d.
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15
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Paton B, Suarez M, Herrero P, Canela N. Glycosylation Biomarkers Associated with Age-Related Diseases and Current Methods for Glycan Analysis. Int J Mol Sci 2021; 22:ijms22115788. [PMID: 34071388 PMCID: PMC8198018 DOI: 10.3390/ijms22115788] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 12/23/2022] Open
Abstract
Ageing is a complex process which implies the accumulation of molecular, cellular and organ damage, leading to an increased vulnerability to disease. In Western societies, the increase in the elderly population, which is accompanied by ageing-associated pathologies such as cardiovascular and mental diseases, is becoming an increasing economic and social burden for governments. In order to prevent, treat and determine which subjects are more likely to develop these age-related diseases, predictive biomarkers are required. In this sense, some studies suggest that glycans have a potential role as disease biomarkers, as they modify the functions of proteins and take part in intra- and intercellular biological processes. As the glycome reflects the real-time status of these interactions, its characterisation can provide potential diagnostic and prognostic biomarkers for multifactorial diseases. This review gathers the alterations in protein glycosylation profiles that are associated with ageing and age-related diseases, such as cancer, type 2 diabetes mellitus, metabolic syndrome and several chronic inflammatory diseases. Furthermore, the review includes the available techniques for the determination and characterisation of glycans, such as liquid chromatography, electrophoresis, nuclear magnetic resonance and mass spectrometry.
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Affiliation(s)
- Beatrix Paton
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
| | - Manuel Suarez
- Nutrigenomics Research Group, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
- Correspondence: (M.S.); (P.H.)
| | - Pol Herrero
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
- Correspondence: (M.S.); (P.H.)
| | - Núria Canela
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), 43204 Reus, Spain; (B.P.); (N.C.)
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16
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Proteomic and Glyco(proteo)mic tools in the profiling of cardiac progenitors and pluripotent stem cell derived cardiomyocytes: Accelerating translation into therapy. Biotechnol Adv 2021; 49:107755. [PMID: 33895330 DOI: 10.1016/j.biotechadv.2021.107755] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 03/15/2021] [Accepted: 04/18/2021] [Indexed: 12/14/2022]
Abstract
Research in stem cells paved the way to an enormous amount of knowledge, increasing expectations on cardio regenerative therapeutic approaches in clinic. While the first generation of clinical trials using cell-based therapies in the heart were performed with bone marrow and adipose tissue derived mesenchymal stem cells, second generation cell therapies moved towards the use of cardiac-committed cell populations, including cardiac progenitor cells and pluripotent stem cell derived cardiomyocytes. Despite all these progresses, translating the aptitudes of R&D and pre-clinical data into effective clinical treatments is still highly challenging, partially due to the demanding regulatory and safety concerns but also because of the lack of knowledge on the regenerative mechanisms of action of these therapeutic products. Thus, the need of analytical methodologies that enable a complete characterization of such complex products and a deep understanding of their therapeutic effects, at the cell and molecular level, is imperative to overcome the hurdles of these advanced therapies. Omics technologies, such as proteomics and glyco(proteo)mics workflows based on state of the art mass-spectrometry, have prompted some major breakthroughs, providing novel data on cell biology and a detailed assessment of cell based-products applied in cardiac regeneration strategies. These advanced 'omics approaches, focused on the profiling of protein and glycan signatures are excelling the identification and characterization of cell populations under study, namely unveiling pluripotency and differentiation markers, as well as paracrine mechanisms and signaling cascades involved in cardiac repair. The leading knowledge generated is supporting a more rational therapy design and the rethinking of challenges in Advanced Therapy Medicinal Products development. Herein, we review the most recent methodologies used in the fields of proteomics, glycoproteomics and glycomics and discuss their impact on the study of cardiac progenitor cells and pluripotent stem cell derived cardiomyocytes biology. How these discoveries will impact the speed up of novel therapies for cardiovascular diseases is also addressed.
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17
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Kearney CJ, Vervoort SJ, Ramsbottom KM, Todorovski I, Lelliott EJ, Zethoven M, Pijpers L, Martin BP, Semple T, Martelotto L, Trapani JA, Parish IA, Scott NE, Oliaro J, Johnstone RW. SUGAR-seq enables simultaneous detection of glycans, epitopes, and the transcriptome in single cells. SCIENCE ADVANCES 2021; 7:7/8/eabe3610. [PMID: 33608275 PMCID: PMC7895430 DOI: 10.1126/sciadv.abe3610] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/05/2021] [Indexed: 05/08/2023]
Abstract
Multimodal single-cell RNA sequencing enables the precise mapping of transcriptional and phenotypic features of cellular differentiation states but does not allow for simultaneous integration of critical posttranslational modification data. Here, we describe SUrface-protein Glycan And RNA-seq (SUGAR-seq), a method that enables detection and analysis of N-linked glycosylation, extracellular epitopes, and the transcriptome at the single-cell level. Integrated SUGAR-seq and glycoproteome analysis identified tumor-infiltrating T cells with unique surface glycan properties that report their epigenetic and functional state.
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Affiliation(s)
- Conor J Kearney
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
| | - Stephin J Vervoort
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
| | - Kelly M Ramsbottom
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Izabela Todorovski
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Emily J Lelliott
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Magnus Zethoven
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Lizzy Pijpers
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Ben P Martin
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Timothy Semple
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Luciano Martelotto
- Centre for Cancer Research, University of Melbourne, Melbourne 3000, VIC, Australia
| | - Joseph A Trapani
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Ian A Parish
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Jane Oliaro
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia.
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Ricky W Johnstone
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
- Cancer Therapeutics Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
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18
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Shibata M, Okamura K, Yura K, Umezawa A. High-precision multiclass cell classification by supervised machine learning on lectin microarray data. Regen Ther 2021; 15:195-201. [PMID: 33426219 PMCID: PMC7770415 DOI: 10.1016/j.reth.2020.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 09/25/2020] [Indexed: 11/27/2022] Open
Abstract
Introduction Establishment of a cell classification platform for evaluation and selection of human pluripotent stem cells (hPSCs) is of great importance to assure the efficacy and safety of cell-based therapy. In our previous work, we introduced a discriminant function that evaluates pluripotency from the cells’ glycome. However, it is not yet suitable for general use. Methods The current study aims to establish a high-precision cell classification platform introducing supervised machine learning and test the platform on glycome analysis as a proof-of-concept study. We employed linear classification and neural network to the lectin microarray data from 1577 human cells and categorized them into five classes including hPSCs. Results The linear-classification-based model and the neural-network-based model successfully predicted the sample type with accuracies of 89% and 97%, respectively. Conclusions Because of the high recognition accuracies and the small amount of computing resources required for these analyses, our platform can be a high precision conventional cell classification system for hPSCs.
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Affiliation(s)
- Mayu Shibata
- Department of Reproductive Biology, National Center for Child Health and Development, Tokyo, 157-8535, Japan.,Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, 112-8610, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Center for Child Health and Development, Tokyo, 157-8535, Japan
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, 112-8610, Japan.,School of Advanced Science and Engineering, Waseda University, Tokyo, 162-0041, Japan
| | - Akihiro Umezawa
- Department of Reproductive Biology, National Center for Child Health and Development, Tokyo, 157-8535, Japan
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19
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Čaval T, Heck AJR, Reiding KR. Meta-heterogeneity: Evaluating and Describing the Diversity in Glycosylation Between Sites on the Same Glycoprotein. Mol Cell Proteomics 2020; 20:100010. [PMID: 33561609 PMCID: PMC8724623 DOI: 10.1074/mcp.r120.002093] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/14/2020] [Accepted: 07/31/2020] [Indexed: 12/26/2022] Open
Abstract
Mass spectrometry-based glycoproteomics has gone through some incredible developments over the last few years. Technological advances in glycopeptide enrichment, fragmentation methods, and data analysis workflows have enabled the transition of glycoproteomics from a niche application, mainly focused on the characterization of isolated glycoproteins, to a mature technology capable of profiling thousands of intact glycopeptides at once. In addition to numerous biological discoveries catalyzed by the technology, we are also observing an increase in studies focusing on global protein glycosylation and the relationship between multiple glycosylation sites on the same protein. It has become apparent that just describing protein glycosylation in terms of micro- and macro-heterogeneity, respectively, the variation and occupancy of glycans at a given site, is not sufficient to describe the observed interactions between sites. In this perspective we propose a new term, meta-heterogeneity, to describe a higher level of glycan regulation: the variation in glycosylation across multiple sites of a given protein. We provide literature examples of extensive meta-heterogeneity on relevant proteins such as antibodies, erythropoietin, myeloperoxidase, and a number of serum and plasma proteins. Furthermore, we postulate on the possible biological reasons and causes behind the intriguing meta-heterogeneity observed in glycoproteins.
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Affiliation(s)
- Tomislav Čaval
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands; Netherlands Proteomics Center, Utrecht, the Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands; Netherlands Proteomics Center, Utrecht, the Netherlands.
| | - Karli R Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands; Netherlands Proteomics Center, Utrecht, the Netherlands.
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20
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Jordan D, Yang M, Schneekloth JS. Three-Color Imaging Enables Simultaneous Screening of Multiple RNA Targets on Small Molecule Microarrays. ACTA ACUST UNITED AC 2020; 12:e87. [PMID: 33275330 DOI: 10.1002/cpch.87] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Small molecule microarray (SMM) technology has become a powerful tool used in high-throughput screening for target-based drug discovery. One area in which SMMs have found use is the identification of small molecule ligands for RNA. RNAs with unique secondary or tertiary three-dimensional structures are considered to be attractive targets for small molecules. Complex RNA structures can form hydrophobic pockets suitable for small molecule binding, representing an opportunity for developing novel therapeutics. Our lab has previously taken a target-based approach, screening a single target against many small molecules on an SMM platform. Here, we report a screening protocol for SMMs to investigate multiple RNAs simultaneously using multi-color imaging. By introducing a mixture containing different fluorophore-labeled RNAs, the fluorescence signal of each binding event can be observed simultaneously. Thus, the specificity of a hit compound binding to one RNA target over other highly abundant RNAs (such as tRNA or rRNA) can be easily evaluated. © 2020 Wiley Periodicals LLC. Basic Protocol: RNA screening on SMMs by multi-color imaging Support Protocol 1: Preparation of SMM slides Support Protocol 2: Fluorophore labeling of RNA through maleimide chemistry.
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Affiliation(s)
- Deondre Jordan
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland
| | - Mo Yang
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland
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21
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Duan L, Zangiabadi M, Zhao Y. Synthetic lectins for selective binding of glycoproteins in water. Chem Commun (Camb) 2020; 56:10199-10202. [PMID: 32748907 PMCID: PMC7484035 DOI: 10.1039/d0cc02892d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although synthetic mimics of lectins can be extremely useful in biological and biomedical research, molecular recognition of carbohydrates has been hampered by their strong solvation in water and subtle structural differences among analogues. Molecularly imprinted nanoparticle receptors were prepared with glycans directly cleaved from glycoproteins. Functionalized with boroxole groups in the binding sites, these water-soluble synthetic lectins bound the parent glycoproteins selectively in water with an association constant of Ka = 104-105 M-1. The strong binding enabled the receptors to protect the targeted glycans from enzymatic cleavage. When clicked onto magnetic nanoparticles, the receptors enabled facile isolation of glycoproteins from a mixture.
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Affiliation(s)
- Likun Duan
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, USA.
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22
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Tsaneva M, Van Damme EJM. 130 years of Plant Lectin Research. Glycoconj J 2020; 37:533-551. [PMID: 32860551 PMCID: PMC7455784 DOI: 10.1007/s10719-020-09942-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/12/2020] [Accepted: 08/21/2020] [Indexed: 12/15/2022]
Abstract
Lectins are proteins with diverse molecular structures that share the ability to recognize and bind specifically and reversibly to carbohydrate structures without changing the carbohydrate moiety. The history of lectins started with the discovery of ricin about 130 years ago but since then our understanding of lectins has dramatically changed. Over the years the research focus was shifted from 'the characterization of carbohydrate-binding proteins' to 'understanding the biological function of lectins'. Nowadays plant lectins attract a lot of attention especially because of their potential for crop improvement and biomedical research, as well as their application as tools in glycobiology. The present review aims to give an overview of plant lectins and their applications, and how the field evolved in the last decades.
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Affiliation(s)
- Mariya Tsaneva
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Els J M Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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23
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Bonnardel F, Mariethoz J, Salentin S, Robin X, Schroeder M, Perez S, Lisacek F, Imberty A. UniLectin3D, a database of carbohydrate binding proteins with curated information on 3D structures and interacting ligands. Nucleic Acids Res 2020; 47:D1236-D1244. [PMID: 30239928 PMCID: PMC6323968 DOI: 10.1093/nar/gky832] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/07/2018] [Indexed: 01/02/2023] Open
Abstract
Lectins, and related receptors such as adhesins and toxins, are glycan-binding proteins from all origins that decipher the glycocode, i.e. the structural information encoded in the conformation of complex carbohydrates present on the surface of all cells. Lectins are still poorly classified and annotated, but since their functions are based on ligand recognition, their 3D-structures provide a solid foundation for characterization. UniLectin3D is a curated database that classifies lectins on origin and fold, with cross-links to literature, other databases in glycosciences and functional data such as known specificity. The database provides detailed information on lectins, their bound glycan ligands, and features their interactions using the Protein–Ligand Interaction Profiler (PLIP) server. Special care was devoted to the description of the bound glycan ligands with the use of simple graphical representation and numerical format for cross-linking to other databases in glycoscience. We conceived the design of the database architecture and the navigation tools to account for all organisms, as well as to search for oligosaccharide epitopes complexed within specified binding sites. UniLectin3D is accessible at https://www.unilectin.eu/unilectin3D.
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Affiliation(s)
- François Bonnardel
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France.,Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland.,Department of Computer Science, University of Geneva, Route de Drize 7, CH-1227 Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland.,Department of Computer Science, University of Geneva, Route de Drize 7, CH-1227 Geneva, Switzerland
| | - Sebastian Salentin
- Biotechnology Center (BIOTEC), TU Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Xavier Robin
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,Computational Structural Biology Group, SIB Swiss Institute of Bioinformatics, CH-4056 Basel, Switzerland
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), TU Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Serge Perez
- Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland.,Department of Computer Science, University of Geneva, Route de Drize 7, CH-1227 Geneva, Switzerland.,Section of Biology, University of Geneva, CH-1205 Geneva, Switzerland
| | - Anne Imberty
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
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24
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Dang K, Yu HJ, Xu SH, Ma TR, Wang HP, Li Y, Li Z, Gao YF. Remarkable Homeostasis of Protein Sialylation in Skeletal Muscles of Hibernating Daurian Ground Squirrels (Spermophilus dauricus). Front Physiol 2020; 11:37. [PMID: 32116753 PMCID: PMC7020753 DOI: 10.3389/fphys.2020.00037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 01/16/2020] [Indexed: 11/18/2022] Open
Abstract
As the most common post-translational protein modification, glycosylation is intimately linked to muscle atrophy. This study aimed to investigate the performance of protein glycosylation in the soleus muscle (SOL) in Daurian ground squirrels (Spermophilus dauricus) and to determine the potential role of protein glycosylation in the mechanism underlying disuse muscle atrophy prevention. The results showed that (1) seven glycan structures comprising sialic acid α2-3 galactose (SAα2-3Gal) were altered during hibernation; (2) alterations in the SAα2-3Gal structure during hibernation were based on changes in the expression levels of beta-galactoside alpha-2 and 3-sialyltransferases; and (3) α2-3–linked sialylated modifications of heat shock cognate 70 and pyruvate kinase and expression of 14-3-3 epsilon protein were oscillatorily changed during hibernation. Our findings indicate that the skeletal muscles of hibernating Daurian ground squirrels maintain protein sialylation homeostasis by restoring sialylation modification during periodic interbout arousal, which might protect the skeletal muscles against disuse atrophy.
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Affiliation(s)
- Kai Dang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- Laboratory for Bone Metabolism, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Han-Jie Yu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi’an, China
| | - Shen-Hui Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Tian-Ran Ma
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi’an, China
| | - Hui-Ping Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Yang Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi’an, China
- *Correspondence: Zheng Li,
| | - Yun-Fang Gao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- Yun-Fang Gao,
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Yu H, Shu J, Li Z. Lectin microarrays for glycoproteomics: an overview of their use and potential. Expert Rev Proteomics 2020; 17:27-39. [PMID: 31971038 DOI: 10.1080/14789450.2020.1720512] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Glycoproteomics is an important subdiscipline of proteomics, focusing on the role of protein glycosylation in various biological processes. Protein glycosylation is the enzymatic addition of sugars or oligosaccharides to proteins. Altered glycosylation often occurs in the early stages of disease development, for example, certain tumor-associated glycans have been shown to be expressed in precursor lesions of different types of cancer, making them powerful early diagnostic markers. Lectin microarrays have become a powerful tool for both the study of glycosylation and the diagnosis of various diseases including cancer.Areas covered: This review will discuss the most useful features of lectin microarrays, such as their technological advances, their capability for parallel/high-throughput analysis for the important glycopatterns of glycoprotein, and an overview of their use for glycosylation analysis of various complex protein samples, as well as their diagnostic potential in various diseases.Expert opinion: Lectin microarrays have proved to be useful in studying multiple lectin-glycan interactions in a single experiment and, with the advances made in the field, hold a promise of enabling glycopatterns of diseases in a fast and efficient manner. Lectin microarrays will become increasingly powerful early diagnostic tool for a variety of conditions.
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Affiliation(s)
- Hanjie Yu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Jian Shu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, China
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Zhou ZR, Wang XY, Lv J, Chen BB, Tang YB, Qian RC. Nanopipette-assisted single cell metabolic glycan labeling. RSC Adv 2019; 9:30666-30670. [PMID: 35529390 PMCID: PMC9072180 DOI: 10.1039/c9ra06634a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/23/2019] [Indexed: 12/24/2022] Open
Abstract
Here, we report a single cell glycan labeling strategy by combining nanoscale intracellular glass electrodes with bioorthogonal reaction. With the tip diameter less than 100 nm, the nanopipette electrode can be spatially controlled to inject artificial monosaccharides into single living cells with minimal invasion. The injection process can be precisely regulated by electroosmotic flow inside the nanopipette, and fluorescence labeling of sialic acid at single cell level is achieved.
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Affiliation(s)
- Ze-Rui Zhou
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology Shanghai 200237 P. R. China +86 21 64250032
| | - Xiao-Yuan Wang
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology Shanghai 200237 P. R. China +86 21 64250032
| | - Jian Lv
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology Shanghai 200237 P. R. China +86 21 64250032
| | - Bin-Bin Chen
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology Shanghai 200237 P. R. China +86 21 64250032
| | - Yi-Bin Tang
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology Shanghai 200237 P. R. China +86 21 64250032
| | - Ruo-Can Qian
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology Shanghai 200237 P. R. China +86 21 64250032
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Abstract
Many important interactions between bacterial pathogens and their hosts are highly specific binding events that involve host or pathogen carbohydrate structures (glycans). Glycan interactions can mediate adhesion, invasion and immune evasion and can act as receptors for toxins. Several bacterial pathogens can also enzymatically alter host glycans to reveal binding targets, degrade the host cell glycans or alter the function of host glycoproteins. In recent years, high-throughput screening technologies, such as lectin, glycan and mucin microarrays, have transformed the field by identifying new bacterial-host glycointeractions, which are crucial for colonization, persistence and disease. In this Review, we discuss interactions involving both host and bacterial glycans that have a role in bacterial pathogenesis. We also highlight recent technological advances that have illuminated the glycoscience of microbial pathogenesis.
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Chen BB, Wang XY, Qian RC. Rolling "wool-balls": rapid live-cell mapping of membrane sialic acids via poly-p-benzoquinone/ethylenediamine nanoclusters. Chem Commun (Camb) 2019; 55:9681-9684. [PMID: 31347618 DOI: 10.1039/c9cc03338f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Here, we report a convenient, fast labeling strategy for the imaging of cell surface sialic acids (SAs, nine-carbon monosaccharides located at the terminals of cell surface sugar chains). This strategy is based on the synthesis of sticky, furry and fluorescent "wool-balls", which are wound into nanoclusters from p-benzoquinone/ethylenediamine polymer "wires". With abundant amino groups at the surface, the wool-balls can easily stick to the C-7 aldehyde group generated at the ends of periodate treated SAs in less than 30 min.
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Affiliation(s)
- Bin-Bin Chen
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint, Research Center, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
| | - Xiao-Yuan Wang
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint, Research Center, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
| | - Ruo-Can Qian
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint, Research Center, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
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Abstract
Cancer has high incidence and it will continue to increase over the next decades. Detection and quantification of cancer-associated biomarkers is frequently carried out for diagnosis, prognosis and treatment monitoring at various disease stages. It is well-known that glycosylation profiles change significantly during oncogenesis. Aberrant glycans produced during tumorigenesis are, therefore, valuable molecules for detection and characterization of cancer, and for therapeutic design and monitoring. Although glycoproteomics has benefited from the development of analytical tools such as high performance liquid chromatography, two-dimensional gel and capillary electrophoresis and mass spectrometry, these approaches are not well suited for rapid point-of-care (POC) testing easily performed by medical staff. Lectins are biomolecules found in nature with specific affinities toward particular glycan structures and bind them thus forming a relatively strong complex. Because of this characteristic, lectins have been used in analytical techniques for the selective capture or separation of certain glycans in complex samples, namely, in lectin affinity chromatography, or to characterize glycosylation profiles in diverse clinical situations, using lectin microarrays. Lectin-based biosensors have been developed for the detection of specific aberrant and cancer-associated glycostructures to aid diagnosis, prognosis and treatment assessment of these patients. The attractive features of biosensors, such as portability and simple use make them highly suitable for POC testing. Recent developments in lectin biosensors, as well as their potential and pitfalls in cancer glycan biomarker detection, are presented in this chapter.
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Affiliation(s)
- M Luísa S Silva
- Centre of Chemical Research, Autonomous University of Hidalgo State, Pachuca, Hidalgo, México.
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Gizaw ST, Gaunitz S, Novotny MV. Highly Sensitive O-Glycan Profiling for Human Serum Proteins Reveals Gender-Dependent Changes in Colorectal Cancer Patients. Anal Chem 2019; 91:6180-6189. [PMID: 30983323 DOI: 10.1021/acs.analchem.9b00822] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A newly developed microscale protocol for profiling serum O-glycans has been validated here with multiple serum samples obtained from different cohorts of colorectal cancer patients. The simultaneous cleavage and permethylation steps in this procedure preserve the integrity of released minor O-glycans, so that 39 O-linked oligosaccharides could be reliably recorded in a profile. This is far more detected components than shown in any previous studies. The analytical results were further subjected to a battery of statistical tests. Our O-glycan compositions compare favorably with the previous results obtained with solid tumors and cancer cell lines, suggesting that smaller circulatory mucins protruding into the blood circulation may be one source of O-glycans that we observe in the serum samples. While the control vs cancer statistical comparisons generally agree with the expected glycosylation trends, the comparisons of male vs female subjects have led to some surprising results for which we do not have a ready explanation due to lack of any literature describing hormonal control of O-glycosylation. Our results thus underscore the necessity of applying new analytical technologies to clinically interesting sample sets.
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Affiliation(s)
- Solomon T Gizaw
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Stefan Gaunitz
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Milos V Novotny
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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Oswald DM, Sim ES, Baker C, Farhan O, Debanne SM, Morris NJ, Rodriguez BG, Jones MB, Cobb BA. Plasma glycomics predict cardiovascular disease in patients with ART-controlled HIV infections. FASEB J 2019; 33:1852-1859. [PMID: 30183373 PMCID: PMC6338643 DOI: 10.1096/fj.201800923r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/06/2018] [Indexed: 12/30/2022]
Abstract
Despite effective control of HIV infection with antiretroviral drugs, individuals with HIV have high incidences of secondary diseases. These sequelae, such as cardiovascular disease (CVD), are poorly understood and represent a major health burden. To date, predictive biomarkers of HIV-associated secondary disease have been elusive, making preventative clinical management essentially impossible. Here, we applied a newly developed and easy to deploy, multitarget, and high-throughput glycomic analysis to banked HIV+ human plasma samples to determine whether the glycome may include biomarkers that predict future HIV-associated cardiovascular events or CVD diagnoses. Using 324 patient samples, we identified a glycomic fingerprint that was predictive of future CVD events but independent of CD4 counts, diabetes, age, and birth sex, suggesting that the plasma glycome may serve as a biomarker for specific HIV-associated sequelae. Our findings constitute the discovery of novel glycan biomarkers that could classify patients with HIV with elevated risk for CVD and reveal the untapped prognostic potential of the plasma glycome in human disease.-Oswald, D. M., Sim, E. S., Baker, C., Farhan, O., Debanne, S. M., Morris, N. J., Rodriguez, B. G., Jones, M. B., Cobb, B. A. Plasma glycomics predict cardiovascular disease in patients with ART-controlled HIV infections.
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Affiliation(s)
- Douglas M. Oswald
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Edward S. Sim
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Courtney Baker
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Obada Farhan
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Sara M. Debanne
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Nathan J. Morris
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Benigno G. Rodriguez
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Mark B. Jones
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Brian A. Cobb
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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Emerging glycobiology tools: A renaissance in accessibility. Cell Immunol 2018; 333:2-8. [PMID: 29759530 DOI: 10.1016/j.cellimm.2018.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 01/01/2023]
Abstract
The glycobiology of the immune response is a topic that has garnered increased attention due to a number of key discoveries surrounding IgG function, the specificity of some broadly neutralizing anti-HIV antibodies, cancer immunoregulation by galectin molecules and others. This review is the opening article in a Special Edition of Cellular Immunology focused on glycoimmunology, and has the goal of setting the context for these articles by providing a mini-review of how glycans impact immunity. We also focus on some of the technological and methodological advances in the field of glycobiology that are being deployed to lower the barrier of entry into the glycosciences, and to more fully interrogate the glycome and its function.
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Everest-Dass AV, Moh ESX, Ashwood C, Shathili AMM, Packer NH. Human disease glycomics: technology advances enabling protein glycosylation analysis - part 1. Expert Rev Proteomics 2018; 15:165-182. [PMID: 29285957 DOI: 10.1080/14789450.2018.1421946] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
INTRODUCTION Protein glycosylation is recognized as an important post-translational modification, with specific substructures having significant effects on protein folding, conformation, distribution, stability and activity. However, due to the structural complexity of glycans, elucidating glycan structure-function relationships is demanding. The fine detail of glycan structures attached to proteins (including sequence, branching, linkage and anomericity) is still best analysed after the glycans are released from the purified or mixture of glycoproteins (glycomics). The technologies currently available for glycomics are becoming streamlined and standardized and many features of protein glycosylation can now be determined using instruments available in most protein analytical laboratories. Areas covered: This review focuses on the current glycomics technologies being commonly used for the analysis of the microheterogeneity of monosaccharide composition, sequence, branching and linkage of released N- and O-linked glycans that enable the determination of precise glycan structural determinants presented on secreted proteins and on the surface of all cells. Expert commentary: Several emerging advances in these technologies enabling glycomics analysis are discussed. The technological and bioinformatics requirements to be able to accurately assign these precise glycan features at biological levels in a disease context are assessed.
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Affiliation(s)
- Arun V Everest-Dass
- a Biomolecular Discovery and Design Research Centre, Faculty of Science and Engineering , Macquarie University , Sydney , Australia.,b Institute for Glycomics , Griffith University , Gold Coast , Australia.,c ARC Centre for Nanoscale BioPhotonics , Macquarie University , Sydney , Australia
| | - Edward S X Moh
- a Biomolecular Discovery and Design Research Centre, Faculty of Science and Engineering , Macquarie University , Sydney , Australia.,c ARC Centre for Nanoscale BioPhotonics , Macquarie University , Sydney , Australia
| | - Christopher Ashwood
- a Biomolecular Discovery and Design Research Centre, Faculty of Science and Engineering , Macquarie University , Sydney , Australia.,c ARC Centre for Nanoscale BioPhotonics , Macquarie University , Sydney , Australia
| | - Abdulrahman M M Shathili
- a Biomolecular Discovery and Design Research Centre, Faculty of Science and Engineering , Macquarie University , Sydney , Australia.,c ARC Centre for Nanoscale BioPhotonics , Macquarie University , Sydney , Australia
| | - Nicolle H Packer
- a Biomolecular Discovery and Design Research Centre, Faculty of Science and Engineering , Macquarie University , Sydney , Australia.,b Institute for Glycomics , Griffith University , Gold Coast , Australia.,c ARC Centre for Nanoscale BioPhotonics , Macquarie University , Sydney , Australia
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Glycan profiling of proteins using lectin binding by Surface Plasmon Resonance. Anal Biochem 2017; 538:53-63. [PMID: 28947169 DOI: 10.1016/j.ab.2017.09.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 01/21/2023]
Abstract
Glycan profiling of proteins was studied through their lectin binding activity by Surface Plasmon Resonance (SPR). To validate the method, we monitored specific lectin binding with sequential removal of sugar moieties from human transferrin using specific glycosidases. The results clearly indicated that glycans on the protein can be identified by their selective binding activity to various lectins. Using this method, we characterized Fc glycosylation profiles of therapeutic peptibodies and antibodies expressed in mammalian cells (CHO and HEK 293 6E cells), with E. coli expressed proteins as the negative controls. We observed that antibodies expressed in CHO cells did not contain any sialic acid, while antibodies expressed in 293 6E cells contained sialic acid. CHO cell expressed antibodies were also more heavily fucosylated than the ones expressed by 293 6E cells. We further applied this method to measure the fucose composition of glycan engineered mouse antibodies, as well as to determine mannose composition of human antibody variants with depletion or enrichment of high mannose. The glycan profiles generated using this method were comparable to results from 2-AB labeled glycan analysis of normal-phase separated glycans, and Fc gamma receptor binding activity of the glycan engineered antibodies were consistent with their glycan profiles. Hence, we demonstrated that SPR lectin binding analysis can be a quick alternative method to profile protein glycosylation.
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Abstract
Glycans are essential for the maintenance of normal biological function, with alterations in glycan expression being a hallmark of cancer. Cancer stem cells (CSCs) are a subset of cells within a tumour capable of self-renewal, cellular differentiation and resistances to conventional therapies. As is the case with stem cells, marker proteins present on the cell surface are frequently used to identify and enrich CSCs, with the expression of these markers statistical correlating with the likelihood of cancer recurrence and overall patient survival. As such CSC markers are of high clinical relevance. The majority of markers currently used to identify CSC populations are glycoproteins, and although the diverse biological roles for many of these markers are known, the nature and function of the glycan moiety on these glycoproteins remains to be fully elucidated. This mini-review summarises our current knowledge regarding the types and extent of CSC marker glycosylation, and the various roles that these glycans play in CSC biology, including in mediating cell adhesion, metastasis, evading apoptosis, tear shear resistance, tumour growth, maintaining pluripotency, self-renewal, trafficking, maintaining stability, maintaining enzymatic activity and aiding epithelial mesenchymal transitioning. Given that CSCs markers have multiple diverse biological functions, and are potentially of significant diagnostic and therapeutic benefit the search for new markers that are uniquely expressed on CSCs is vital to selectively target/identify this subset of cancer cells. As such we have also outlined how high-throughput lectin microarrays can be used to successfully profile the glycosylation status of CSC and to identify glyco-markers unique to CSCs.
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Dosekova E, Filip J, Bertok T, Both P, Kasak P, Tkac J. Nanotechnology in Glycomics: Applications in Diagnostics, Therapy, Imaging, and Separation Processes. Med Res Rev 2017; 37:514-626. [PMID: 27859448 PMCID: PMC5659385 DOI: 10.1002/med.21420] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 09/08/2016] [Accepted: 09/21/2016] [Indexed: 12/14/2022]
Abstract
This review comprehensively covers the most recent achievements (from 2013) in the successful integration of nanomaterials in the field of glycomics. The first part of the paper addresses the beneficial properties of nanomaterials for the construction of biosensors, bioanalytical devices, and protocols for the detection of various analytes, including viruses and whole cells, together with their key characteristics. The second part of the review focuses on the application of nanomaterials integrated with glycans for various biomedical applications, that is, vaccines against viral and bacterial infections and cancer cells, as therapeutic agents, for in vivo imaging and nuclear magnetic resonance imaging, and for selective drug delivery. The final part of the review describes various ways in which glycan enrichment can be effectively done using nanomaterials, molecularly imprinted polymers with polymer thickness controlled at the nanoscale, with a subsequent analysis of glycans by mass spectrometry. A short section describing an active glycoprofiling by microengines (microrockets) is covered as well.
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Affiliation(s)
- Erika Dosekova
- Department of Glycobiotechnology, Institute of ChemistrySlovak Academy of SciencesDubravska cesta 9845 38BratislavaSlovakia
| | - Jaroslav Filip
- Center for Advanced MaterialsQatar UniversityP.O. Box 2713DohaQatar
| | - Tomas Bertok
- Department of Glycobiotechnology, Institute of ChemistrySlovak Academy of SciencesDubravska cesta 9845 38BratislavaSlovakia
| | - Peter Both
- School of Chemistry, Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Peter Kasak
- Center for Advanced MaterialsQatar UniversityP.O. Box 2713DohaQatar
| | - Jan Tkac
- Department of Glycobiotechnology, Institute of ChemistrySlovak Academy of SciencesDubravska cesta 9845 38BratislavaSlovakia
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Affiliation(s)
- Stefan Gaunitz
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Gabe Nagy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Nicola L. B. Pohl
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- Regional Center for Applied Molecular Oncology, Masaryk Memorial Oncological Institute, 656 53 Brno, Czech Republic
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Wu Z, Liu Y, Ma C, Li L, Bai J, Byrd-Leotis L, Lasanajak Y, Guo Y, Wen L, Zhu H, Song J, Li Y, Steinhauer DA, Smith DF, Zhao B, Chen X, Guan W, Wang PG. Identification of the binding roles of terminal and internal glycan epitopes using enzymatically synthesized N-glycans containing tandem epitopes. Org Biomol Chem 2016; 14:11106-11116. [PMID: 27752690 PMCID: PMC5951163 DOI: 10.1039/c6ob01982j] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glycans play diverse roles in a wide range of biological processes. Research on glycan-binding events is essential for learning their biological and pathological functions. However, the functions of terminal and internal glycan epitopes exhibited during binding with glycan-binding proteins (GBPs) and/or viruses need to be further identified. Therefore, a focused library of 36 biantennary asparagine (Asn)-linked glycans with some presenting tandem glycan epitopes was synthesized via a combined Core Isolation/Enzymatic Extension (CIEE) and one-pot multienzyme (OPME) synthetic strategy. These N-glycans include those containing a terminal sialyl N-acetyllactosamine (LacNAc), sialyl Lewis x (sLex) and Siaα2-8-Siaα2-3/6-R structures with N-acetylneuraminic acid (Neu5Ac) or N-glycolylneuraminic acid (Neu5Gc) sialic acid form, LacNAc, Lewis x (Lex), α-Gal, and Galα1-3-Lex; and tandem epitopes including α-Gal, Lex, Galα1-3-Lex, LacNAc, and sialyl LacNAc, presented with an internal sialyl LacNAc or 1-2 repeats of an internal LacNAc or Lex component. They were synthesized in milligram-scale, purified to over 98% purity, and used to prepare a glycan microarray. Binding studies using selected plant lectins, antibodies, and viruses demonstrated, for the first time, that when interpreting the binding between glycans and GBPs/viruses, not only the structure of the terminal glycan epitopes, but also the internal epitopes and/or modifications of terminal epitopes needs to be taken into account.
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Affiliation(s)
- Zhigang Wu
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
| | - Yunpeng Liu
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
| | - Cheng Ma
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
| | - Lei Li
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
| | - Jing Bai
- College of Life Science, Hebei Normal University, Shijiazhuang, Hebei 050024, China.
| | - Lauren Byrd-Leotis
- Departments of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yi Lasanajak
- Department of Biochemistry and Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yuxi Guo
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
| | - Liuqing Wen
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
| | - He Zhu
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
| | - Jing Song
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
| | - Yanhong Li
- Department of Chemistry, University of California, Davis, CA 95616, USA.
| | - David A Steinhauer
- Departments of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David F Smith
- Department of Biochemistry and Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Baohua Zhao
- College of Life Science, Hebei Normal University, Shijiazhuang, Hebei 050024, China.
| | - Xi Chen
- Department of Chemistry, University of California, Davis, CA 95616, USA.
| | - Wanyi Guan
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, USA. and College of Life Science, Hebei Normal University, Shijiazhuang, Hebei 050024, China.
| | - Peng George Wang
- Department of Chemistry and Center of Diagnostics & Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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Saldova R, Kilcoyne M, Stöckmann H, Millán Martín S, Lewis AM, Tuite CME, Gerlach JQ, Le Berre M, Borys MC, Li ZJ, Abu-Absi NR, Leister K, Joshi L, Rudd PM. Advances in analytical methodologies to guide bioprocess engineering for bio-therapeutics. Methods 2016; 116:63-83. [PMID: 27832969 DOI: 10.1016/j.ymeth.2016.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/27/2016] [Accepted: 11/03/2016] [Indexed: 12/15/2022] Open
Abstract
This study was performed to monitor the glycoform distribution of a recombinant antibody fusion protein expressed in CHO cells over the course of fed-batch bioreactor runs using high-throughput methods to accurately determine the glycosylation status of the cell culture and its product. Three different bioreactors running similar conditions were analysed at the same five time-points using the advanced methods described here. N-glycans from cell and secreted glycoproteins from CHO cells were analysed by HILIC-UPLC and MS, and the total glycosylation (both N- and O-linked glycans) secreted from the CHO cells were analysed by lectin microarrays. Cell glycoproteins contained mostly high mannose type N-linked glycans with some complex glycans; sialic acid was α-(2,3)-linked, galactose β-(1,4)-linked, with core fucose. Glycans attached to secreted glycoproteins were mostly complex with sialic acid α-(2,3)-linked, galactose β-(1,4)-linked, with mostly core fucose. There were no significant differences noted among the bioreactors in either the cell pellets or supernatants using the HILIC-UPLC method and only minor differences at the early time-points of days 1 and 3 by the lectin microarray method. In comparing different time-points, significant decreases in sialylation and branching with time were observed for glycans attached to both cell and secreted glycoproteins. Additionally, there was a significant decrease over time in high mannose type N-glycans from the cell glycoproteins. A combination of the complementary methods HILIC-UPLC and lectin microarrays could provide a powerful and rapid HTP profiling tool capable of yielding qualitative and quantitative data for a defined biopharmaceutical process, which would allow valuable near 'real-time' monitoring of the biopharmaceutical product.
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Affiliation(s)
- Radka Saldova
- NIBRT GlycoScience Group, The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin 4, Ireland.
| | - Michelle Kilcoyne
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland; Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
| | - Henning Stöckmann
- NIBRT GlycoScience Group, The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin 4, Ireland.
| | - Silvia Millán Martín
- NIBRT GlycoScience Group, The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin 4, Ireland.
| | - Amanda M Lewis
- Bristol-Myers Squibb, BMS, Biologics Development, 38 Jackson Road, Devens, MA 01434, USA.
| | - Catherine M E Tuite
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland.
| | - Jared Q Gerlach
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland; Regenerative Medicine Institute, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland.
| | - Marie Le Berre
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland.
| | - Michael C Borys
- Bristol-Myers Squibb, BMS, Biologics Development, 38 Jackson Road, Devens, MA 01434, USA.
| | - Zheng Jian Li
- Bristol-Myers Squibb, BMS, Biologics Development, 38 Jackson Road, Devens, MA 01434, USA.
| | - Nicholas R Abu-Absi
- Bristol-Myers Squibb, BMS, Biologics Development, 38 Jackson Road, Devens, MA 01434, USA.
| | - Kirk Leister
- Bristol-Myers Squibb, BMS, Biologics Development, 38 Jackson Road, Devens, MA 01434, USA.
| | - Lokesh Joshi
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland.
| | - Pauline M Rudd
- NIBRT GlycoScience Group, The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin 4, Ireland.
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41
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Varki A. Biological roles of glycans. Glycobiology 2016; 27:3-49. [PMID: 27558841 PMCID: PMC5884436 DOI: 10.1093/glycob/cww086] [Citation(s) in RCA: 1433] [Impact Index Per Article: 179.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 02/07/2023] Open
Abstract
Simple and complex carbohydrates (glycans) have long been known to play major metabolic, structural and physical roles in biological systems. Targeted microbial binding to host glycans has also been studied for decades. But such biological roles can only explain some of the remarkable complexity and organismal diversity of glycans in nature. Reviewing the subject about two decades ago, one could find very few clear-cut instances of glycan-recognition-specific biological roles of glycans that were of intrinsic value to the organism expressing them. In striking contrast there is now a profusion of examples, such that this updated review cannot be comprehensive. Instead, a historical overview is presented, broad principles outlined and a few examples cited, representing diverse types of roles, mediated by various glycan classes, in different evolutionary lineages. What remains unchanged is the fact that while all theories regarding biological roles of glycans are supported by compelling evidence, exceptions to each can be found. In retrospect, this is not surprising. Complex and diverse glycans appear to be ubiquitous to all cells in nature, and essential to all life forms. Thus, >3 billion years of evolution consistently generated organisms that use these molecules for many key biological roles, even while sometimes coopting them for minor functions. In this respect, glycans are no different from other major macromolecular building blocks of life (nucleic acids, proteins and lipids), simply more rapidly evolving and complex. It is time for the diverse functional roles of glycans to be fully incorporated into the mainstream of biological sciences.
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Affiliation(s)
- Ajit Varki
- Departments of Medicine and Cellular & Molecular Medicine, Glycobiology Research and Training Center, University of California at San Diego, La Jolla, CA 92093-0687, USA
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42
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Hemmi H, Kuno A, Unno S, Hirabayashi J. NMR analysis on the sialic acid-binding mechanism of an R-type lectin mutant by natural evolution-mimicry. FEBS Lett 2016; 590:1720-8. [PMID: 27172906 DOI: 10.1002/1873-3468.12212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 05/02/2016] [Accepted: 05/05/2016] [Indexed: 11/05/2022]
Abstract
A sialic acid-binding lectin (SRC) was created from the C-terminal domain of an R-type N-acetyl lactosamine-binding lectin (EW29Ch) by natural evolution-mimicry. Here, we clarified its sialic acid-binding mechanism using NMR spectroscopy. The NMR analysis showed differences between conformations of the 6'-sialyllactose-bound SRC in the solution state and that in the crystal state, and differences between the internal motion of the loop region in subdomain γ in SRC and that of the corresponding region in EW29Ch. The NMR analysis thus provided useful information to explain the manner of binding to 6'-sialyllactose in solution, which the previous X-ray crystal structure analysis lacked.
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Affiliation(s)
- Hikaru Hemmi
- Food Research Institute, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Atsushi Kuno
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.,Glycomedicine Technology Research Center (GTRC), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Sachiko Unno
- Glycomedicine Technology Research Center (GTRC), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Jun Hirabayashi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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43
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Syed P, Gidwani K, Kekki H, Leivo J, Pettersson K, Lamminmäki U. Role of lectin microarrays in cancer diagnosis. Proteomics 2016; 16:1257-65. [PMID: 26841254 DOI: 10.1002/pmic.201500404] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/25/2016] [Accepted: 01/28/2016] [Indexed: 12/22/2022]
Abstract
The majority of cell differentiation associated tumor markers reported to date are either glycoproteins or glycolipids. Despite there being a large number of glycoproteins reported as candidate markers for various cancers, only a handful are approved by the US Food and Drug Administration. Lectins, which bind to the glycan part of the glycoproteins, can be exploited to identify aberrant glycosylation patterns, which in turn would help in enhancing the specificity of cancer diagnosis. Although conventional techniques such as HPLC and MS have been instrumental in performing the glycomic analyses, these techniques lack multiplexity. Lectin microarrays have proved to be useful in studying multiple lectin-glycan interactions in a single experiment and, with the advances made in the field, hold a promise of enabling glycomic profiling of cancers in a fast and efficient manner.
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Affiliation(s)
- Parvez Syed
- Department of Biochemistry/Biotechnology, University of Turku, Turun yliopisto, Finland
| | - Kamlesh Gidwani
- Department of Biochemistry/Biotechnology, University of Turku, Turun yliopisto, Finland
| | - Henna Kekki
- Department of Biochemistry/Biotechnology, University of Turku, Turun yliopisto, Finland
| | - Janne Leivo
- Department of Biochemistry/Biotechnology, University of Turku, Turun yliopisto, Finland
| | - Kim Pettersson
- Department of Biochemistry/Biotechnology, University of Turku, Turun yliopisto, Finland
| | - Urpo Lamminmäki
- Department of Biochemistry/Biotechnology, University of Turku, Turun yliopisto, Finland
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44
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Šunderić M, Šedivá A, Robajac D, Miljuš G, Gemeiner P, Nedić O, Katrlík J. Lectin-based protein microarray analysis of differences in serum alpha-2-macroglobulin glycosylation between patients with colorectal cancer and persons without cancer. Biotechnol Appl Biochem 2015; 63:457-64. [PMID: 26075587 DOI: 10.1002/bab.1407] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/10/2015] [Indexed: 11/11/2022]
Abstract
Glycosylation is co- and posttranslational modifications affecting proteins. The glycopattern changes are associated with changes in biological function and are involved in many diseases including cancer. We present the lectin-based protein microarray method enabling determination of differences in protein glycosylation. The method involves isolation of targeted protein from samples by immunoprecipitation, spotting of protein from multiple samples into arrays on a microarray slide, incubation with set of biotinylated lectins, the reaction with fluorescent conjugate of streptavidin, and detection of fluorescent intensities by microarray scanner. Lectin-based protein microarray was applied in investigation of differences in alpha-2-macroglobulin (α2M) glycosylation isolated from sera samples of healthy persons and patients with colorectal cancer (CC). From 14 lectins used in analysis, statistically significant differences (Student's t-test, P < 0.05) between two groups of samples (persons without cancer and CC patients) were found for 5 of them. α2M molecules isolated from sera of CC patients have higher content of α2,6 sialic acid, N-acetylglucosamine and mannose residues, and tri-/tetraantennary complex type high-mannose N-glycans. A novel lectin-based protein microarray developed and described can serve as a suitable analytical technique for sensitive, simple, fast, and high-throughput determination of differences in protein glycosylation isolated from serum or other samples.
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Affiliation(s)
- Miloš Šunderić
- Institute for the Application of Nuclear Energy, University of Belgrade, Belgrade, Serbia
| | - Alena Šedivá
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Dragana Robajac
- Institute for the Application of Nuclear Energy, University of Belgrade, Belgrade, Serbia
| | - Goran Miljuš
- Institute for the Application of Nuclear Energy, University of Belgrade, Belgrade, Serbia
| | - Peter Gemeiner
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Olgica Nedić
- Institute for the Application of Nuclear Energy, University of Belgrade, Belgrade, Serbia
| | - Jaroslav Katrlík
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
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45
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Calle LP, Echeverria B, Franconetti A, Serna S, Fernández‐Alonso MC, Diercks T, Cañada FJ, Ardá A, Reichardt N, Jiménez‐Barbero J. Monitoring Glycan–Protein Interactions by NMR Spectroscopic Analysis: A Simple Chemical Tag That Mimics Natural CH–π Interactions. Chemistry 2015; 21:11408-16. [DOI: 10.1002/chem.201501248] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Luis P. Calle
- Department of Chemical and Physical Biology, CIB‐CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain)
| | - Begoña Echeverria
- Department of Glycotechnology, CICbiomaGUNE, Paseo Miramón 182, 20009 San Sebastián (Spain)
| | - Antonio Franconetti
- Department of Organic Chemistry, University of Sevilla, Profesor García González 1, 41012 Sevilla (Spain)
| | - Sonia Serna
- Department of Glycotechnology, CICbiomaGUNE, Paseo Miramón 182, 20009 San Sebastián (Spain)
| | | | - Tammo Diercks
- Structural Biology Unit, CIC bioGUNE, Parque Tecnologico de Bizkaia, Building 801a, 48160 Derio (Spain)
| | - F. Javier Cañada
- Department of Chemical and Physical Biology, CIB‐CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain)
| | - Ana Ardá
- Structural Biology Unit, CIC bioGUNE, Parque Tecnologico de Bizkaia, Building 801a, 48160 Derio (Spain)
| | | | - Jesús Jiménez‐Barbero
- Structural Biology Unit, CIC bioGUNE, Parque Tecnologico de Bizkaia, Building 801a, 48160 Derio (Spain)
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao (Spain)
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46
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Srinivasan K, Roy S, Washburn N, Sipsey SF, Meccariello R, Meador JW, Ling LE, Manning AM, Kaundinya GV. A Quantitative Microtiter Assay for Sialylated Glycoform Analyses Using Lectin Complexes. JOURNAL OF BIOMOLECULAR SCREENING 2015; 20:768-78. [PMID: 25851037 PMCID: PMC4512520 DOI: 10.1177/1087057115577597] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/20/2015] [Accepted: 02/22/2015] [Indexed: 12/12/2022]
Abstract
Fidelity of glycan structures is a key requirement for biotherapeutics, with carbohydrates playing an important role for therapeutic efficacy. Comprehensive glycan profiling techniques such as liquid chromatography (LC) and mass spectrometry (MS), while providing detailed description of glycan structures, require glycan cleavage, labeling, and paradigms to deconvolute the considerable data sets they generate. On the other hand, lectins as probes on microarrays have recently been used in orthogonal approaches for in situ glycoprofiling but require analyte labeling to take advantage of the capabilities of automated microarray readers and data analysis they afford. Herein, we describe a lectin-based microtiter assay (lectin-enzyme-linked immunosorbent assay [ELISA]) to quantify terminal glycan moieties, applicable to in vitro and in-cell glycan-engineered Fc proteins as well as intact IgGs from intravenous immunoglobulin (IVIG), a blood product containing pooled polyvalent IgG antibodies extracted from plasma from healthy human donors. We corroborate our findings with industry-standard LC-MS profiling. This "customizable" ELISA juxtaposes readouts from multiple lectins, focusing on a subset of glycoforms, and provides the ability to discern single- versus dual-arm glycosylation while defining levels of epitopes at sensitivities comparable to MS. Extendable to other biologics, this ELISA can be used stand-alone or complementary to MS for quantitative glycan analysis.
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Affiliation(s)
| | | | | | | | | | | | - Leona E Ling
- Momenta Pharmaceuticals, Inc., Cambridge, MA, USA
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47
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Lockett MR, Smith LM. Carbon Substrates: A Stable Foundation for Biomolecular Arrays. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:263-285. [PMID: 26048550 PMCID: PMC6287745 DOI: 10.1146/annurev-anchem-071114-040146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Since their advent in the early 1990s, microarray technologies have developed into a powerful and ubiquitous platform for biomolecular analysis. Microarrays consist of three major elements: the substrate upon which they are constructed, the chemistry employed to attach biomolecules, and the biomolecules themselves. Although glass substrates and silane-based attachment chemistries are used for the vast majority of current microarray platforms, these materials suffer from severe limitations in stability, due to hydrolysis of both the substrate material itself and of the silyl ether linkages employed for attachment. These limitations in stability compromise assay performance and render impossible many potential microarray applications. We describe here a suite of alternative carbon-based substrates and associated attachment chemistries for microarray fabrication. The substrates themselves, as well as the carbon-carbon bond-based attachment chemistries, offer greatly increased chemical stability, enabling a myriad of novel applications.
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Affiliation(s)
- Matthew R Lockett
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599;
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48
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Paleček E, Tkáč J, Bartošík M, Bertók T, Ostatná V, Paleček J. Electrochemistry of nonconjugated proteins and glycoproteins. Toward sensors for biomedicine and glycomics. Chem Rev 2015; 115:2045-108. [PMID: 25659975 PMCID: PMC4360380 DOI: 10.1021/cr500279h] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Emil Paleček
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Tkáč
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Martin Bartošík
- Regional
Centre for Applied Molecular Oncology, Masaryk
Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Tomáš Bertók
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Veronika Ostatná
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Paleček
- Central
European Institute of Technology, Masaryk
University, Kamenice
5, 625 00 Brno, Czech Republic
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49
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do Nascimento ASF, Serna S, Beloqui A, Arda A, Sampaio AH, Walcher J, Ott D, Unverzagt C, Reichardt NC, Jimenez-Barbero J, Nascimento KS, Imberty A, Cavada BS, Varrot A. Algal lectin binding to core (α1-6) fucosylated N-glycans: structural basis for specificity and production of recombinant protein. Glycobiology 2015; 25:607-16. [PMID: 25573275 DOI: 10.1093/glycob/cwv002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 01/05/2015] [Indexed: 12/11/2022] Open
Abstract
We determined the specificity of BTL, a lectin from the red marine alga Bryothamnion triquetrum, toward fucosylated oligosaccharides. BTL showed a strict specificity for the core α1,6-fucosylation, which is an important marker for cancerogenesis and quality control of therapeutical antibodies. The double fucosylation α1,6 and α1,3 was also recognized, but the binding was totally abolished in the sole presence of the α1,3-fucosylation. A more detailed analysis of the specificity of BTL showed a preference for bi- and tri-antennary nonbisected N-glycans. Sialylation or fucosylation at the nonreducing end of N-glycans did not affect the recognition by the lectin. BTL displayed a strong affinity for a core α1,6-fucosylated octasaccharide with a Kd of 12 μM by titration microcalorimetry. The structural characterization of the interaction between BTL and the octasaccharide was obtained by STD-NMR. It demonstrated an extended epitope for recognition that includes the fucose residue, the distal GlcNAc and one mannose residue. Recombinant rBTL was obtained in Escherichia coli and characterized. Its binding properties for carbohydrates were studied using hemagglutination tests and glycan array analysis. rBTL was able to agglutinate rabbit erythrocytes with strong hemagglutination activity only after treatment with papain and trypsin, indicating that its ligands were not directly accessible at the cell surface. The hemagglutinating properties of rBTL confirm the correct folding and functional state of the protein. The results show BTL as a potent candidate for cancer diagnosis and as a reagent for the preparation and quality control of antibodies lacking core α1,6-fucosylated N-glycans.
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Affiliation(s)
- Antônia S F do Nascimento
- CERMAV, UPR5301, CNRS and Université Grenoble Alpes, 38041 Grenoble, France Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Sonia Serna
- Glycotechnology Laboratory, CICbiomaGUNE, 20009 San Sebastian, Spain
| | - Ana Beloqui
- Glycotechnology Laboratory, CICbiomaGUNE, 20009 San Sebastian, Spain
| | - Ana Arda
- Chemical and Physical Biology, Centro de Investigaciones Biologicas, CSIC, 28040 Madrid, Spain
| | - Alexandre H Sampaio
- Laboratório de Biotecnologia Marinha-BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Janika Walcher
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Dimitri Ott
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Carlo Unverzagt
- Bioorganische Chemie, Gebäude NW1, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Niels-Christian Reichardt
- Glycotechnology Laboratory, CICbiomaGUNE, 20009 San Sebastian, Spain CIBER-BBN, Paseo Miramon 182, 20009 San Sebastian, Spain
| | - Jesus Jimenez-Barbero
- Chemical and Physical Biology, Centro de Investigaciones Biologicas, CSIC, 28040 Madrid, Spain
| | - Kyria S Nascimento
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Anne Imberty
- CERMAV, UPR5301, CNRS and Université Grenoble Alpes, 38041 Grenoble, France
| | - Benildo S Cavada
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Annabelle Varrot
- CERMAV, UPR5301, CNRS and Université Grenoble Alpes, 38041 Grenoble, France
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50
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Wang SK, Cheng CM. Glycan-based diagnostic devices: current progress, challenges and perspectives. Chem Commun (Camb) 2015; 51:16750-62. [DOI: 10.1039/c5cc06876b] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The development of glycan-based diagnostic devices is illustrated with recent examples from both carbohydrate recognition and device design aspects.
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Affiliation(s)
- Sheng-Kai Wang
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 300
- Taiwan
| | - Chao-Min Cheng
- Institute of Biomedical Engineering
- National Tsing Hua University
- Taiwan
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