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Yom A, Chiang A, Lewis NE. Boltzmann Model Predicts Glycan Structures from Lectin Binding. Anal Chem 2024; 96:8332-8341. [PMID: 38720429 PMCID: PMC11162346 DOI: 10.1021/acs.analchem.3c04992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
Glycans are complex oligosaccharides that are involved in many diseases and biological processes. Unfortunately, current methods for determining glycan composition and structure (glycan sequencing) are laborious and require a high level of expertise. Here, we assess the feasibility of sequencing glycans based on their lectin binding fingerprints. By training a Boltzmann model on lectin binding data, we predict the approximate structures of 88 ± 7% of N-glycans and 87 ± 13% of O-glycans in our test set. We show that our model generalizes well to the pharmaceutically relevant case of Chinese hamster ovary (CHO) cell glycans. We also analyze the motif specificity of a wide array of lectins and identify the most and least predictive lectins and glycan features. These results could help streamline glycoprotein research and be of use to anyone using lectins for glycobiology.
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Affiliation(s)
- Aria Yom
- Department of Physics, University of California, San Diego, California 92093, United States
| | - Austin Chiang
- Department of Pediatrics, University of California, San Diego, California 92093, United States
- Immunology Center of Georgia, Augusta University, Augusta, Georgia 30912, United States
- Department of Medicine, Augusta University, Augusta, Georgia 30912, United States
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, California 92093, United States
- Department of Bioengineering, University of California, San Diego, California 92093, United States
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2
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Yom A, Chiang A, Lewis NE. A Boltzmann model predicts glycan structures from lectin binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.03.543532. [PMID: 37333412 PMCID: PMC10274649 DOI: 10.1101/2023.06.03.543532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Glycans are complex oligosaccharides involved in many diseases and biological processes. Unfortunately, current methods for determining glycan composition and structure (glycan sequencing) are laborious and require a high level of expertise. Here, we assess the feasibility of sequencing glycans based on their lectin binding fingerprints. By training a Boltzmann model on lectin binding data, we predict the approximate structures of 88 ± 7% of N-glycans and 87 ± 13% of O-glycans in our test set. We show that our model generalizes well to the pharmaceutically relevant case of Chinese Hamster Ovary (CHO) cell glycans. We also analyze the motif specificity of a wide array of lectins and identify the most and least predictive lectins and glycan features. These results could help streamline glycoprotein research and be of use to anyone using lectins for glycobiology.
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Affiliation(s)
- Aria Yom
- Department of Physics, University of California, San Diego. CA 92093, USA
| | - Austin Chiang
- Department of Pediatrics, University of California, San Diego. CA 92093, USA
- Immunology Center of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Medicine, Augusta University, Augusta, GA 30912, USA
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego. CA 92093, USA
- Department of Pediatrics, University of California, San Diego. CA 92093, USA
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3
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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: 96] [Impact Index Per Article: 48.0] [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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4
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Srivastava S, Verhagen A, Sasmal A, Wasik BR, Diaz S, Yu H, Bensing BA, Khan N, Khedri Z, Secrest P, Sullam P, Varki N, Chen X, Parrish CR, Varki A. Development and applications of sialoglycan-recognizing probes (SGRPs) with defined specificities: exploring the dynamic mammalian sialoglycome. Glycobiology 2022; 32:1116-1136. [PMID: 35926090 PMCID: PMC9680117 DOI: 10.1093/glycob/cwac050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/20/2022] [Accepted: 07/14/2022] [Indexed: 01/07/2023] Open
Abstract
Glycans that are abundantly displayed on vertebrate cell surface and secreted molecules are often capped with terminal sialic acids (Sias). These diverse 9-carbon-backbone monosaccharides are involved in numerous intrinsic biological processes. They also interact with commensals and pathogens, while undergoing dynamic changes in time and space, often influenced by environmental conditions. However, most of this sialoglycan complexity and variation remains poorly characterized by conventional techniques, which often tend to destroy or overlook crucial aspects of Sia diversity and/or fail to elucidate native structures in biological systems, i.e. in the intact sialome. To date, in situ detection and analysis of sialoglycans has largely relied on the use of plant lectins, sialidases, or antibodies, whose preferences (with certain exceptions) are limited and/or uncertain. We took advantage of naturally evolved microbial molecules (bacterial adhesins, toxin subunits, and viral hemagglutinin-esterases) that recognize sialoglycans with defined specificity to delineate 9 classes of sialoglycan recognizing probes (SGRPs: SGRP1-SGRP9) that can be used to explore mammalian sialome changes in a simple and systematic manner, using techniques common in most laboratories. SGRP candidates with specificity defined by sialoglycan microarray studies were engineered as tagged probes, each with a corresponding nonbinding mutant probe as a simple and reliable negative control. The optimized panel of SGRPs can be used in methods commonly available in most bioscience labs, such as ELISA, western blot, flow cytometry, and histochemistry. To demonstrate the utility of this approach, we provide examples of sialoglycome differences in tissues from C57BL/6 wild-type mice and human-like Cmah-/- mice.
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Affiliation(s)
- Saurabh Srivastava
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Andrea Verhagen
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Aniruddha Sasmal
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Brian R Wasik
- College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Sandra Diaz
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Hai Yu
- Department of Chemistry, University of California at Davis, Davis, CA, USA
| | - Barbara A Bensing
- Department of Medicine, University of California, San Francisco, CA, USA,VA Medical Center, San Francisco, CA, USA
| | - Naazneen Khan
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Zahra Khedri
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Patrick Secrest
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Paul Sullam
- Department of Medicine, University of California, San Francisco, CA, USA,VA Medical Center, San Francisco, CA, USA
| | - Nissi Varki
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Xi Chen
- Department of Chemistry, University of California at Davis, Davis, CA, USA
| | - Colin R Parrish
- College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Ajit Varki
- Corresponding author: UCSD School of Medicine, La Jolla, CA 92093-0687, USA.
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5
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Lundstrøm J, Korhonen E, Lisacek F, Bojar D. LectinOracle: A Generalizable Deep Learning Model for Lectin-Glycan Binding Prediction. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103807. [PMID: 34862760 PMCID: PMC8728848 DOI: 10.1002/advs.202103807] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/03/2021] [Indexed: 05/07/2023]
Abstract
Ranging from bacterial cell adhesion over viral cell entry to human innate immunity, glycan-binding proteins or lectins are abound in nature. Widely used as staining and characterization reagents in cell biology and crucial for understanding the interactions in biological systems, lectins are a focal point of study in glycobiology. Yet the sheer breadth and depth of specificity for diverse oligosaccharide motifs has made studying lectins a largely piecemeal approach, with few options to generalize. Here, LectinOracle, a model combining transformer-based representations for proteins and graph convolutional neural networks for glycans to predict their interaction, is presented. Using a curated data set of 564,647 unique protein-glycan interactions, it is shown that LectinOracle predictions agree with literature-annotated specificities for a wide range of lectins. Using a range of specialized glycan arrays, it is shown that LectinOracle predictions generalize to new glycans and lectins, with qualitative and quantitative agreement with experimental data. It is further demonstrated that LectinOracle can be used to improve lectin classification, accelerate lectin directed evolution, predict epidemiological outcomes in the context of influenza virus, and analyze whole lectomes in host-microbe interactions. It is envisioned that the herein presented platform will advance both the study of lectins and their role in (glyco)biology.
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Affiliation(s)
- Jon Lundstrøm
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburg41390Sweden
- Wallenberg Centre for Molecular and Translational MedicineUniversity of GothenburgGothenburg41390Sweden
| | - Emma Korhonen
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburg41390Sweden
- Wallenberg Centre for Molecular and Translational MedicineUniversity of GothenburgGothenburg41390Sweden
| | - Frédérique Lisacek
- Swiss Institute of BioinformaticsGeneva1227Switzerland
- Computer Science DepartmentUniGeGeneva1227Switzerland
- Section of BiologyUniGeGeneva1205Switzerland
| | - Daniel Bojar
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburg41390Sweden
- Wallenberg Centre for Molecular and Translational MedicineUniversity of GothenburgGothenburg41390Sweden
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6
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Effects of Dietary Doum Palm Fruit Powder on Growth, Antioxidant Capacity, Immune Response, and Disease Resistance of African Catfish, Clarias gariepinus (B.). Animals (Basel) 2020; 10:ani10081407. [PMID: 32823515 PMCID: PMC7460004 DOI: 10.3390/ani10081407] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 12/21/2022] Open
Abstract
Application of herbal immune-stimulants for modulation of fish growth and immune response has received great interest during the past decades. With several pharmacological properties, Doum palm, Hyphaene thebaica (Mart.) is known to be a beneficial medicinal plant. The objective of this study was to investigate the effects of the dietary addition of doum palm fruit powder (DPFP) on growth performance, non-specific immune response, and antioxidant parameters of African catfish, Clarias gariepinus (B.). A total of 120 fish (average initial weight 60.50 ± 0.04 g) were randomly allocated to four groups (three replicates/group, 10 fish/aquarium); a basal diet without DPFP supplementation was used as a control, and three other diets were prepared by supplementing 5, 10, or 15 g kg-1 DPFP for a ten-week feeding period. Following ten weeks of feeding, the fish were challenged with Aeromonas hydrophila (as an immune challenge test), and mortalities were recorded. In comparison to the control diet, dietary DPFP significantly improved growth parameters, including final body weight, body weight gain (WG), specific growth rate (SGR), feed conversion ratio (FCR), and protein efficiency ratio (PER), along with an increase in the content of dry matter of the whole body, in a concentration-dependent manner. Moreover, the heights of intestinal villi, numbers of goblet cells, and intraepithelial lymphocytes (IEL) exhibited marked escalation in all parts of the intestine by increasing the level of DPFP, except for numbers of IEL in the proximal part. The decline in serum glucose, cholesterol, and triglyceride levels was prominent in DPFP10 and DPFP15 groups respective to the DPFP0 group. Furthermore, DPFP boosted the hepatic level of catalase (CAT) in the fish, in a dose-dependent manner; meanwhile, the activity of superoxide dismutase (SOD) and reduced glutathione (GSH) content were also augmented in DPFP10 and DPFP15 groups respective to the DPFP0 group. Dietary DPFP (DPFP15 followed by DPFP10 then DPFP5) led to a pronounced enhancement in the innate immune response (phagocytic percent and index, lysozyme activity, nitric oxide (NO) production, and sialoglycans, namely α 2,3-sialyltransferase and α 2,6-sialyltransferase content); however, the myeloperoxidase (MPO) activity was reduced. Significantly higher relative percentage survival (RPS, 88.56%) of the fish, following the A. hydrophila challenge, was observed for the DPFP15 group. We can suggest that DPFP can beneficially influence fish growth, intestinal histomorphology, hepatic levels of catalase (CAT), superoxide dismutase (SOD) activity and glutathione (GSH) content, immune response, and disease resistance against A. hydrophila challenge.
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7
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Li L, Guan W, Zhang G, Wu Z, Yu H, Chen X, Wang PG. Microarray analyses of closely related glycoforms reveal different accessibilities of glycan determinants on N-glycan branches. Glycobiology 2020; 30:334-345. [PMID: 32026940 PMCID: PMC7175966 DOI: 10.1093/glycob/cwz100] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 01/03/2023] Open
Abstract
Glycans mediate a wide variety of biological roles via recognition by glycan-binding proteins (GBPs). Comprehensive knowledge of such interaction is thus fundamental to glycobiology. While the primary binding feature of GBPs can be easily uncovered by using a simple glycan microarray harboring limited numbers of glycan motifs, their fine specificities are harder to interpret. In this study, we prepared 98 closely related N-glycoforms that contain 5 common glycan epitopes which allowed the determination of the fine binding specificities of several plant lectins and anti-glycan antibodies. These N-glycoforms differ from each other at the monosaccharide level and were presented in an identical format to ensure comparability. With the analysis platform we used, it was found that most tested GBPs have preferences toward only one branch of the complex N-glycans, and their binding toward the epitope-presenting branch can be significantly affected by structures on the other branch. Fine specificities described here are valuable for a comprehensive understanding and applications of GBPs.
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Affiliation(s)
- Lei Li
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Wanyi Guan
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Gaolan Zhang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Zhigang Wu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Hai Yu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Xi Chen
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Peng G Wang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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8
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Coff L, Chan J, Ramsland PA, Guy AJ. Identifying glycan motifs using a novel subtree mining approach. BMC Bioinformatics 2020; 21:42. [PMID: 32019496 PMCID: PMC7001330 DOI: 10.1186/s12859-020-3374-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 01/20/2020] [Indexed: 11/17/2022] Open
Abstract
Background Glycans are complex sugar chains, crucial to many biological processes. By participating in binding interactions with proteins, glycans often play key roles in host–pathogen interactions. The specificities of glycan-binding proteins, such as lectins and antibodies, are governed by motifs within larger glycan structures, and improved characterisations of these determinants would aid research into human diseases. Identification of motifs has previously been approached as a frequent subtree mining problem, and we extend these approaches with a glycan notation that allows recognition of terminal motifs. Results In this work, we customised a frequent subtree mining approach by altering the glycan notation to include information on terminal connections. This allows specific identification of terminal residues as potential motifs, better capturing the complexity of glycan-binding interactions. We achieved this by including additional nodes in a graph representation of the glycan structure to indicate the presence or absence of a linkage at particular backbone carbon positions. Combining this frequent subtree mining approach with a state-of-the-art feature selection algorithm termed minimum-redundancy, maximum-relevance (mRMR), we have generated a classification pipeline that is trained on data from a glycan microarray. When applied to a set of commonly used lectins, the identified motifs were consistent with known binding determinants. Furthermore, logistic regression classifiers trained using these motifs performed well across most lectins examined, with a median AUC value of 0.89. Conclusions We present here a new subtree mining approach for the classification of glycan binding and identification of potential binding motifs. The Carbohydrate Classification Accounting for Restricted Linkages (CCARL) method will assist in the interpretation of glycan microarray experiments and will aid in the discovery of novel binding motifs for further experimental characterisation.
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Affiliation(s)
- Lachlan Coff
- School of Science, College of Science, Engineering and Health, RMIT University, 3000, Melbourne, Australia
| | - Jeffrey Chan
- School of Science, College of Science, Engineering and Health, RMIT University, 3000, Melbourne, Australia
| | - Paul A Ramsland
- School of Science, College of Science, Engineering and Health, RMIT University, 3000, Melbourne, Australia.,Department of Immunology, Monash University, 3004, Melbourne, Australia.,Department of Surgery Austin Health, University of Melbourne, 3084, Heidelberg, Australia
| | - Andrew J Guy
- School of Science, College of Science, Engineering and Health, RMIT University, 3000, Melbourne, Australia.
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9
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Haab BB, Klamer Z. Advances in Tools to Determine the Glycan-Binding Specificities of Lectins and Antibodies. Mol Cell Proteomics 2020; 19:224-232. [PMID: 31848260 PMCID: PMC7000120 DOI: 10.1074/mcp.r119.001836] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/13/2019] [Indexed: 01/17/2023] Open
Abstract
Proteins that bind carbohydrate structures can serve as tools to quantify or localize specific glycans in biological specimens. Such proteins, including lectins and glycan-binding antibodies, are particularly valuable if accurate information is available about the glycans that a protein binds. Glycan arrays have been transformational for uncovering rich information about the nuances and complexities of glycan-binding specificity. A challenge, however, has been the analysis of the data. Because protein-glycan interactions are so complex, simplistic modes of analyzing the data and describing glycan-binding specificities have proven inadequate in many cases. This review surveys the methods for handling high-content data on protein-glycan interactions. We contrast the approaches that have been demonstrated and provide an overview of the resources that are available. We also give an outlook on the promising experimental technologies for generating new insights into protein-glycan interactions, as well as a perspective on the limitations that currently face the field.
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10
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Khasbiullina NR, Shilova NV, Navakouski MJ, Nokel AY, Blixt O, Kononov LO, Knirel YA, Bovin NV. The Repertoire of Human Antiglycan Antibodies and Its Dynamics in the First Year of Life. BIOCHEMISTRY (MOSCOW) 2019; 84:608-616. [PMID: 31238860 DOI: 10.1134/s0006297919060038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The repertoire of antiglycan antibodies of peripheral blood was studied using a microarray containing 487 glycan antigens: fragments of mammalian glycans (N- and O-chains of glycoproteins, as well as glycolipids) and also bacterial polysaccharides. The sera samples correspond to the third, sixth, and twelfth months of life. The infants were divided into four groups according to their nutrition type: breast milk, standard formula, and partially or extensively hydrolyzed formula. During the first year of life, the total amount of IgG decreased; presumably, the lifetime of maternal IgG in the newborns' bloodstream is much greater than is generally assumed. At the same time, the IgM content was low during the first six months and increased significantly by the twelfth month. The antiglycan IgM repertoire of one-year-old infants was still different from that of their mothers, as well as from the repertoire of unrelated donors, in particular, by the absence of antibodies against the Galβ1-3GlcNAc (LeC) disaccharide, which is found in almost all healthy humans. It is noteworthy that the level of IgM of breast-fed infants was significantly lower than that of formula-fed by the twelfth month.
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Affiliation(s)
- N R Khasbiullina
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia. .,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - N V Shilova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - M J Navakouski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - A Yu Nokel
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - O Blixt
- University of Copenhagen, Frederiksberg, T4221871, Denmark
| | - L O Kononov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Yu A Knirel
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 119991, Russia
| | - N V Bovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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11
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Ahmad F, Döbel T, Schmitz M, Schäkel K. Current Concepts on 6-sulfo LacNAc Expressing Monocytes (slanMo). Front Immunol 2019; 10:948. [PMID: 31191513 PMCID: PMC6540605 DOI: 10.3389/fimmu.2019.00948] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 04/12/2019] [Indexed: 12/25/2022] Open
Abstract
The human mononuclear phagocytes system consists of dendritic cells (DCs), monocytes, and macrophages having different functions in bridging innate and adaptive immunity. Among the heterogeneous population of monocytes the cell surface marker slan (6-sulfo LacNAc) identifies a specific subset of human CD14- CD16+ non-classical monocytes, called slan+ monocytes (slanMo). In this review we discuss the identity and functions of slanMo, their contributions to immune surveillance by pro-inflammatory cytokine production, and cross talk with T cells and NK cells. We also consider the role of slanMo in the regulation of chronic inflammatory diseases and cancer. Finally, we highlight unresolved questions that should be the focus of future research.
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Affiliation(s)
- Fareed Ahmad
- Department of Dermatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Döbel
- Department of Dermatology, Heidelberg University Hospital, Heidelberg, Germany.,Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, United States
| | - Marc Schmitz
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, Technische Universtät Dresden, Dresden, Germany.,Partner Site Dresden, National Center for Tumor Diseases (NCT), Dresden, Germany
| | - Knut Schäkel
- Department of Dermatology, Heidelberg University Hospital, Heidelberg, Germany
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12
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Metabolomic and glycomic findings in posttraumatic stress disorder. Prog Neuropsychopharmacol Biol Psychiatry 2019; 88:181-193. [PMID: 30025792 DOI: 10.1016/j.pnpbp.2018.07.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/21/2018] [Accepted: 07/14/2018] [Indexed: 01/10/2023]
Abstract
Posttraumatic stress disorder (PTSD) is a stressor-related disorder that develops in a subset of individuals exposed to a traumatic experience. Factors associated with vulnerability to PTSD are still not fully understood. PTSD is frequently comorbid with various psychiatric and somatic disorders, moderate response to treatment and remission rates. The term "theranostics" combines diagnosis, prognosis, and therapy and offers targeted therapy based on specific analyses. Theranostics, combined with novel techniques and approaches called "omics", which integrate genomics, transcriptomic, proteomics and metabolomics, might improve knowledge about biological underpinning of PTSD, and offer novel therapeutic strategies. The focus of this review is on metabolomic and glycomic data in PTSD. Metabolomics evaluates changes in the metabolome of an organism by exploring the set of small molecules (metabolites), while glycomics studies the glycome, a complete repertoire of glycan structures with their functional roles in biological systems. Both metabolome and glycome reflect the physiological and pathological conditions in individuals. Only a few studies evaluated metabolic and glycomic changes in patients with PTSD. The metabolomics studies in PTSD patients uncovered different metabolites that might be associated with psychopathological alterations in PTSD. The glycomics study in PTSD patients determined nine N-glycan structures and found accelerated and premature aging in traumatized subjects and subjects with PTSD based on a GlycoAge index. Therefore, further larger studies and replications are needed. Better understanding of the biological basis of PTSD, including metabolomic and glycomic data, and their integration with other "omics" approaches, might identify new molecular targets and might provide improved therapeutic approaches.
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13
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Yu SY, Hsiao CT, Izawa M, Yusa A, Ishida H, Nakamura S, Yagi H, Kannagi R, Khoo KH. Distinct substrate specificities of human GlcNAc-6-sulfotransferases revealed by mass spectrometry-based sulfoglycomic analysis. J Biol Chem 2018; 293:15163-15177. [PMID: 30093410 PMCID: PMC6166739 DOI: 10.1074/jbc.ra118.001937] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 08/08/2018] [Indexed: 12/19/2022] Open
Abstract
Sulfated glycans are known to be involved in several glycan-mediated cell adhesion and recognition pathways. Our mRNA transcript analyses on the genes involved in synthesizing GlcNAc-6-O-sulfated glycans in human colon cancer tissues indicated that GlcNAc6ST-2 (CHST4) is preferentially expressed in cancer cells compared with nonmalignant epithelial cells among the three known major GlcNAc-6-O-sulfotransferases. On the contrary, GlcNAc6ST-3 (CHST5) was only expressed in nonmalignant epithelial cells, whereas GlcNAc6ST-1 (CHST2) was expressed equally in both cancerous and nonmalignant epithelial cells. These results suggest that 6-O-sulfated glycans that are synthesized only by GlcNAc6ST-2 may be highly colon cancer-specific, as supported by immunohistochemical staining of cancer cells using the MECA-79 antibody known to be relatively specific to the enzymatic reaction products of GlcNAc6ST-2. By more precise MS-based sulfoglycomic analyses, we sought to further infer the substrate specificities of GlcNAc6STs via a definitive mapping of various sulfo-glycotopes and O-glycan structures expressed in response to overexpression of transfected GlcNAc6STs in the SW480 colon cancer cell line. By detailed MS/MS sequencing, GlcNAc6ST-3 was shown to preferentially add sulfate onto core 2-based O-glycan structures, but it does not act on extended core 1 structures, whereas GlcNAc6ST-1 prefers core 2-based O-glycans to extended core 1 structures. In contrast, GlcNAc6ST-2 could efficiently add sulfate onto both extended core 1- and core 2-based O-glycans, leading to the production of unique sulfated extended core 1 structures such as R-GlcNAc(6-SO3-)β1-3Galβ1-4GlcNAc(6-SO3-)β1-3Galβ1-3GalNAcα, which are good candidates to be targeted as cancer-specific glycans.
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Affiliation(s)
- Shin-Yi Yu
- From the Institute of Biological Chemistry and
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 115, Taiwan
| | | | | | - Akiko Yusa
- the Department of Molecular Pathology and
| | - Hiroji Ishida
- Laboratory for Clinical Pathology, Aichi Cancer Center, Nagoya 464-8681, Japan, and
| | - Shigeo Nakamura
- Laboratory for Clinical Pathology, Aichi Cancer Center, Nagoya 464-8681, Japan, and
| | - Hirokazu Yagi
- the Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Reiji Kannagi
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 115, Taiwan,
- the Department of Molecular Pathology and
- Laboratory for Clinical Pathology, Aichi Cancer Center, Nagoya 464-8681, Japan, and
- the Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
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14
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Abstract
Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.
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Affiliation(s)
- Robert J Woods
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States
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15
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Dingjan T, Gillon É, Imberty A, Pérez S, Titz A, Ramsland PA, Yuriev E. Virtual Screening Against Carbohydrate-Binding Proteins: Evaluation and Application to Bacterial Burkholderia ambifaria Lectin. J Chem Inf Model 2018; 58:1976-1989. [DOI: 10.1021/acs.jcim.8b00185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Tamir Dingjan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Émilie Gillon
- University Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Anne Imberty
- University Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Serge Pérez
- University Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France
| | - Alexander Titz
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, D-66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany
- Department of Pharmacy, Saarland University, D-66123 Saarbrücken, Germany
| | - Paul A. Ramsland
- School of Science, RMIT University, Bundoora, Victoria 3083, Australia
- Department of Surgery Austin Health, University of Melbourne, Heidelberg, Victoria 3084, Australia
- Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria 3004, Australia
- Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
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16
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Boziki M, Polyzos SA, Deretzi G, Kazakos E, Katsinelos P, Doulberis M, Kotronis G, Giartza-Taxidou E, Laskaridis L, Tzivras D, Vardaka E, Kountouras C, Grigoriadis N, Thomann R, Kountouras J. A potential impact of Helicobacter pylori-related galectin-3 in neurodegeneration. Neurochem Int 2017; 113:137-151. [PMID: 29246761 DOI: 10.1016/j.neuint.2017.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/03/2017] [Accepted: 12/11/2017] [Indexed: 02/07/2023]
Abstract
Neurodegeneration represents a component of the central nervous system (CNS) diseases pathogenesis, either as a disability primary source in the frame of prototype neurodegenerative disorders, or as a secondary effect, following inflammation, hypoxia or neurotoxicity. Galectins are members of the lectin superfamily, a group of endogenous glycan-binding proteins, able to interact with glycosylated receptors expressed by several immune cell types. Glycan-lectin interactions play critical roles in the living systems by involving and mediating a variety of biologically important normal and pathological processes, including cell-cell signaling shaping cell communication, proliferation and migration, immune responses and fertilization, host-pathogen interactions and diseases such as neurodegenerative disorders and tumors. This review focuses in the role of Galectin-3 in shaping responses of the immune system against microbial agents, and concretely, Helicobacter pylori (Hp), thereby potentiating effect of the microbe in areas distant from the ordinary site of colonization, like the CNS. We hereby postulate that gastrointestinal Hp alterations in terms of immune cell functional phenotype, cytokine and chemokine secretion, may trigger systemic responses, thereby conferring implications for remote processes susceptible in immunity disequilibrium, namely, the CNS inflammation and/or neurodegeneration.
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Affiliation(s)
- Marina Boziki
- Department of Medicine, Second Medical Clinic, Aristotle University of Thessaloniki, Ippokration Hospital, Thessaloniki, Greece; Department of Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Stergios A Polyzos
- Department of Medicine, Second Medical Clinic, Aristotle University of Thessaloniki, Ippokration Hospital, Thessaloniki, Greece
| | - Georgia Deretzi
- Department of Neurology, Multiple Sclerosis Unit, Papageorgiou Hospital, Thessaloniki, Greece
| | - Evangelos Kazakos
- Department of Medicine, Second Medical Clinic, Aristotle University of Thessaloniki, Ippokration Hospital, Thessaloniki, Greece
| | - Panagiotis Katsinelos
- Department of Medicine, Second Medical Clinic, Aristotle University of Thessaloniki, Ippokration Hospital, Thessaloniki, Greece
| | - Michael Doulberis
- Department of Medicine, Second Medical Clinic, Aristotle University of Thessaloniki, Ippokration Hospital, Thessaloniki, Greece; Department of Internal Medicine, Bürgerspital Solothurn, Solothurn, Switzerland
| | - Georgios Kotronis
- Department of Medicine, Second Medical Clinic, Aristotle University of Thessaloniki, Ippokration Hospital, Thessaloniki, Greece
| | - Evaggelia Giartza-Taxidou
- Department of Medicine, Second Medical Clinic, Aristotle University of Thessaloniki, Ippokration Hospital, Thessaloniki, Greece
| | - Leonidas Laskaridis
- Department of Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitri Tzivras
- Department of Medicine, Second Medical Clinic, Aristotle University of Thessaloniki, Ippokration Hospital, Thessaloniki, Greece
| | - Elisabeth Vardaka
- Department of Medicine, Second Medical Clinic, Aristotle University of Thessaloniki, Ippokration Hospital, Thessaloniki, Greece
| | - Constantinos Kountouras
- Department of Medicine, Second Medical Clinic, Aristotle University of Thessaloniki, Ippokration Hospital, Thessaloniki, Greece
| | - Nikolaos Grigoriadis
- Department of Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Robert Thomann
- Department of Internal Medicine, Bürgerspital Solothurn, Solothurn, Switzerland
| | - Jannis Kountouras
- Department of Medicine, Second Medical Clinic, Aristotle University of Thessaloniki, Ippokration Hospital, Thessaloniki, Greece.
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17
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Lectins identify distinct populations of coelomocytes in Strongylocentrotus purpuratus. PLoS One 2017; 12:e0187987. [PMID: 29125863 PMCID: PMC5695280 DOI: 10.1371/journal.pone.0187987] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 10/30/2017] [Indexed: 11/20/2022] Open
Abstract
Coelomocytes represent the immune cells of echinoderms, but detailed knowledge about their roles during immune responses is very limited. One major challenge for studying coelomocyte biology is the lack of reagents to identify and purify distinct populations defined by objective molecular markers rather than by morphology-based classifications that are subjective at times. Glycosylation patterns are known to differ significantly between cell types in vertebrates, and furthermore they can vary depending on the developmental stage and activation states within a given lineage. Thus fluorescently labeled lectins that recognize distinct glycan structures on cell surface proteins are routinely used to identify discrete cell populations in the vertebrate immune system. Here we now employed a panel of fifteen fluorescently-labeled lectins to determine differences in the glycosylation features on the surface of Strongylocentrotus purpuratus coelomocytes by fluorescence microscopy and flow cytometry. Eight of the lectins (succinylated wheat germ agglutinin, Len culinaris lectin, Pisum sativum agglutinin, Saphora japonica agglutinin, Solanum tuberosum lectin, Lycopersicon esculentum lectin, Datura stramonium lectin, Vicia villosa lectin) showed distinct binding patterns to fixed and live cells of three major coelomocyte classes: phagocytic cells, red spherule cells, and vibratile cells. Importantly, almost all lectins bound only to a subgroup of cells within each cell type. Lastly, we established fluorescently-labeled lectin-based fluorescence activated cell sorting as a strategy to purify distinct S. purpuratus coelomocyte (sub-)populations based on molecular markers. We anticipate that this will become a routine approach in future studies focused on dissecting the roles of different coelomocytes in echinoderm immunity.
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18
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Klamer Z, Staal B, Prudden AR, Liu L, Smith DF, Boons GJ, Haab B. Mining High-Complexity Motifs in Glycans: A New Language To Uncover the Fine Specificities of Lectins and Glycosidases. Anal Chem 2017; 89:12342-12350. [PMID: 29058413 PMCID: PMC5700451 DOI: 10.1021/acs.analchem.7b04293] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Knowledge of lectin
and glycosidase specificities is fundamental
to the study of glycobiology. The primary specificities of such molecules
can be uncovered using well-established tools, but the complex details
of their specificities are difficult to determine and describe. Here
we present a language and algorithm for the analysis and description
of glycan motifs with high complexity. The language uses human-readable
notation and wildcards, modifiers, and logical operators to define
motifs of nearly any complexity. By applying the syntax to the analysis
of glycan-array data, we found that the lectin AAL had higher binding
where fucose groups are displayed on separate branches. The lectin
SNA showed gradations in binding based on the length of the extension
displaying sialic acid and on characteristics of the opposing branches.
A new algorithm to evaluate changes in lectin binding upon treatment
with exoglycosidases identified the primary specificities and potential
fine specificities of an α1–2-fucosidase and an α2–3,6,8-neuraminidase.
The fucosidase had significantly lower action where sialic acid neighbors
the fucose, and the neuraminidase showed statistically lower action
where α1–2 fucose neighbors the sialic acid or is on
the opposing branch. The complex features identified here would have
been inaccessible to analysis using previous methods. The new language
and algorithms promise to facilitate the precise determination and
description of lectin and glycosidase specificities.
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Affiliation(s)
- Zachary Klamer
- Van Andel Research Institute , 333 Bostwick NE, Grand Rapids, Michigan 49503, United States
| | - Ben Staal
- Van Andel Research Institute , 333 Bostwick NE, Grand Rapids, Michigan 49503, United States
| | - Anthony R Prudden
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Lin Liu
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - David F Smith
- Emory Comprehensive Glycomics Core, Emory University School of Medicine , Atlanta, Georgia 30322, United States
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Brian Haab
- Van Andel Research Institute , 333 Bostwick NE, Grand Rapids, Michigan 49503, United States
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19
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Shi Z, Li WW, Tang Y, Cheng LJ. A Novel Molecular Model of Plant Lectin-Induced Programmed Cell Death in Cancer. Biol Pharm Bull 2017; 40:1625-1629. [PMID: 28768938 DOI: 10.1248/bpb.b17-00363] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Plant lectin, a class of highly diverse non-immune origin and carbohydrate-binding proteins, has been reported to specially induce cancer cell through programmed cell death (PCD) pathways (apoptosis and/or autophagy), shedding lights on screening promising anti-cancer candidate agent for further therapeutic trials. However, the complicated molecular mechanisms by which plant lectins induced the programmed death of tumor cells, have not yet been fully clarified. Here, we summarized a novel model, based on vast amount of research, by which plant lectins eliminate various types of cancer cells via three major pathways, including a) direct ribosome inactivating, b) endocytosis-dependent mitochondrial dysfunction and c) sugar-containing receptors binding. A better understanding of the role of plant lectins played and further elucidation of the strategies targeting PCD would provide a new clue for the applications and modifications of plant lectin as a potential anti-cancer agent from bench to clinic.
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Affiliation(s)
- Zheng Shi
- School of Medicine, Chengdu University
| | | | - Yong Tang
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine
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20
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Reatini BS, Ensink E, Liau B, Sinha JY, Powers TW, Partyka K, Bern M, Brand RE, Rudd PM, Kletter D, Drake R, Haab BB. Characterizing Protein Glycosylation through On-Chip Glycan Modification and Probing. Anal Chem 2016; 88:11584-11592. [PMID: 27809484 PMCID: PMC5290727 DOI: 10.1021/acs.analchem.6b02998] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Glycans are critical to protein biology and are useful as disease biomarkers. Many studies of glycans rely on clinical specimens, but the low amount of sample available for some specimens limits the experimental options. Here we present a method to obtain information about protein glycosylation using a minimal amount of protein. We treat proteins that were captured or directly spotted in small microarrays (2.2 mm × 2.2 mm) with exoglycosidases to successively expose underlying features, and then we probe the native or exposed features using a panel of lectins or glycan-binding reagents. We developed an algorithm to interpret the data and provide predictions about the glycan motifs that are present in the sample. We demonstrated the efficacy of the method to characterize differences between glycoproteins in their sialic acid linkages and N-linked glycan branching, and we validated the assignments by comparing results from mass spectrometry and chromatography. The amount of protein used on-chip was about 11 ng. The method also proved effective for analyzing the glycosylation of a cancer biomarker in human plasma, MUC5AC, using only 20 μL of the plasma. A glycan on MUC5AC that is associated with cancer had mostly 2,3-linked sialic acid, whereas other glycans on MUC5AC had a 2,6 linkage of sialic acid. The on-chip glycan modification and probing (on-chip GMAP) method provides a platform for analyzing protein glycosylation in clinical specimens and could complement the existing toolkit for studying glycosylation in disease.
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Affiliation(s)
| | - Elliot Ensink
- Van Andel Research Institute, Grand Rapids, Michigan
| | - Brian Liau
- Bioprocessing Technology Institute, Singapore
| | | | - Thomas W. Powers
- Medical University of South Carolina, Charleston, South Carolina
| | - Katie Partyka
- Van Andel Research Institute, Grand Rapids, Michigan
| | | | - Randall E. Brand
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Pauline M. Rudd
- Bioprocessing Technology Institute, Singapore
- National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | | | | | - Brian B. Haab
- Van Andel Research Institute, Grand Rapids, Michigan
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21
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Multi-level regulation of cellular glycosylation: from genes to transcript to enzyme to structure. Curr Opin Struct Biol 2016; 40:145-152. [PMID: 27744149 DOI: 10.1016/j.sbi.2016.09.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/08/2016] [Accepted: 09/27/2016] [Indexed: 12/29/2022]
Abstract
Glycosylation is a ubiquitous mammalian post-translational modification that both decorates a majority of expressed proteins and regulates their function. Cellular glycan biosynthesis is facilitated by a few hundred enzymes that are collectively termed 'glycoenzymes'. The expression and activity of these enzymes is controlled at the transcription, translation and post-translation levels. New wet-lab advances are providing analytical methods to collect large-scale data at these multiple levels, relational databases are starting to collate these results, and computer models are beginning to integrate this information across scales in order to gain new knowledge. These activities are likely to enable the qualitative and quantitative mapping of pathways regulating glycan production and function in proteins, cells and tissue.
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Structural basis for sulfation-dependent self-glycan recognition by the human immune-inhibitory receptor Siglec-8. Proc Natl Acad Sci U S A 2016; 113:E4170-9. [PMID: 27357658 DOI: 10.1073/pnas.1602214113] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Siglec-8 is a human immune-inhibitory receptor that, when engaged by specific self-glycans, triggers eosinophil apoptosis and inhibits mast cell degranulation, providing an endogenous mechanism to down-regulate immune responses of these central inflammatory effector cells. Here we used solution NMR spectroscopy to dissect the fine specificity of Siglec-8 toward different sialylated and sulfated carbohydrate ligands and determined the structure of the Siglec-8 lectin domain in complex with its prime glycan target 6'-sulfo sialyl Lewis(x) A canonical motif for sialic acid recognition, extended by a secondary motif formed by unique loop regions, recognizing 6-O-sulfated galactose dictates tight specificity distinct from other Siglec family members and any other endogenous glycan recognition receptors. Structure-guided mutagenesis revealed key contacts of both interfaces to be equally essential for binding. Our work provides critical structural and mechanistic insights into how Siglec-8 selectively recognizes its glycan target, rationalizes the functional impact of site-specific glycan sulfation in modulating this lectin-glycan interaction, and will enable the rational design of Siglec-8-targeted agonists to treat eosinophil- and mast cell-related allergic and inflammatory diseases, such as asthma.
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23
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Mereiter S, Balmaña M, Gomes J, Magalhães A, Reis CA. Glycomic Approaches for the Discovery of Targets in Gastrointestinal Cancer. Front Oncol 2016; 6:55. [PMID: 27014630 PMCID: PMC4783390 DOI: 10.3389/fonc.2016.00055] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 02/24/2016] [Indexed: 12/22/2022] Open
Abstract
Gastrointestinal (GI) cancer is the most common group of malignancies and many of its types are among the most deadly. Various glycoconjugates have been used in clinical practice as serum biomarker for several GI tumors, however, with limited diagnose application. Despite the good accessibility by endoscopy of many GI organs, the lack of reliable serum biomarkers often leads to late diagnosis of malignancy and consequently low 5-year survival rates. Recent advances in analytical techniques have provided novel glycoproteomic and glycomic data and generated functional information and putative biomarker targets in oncology. Glycosylation alterations have been demonstrated in a series of glycoconjugates (glycoproteins, proteoglycans, and glycosphingolipids) that are involved in cancer cell adhesion, signaling, invasion, and metastasis formation. In this review, we present an overview on the major glycosylation alterations in GI cancer and the current serological biomarkers used in the clinical oncology setting. We further describe recent glycomic studies in GI cancer, namely gastric, colorectal, and pancreatic cancer. Moreover, we discuss the role of glycosylation as a modulator of the function of several key players in cancer cell biology. Finally, we address several state-of-the-art techniques currently applied in this field, such as glycomic and glycoproteomic analyses, the application of glycoengineered cell line models, microarray and proximity ligation assay, and imaging mass spectrometry, and provide an outlook to future perspectives and clinical applications.
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Affiliation(s)
- Stefan Mereiter
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Institute of Biomedical Sciences of Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Meritxell Balmaña
- Biochemistry and Molecular Biology Unit, Department of Biology, University of Girona , Girona , Spain
| | - Joana Gomes
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Ana Magalhães
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Celso A Reis
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Institute of Biomedical Sciences of Abel Salazar (ICBAS), University of Porto, Porto, Portugal; Medical Faculty, University of Porto, Porto, Portugal
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24
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A Panel of Recombinant Mucins Carrying a Repertoire of Sialylated O-Glycans Based on Different Core Chains for Studies of Glycan Binding Proteins. Biomolecules 2015; 5:1810-31. [PMID: 26274979 PMCID: PMC4598776 DOI: 10.3390/biom5031810] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 01/26/2023] Open
Abstract
Sialylated glycans serve as key elements of receptors for many viruses, bacteria, and bacterial toxins. The microbial recognition and their binding specificity can be affected by the linkage of the terminal sugar residue, types of underlying sugar chains, and the nature of the entire glycoconjugate. Owing to the pathobiological significance of sialylated glycans, we have engineered Chinese hamster ovary (CHO) cells to secrete mucin-type immunoglobulin-fused proteins carrying terminal α2,3- or α2,6-linked sialic acid on defined O-glycan core saccharide chains. Besides stably expressing P-selectin glycoprotein ligand-1/mouse immunoglobulin G2b cDNA (PSGL-1/mIgG2b), CHO cells were stably transfected with plasmids encoding glycosyltransferases to synthesize core 2 (GCNT1), core 3 (B3GNT6), core 4 (GCNT1 and B3GNT6), or extended core 1 (B3GNT3) chains with or without the type 1 chain-encoding enzyme B3GALT5 and ST6GAL1. Western blot and liquid chromatography-mass spectrometry analysis confirmed the presence of core 1, 2, 3, 4, and extended core 1 chains carrying either type 1 (Galb3GlcNAc) or type 2 (Galb4GlcNAc) outer chains with or without α2,6-linked sialic acids. This panel of recombinant mucins carrying a repertoire of sialylated O-glycans will be important tools in studies aiming at determining the fine O-glycan binding specificity of sialic acid-specific microbial adhesins and mammalian lectins.
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Defaus S, Gupta P, Andreu D, Gutiérrez-Gallego R. Mammalian protein glycosylation--structure versus function. Analyst 2015; 139:2944-67. [PMID: 24779027 DOI: 10.1039/c3an02245e] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Carbohydrates fulfil many common as well as extremely important functions in nature. They show a variety of molecular displays--e.g., free mono-, oligo-, and polysaccharides, glycolipids, proteoglycans, glycoproteins, etc.--with particular roles and localizations in living organisms. Structure-specific peculiarities are so many and diverse that it becomes virtually impossible to cover them all from an analytical perspective. Hence this manuscript, focused on mammalian glycosylation, rather than a complete list of analytical descriptors or recognized functions for carbohydrate structures, comprehensively reviews three central issues in current glycoscience, namely (i) structural analysis of glycoprotein glycans, covering both classical and novel approaches for teasing out the structural puzzle as well as potential pitfalls of these processes; (ii) an overview of functions attributed to carbohydrates, covering from monosaccharide to complex, well-defined epitopes and full glycans, including post-glycosylational modifications, and (iii) recent technical advances allowing structural identification of glycoprotein glycans with simultaneous assignation of biological functions.
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Affiliation(s)
- S Defaus
- Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona Biomedical Research Park, 08003 Barcelona, Spain.
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26
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Singh S, Pal K, Yadav J, Tang H, Partyka K, Kletter D, Hsueh P, Ensink E, Kc B, Hostetter G, Xu HE, Bern M, Smith DF, Mehta AS, Brand R, Melcher K, Haab BB. Upregulation of glycans containing 3' fucose in a subset of pancreatic cancers uncovered using fusion-tagged lectins. J Proteome Res 2015; 14:2594-605. [PMID: 25938165 DOI: 10.1021/acs.jproteome.5b00142] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The fucose post-translational modification is frequently increased in pancreatic cancer, thus forming the basis for promising biomarkers, but a subset of pancreatic cancer patients does not elevate the known fucose-containing biomarkers. We hypothesized that such patients elevate glycan motifs with fucose in linkages and contexts different from the known fucose-containing biomarkers. We used a database of glycan array data to identify the lectins CCL2 to detect glycan motifs with fucose in a 3' linkage; CGL2 for motifs with fucose in a 2' linkage; and RSL for fucose in all linkages. We used several practical methods to test the lectins and determine the optimal mode of detection, and we then tested whether the lectins detected glycans in pancreatic cancer patients who did not elevate the sialyl-Lewis A glycan, which is upregulated in ∼75% of pancreatic adenocarcinomas. Patients who did not upregulate sialyl-Lewis A, which contains fucose in a 4' linkage, tended to upregulate fucose in a 3' linkage, as detected by CCL2, but they did not upregulate total fucose or fucose in a 2' linkage. CCL2 binding was high in cancerous epithelia from pancreatic tumors, including areas negative for sialyl-Lewis A and a related motif containing 3' fucose, sialyl-Lewis X. Thus, glycans containing 3' fucose may complement sialyl-Lewis A to contribute to improved detection of pancreatic cancer. Furthermore, the use of panels of recombinant lectins may uncover details about glycosylation that could be important for characterizing and detecting cancer.
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Affiliation(s)
- Sudhir Singh
- †Van Andel Research Institute, Grand Rapids, Michigan 49503, United States
| | - Kuntal Pal
- †Van Andel Research Institute, Grand Rapids, Michigan 49503, United States
| | - Jessica Yadav
- †Van Andel Research Institute, Grand Rapids, Michigan 49503, United States
| | - Huiyuan Tang
- †Van Andel Research Institute, Grand Rapids, Michigan 49503, United States
| | - Katie Partyka
- †Van Andel Research Institute, Grand Rapids, Michigan 49503, United States
| | - Doron Kletter
- ‡Palo Alto Research Center, Palo Alto, California 94304, United States
| | - Peter Hsueh
- †Van Andel Research Institute, Grand Rapids, Michigan 49503, United States
| | - Elliot Ensink
- †Van Andel Research Institute, Grand Rapids, Michigan 49503, United States
| | - Birendra Kc
- §Spectrum Health, Grand Rapids, Michigan 49503, United States
| | - Galen Hostetter
- †Van Andel Research Institute, Grand Rapids, Michigan 49503, United States
| | - H Eric Xu
- †Van Andel Research Institute, Grand Rapids, Michigan 49503, United States
| | - Marshall Bern
- ‡Palo Alto Research Center, Palo Alto, California 94304, United States
| | - David F Smith
- ∥Emory University, Atlanta, Georgia 30322, United States
| | - Anand S Mehta
- ⊥Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Randall Brand
- #University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania 15213, United States
| | - Karsten Melcher
- †Van Andel Research Institute, Grand Rapids, Michigan 49503, United States
| | - Brian B Haab
- †Van Andel Research Institute, Grand Rapids, Michigan 49503, United States
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27
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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: 214] [Impact Index Per Article: 23.8] [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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28
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Tang H, Singh S, Partyka K, Kletter D, Hsueh P, Yadav J, Ensink E, Bern M, Hostetter G, Hartman D, Huang Y, Brand RE, Haab BB. Glycan motif profiling reveals plasma sialyl-lewis x elevations in pancreatic cancers that are negative for sialyl-lewis A. Mol Cell Proteomics 2015; 14:1323-33. [PMID: 25733690 DOI: 10.1074/mcp.m114.047837] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Indexed: 12/24/2022] Open
Abstract
The sialyl-Lewis A (sLeA) glycan forms the basis of the CA19-9 assay and is the current best biomarker for pancreatic cancer, but because it is not elevated in ∼25% of pancreatic cancers, it is not useful for early diagnosis. We hypothesized that sLeA-low tumors secrete glycans that are related to sLeA but not detectable by CA19-9 antibodies. We used a method called motif profiling to predict that a structural isomer of sLeA called sialyl-Lewis X (sLeX) is elevated in the plasma of some sLeA-low cancers. We corroborated this prediction in a set of 48 plasma samples and in a blinded set of 200 samples. An antibody sandwich assay formed by the capture and detection of sLeX was elevated in 13 of 69 cancers that were not elevated in sLeA, and a novel hybrid assay of sLeA capture and sLeX detected 24 of 69 sLeA-low cancers. A two-marker panel based on combined sLeA and sLeX detection differentiated 109 pancreatic cancers from 91 benign pancreatic diseases with 79% accuracy (74% sensitivity and 78% specificity), significantly better than sLeA alone, which yielded 68% accuracy (65% sensitivity and 71% specificity). Furthermore, sLeX staining was evident in tumors that do not elevate plasma sLeA, including those with poorly differentiated ductal adenocarcinoma. Thus, glycan-based biomarkers could characterize distinct subgroups of patients. In addition, the combined use of sLeA and sLeX, or related glycans, could lead to a biomarker panel that is useful in the clinical diagnosis of pancreatic cancer. Précis: This paper shows that a structural isomer of the current best biomarker for pancreatic cancer, CA19-9, is elevated in the plasma of patients who are low in CA19-9, potentially enabling more comprehensive detection and classification of pancreatic cancers.
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Affiliation(s)
| | | | | | | | - Peter Hsueh
- §Van Andel Research Institute, Grand Rapids, MI
| | | | | | | | | | | | - Ying Huang
- **University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | - Brian B Haab
- §Van Andel Research Institute, Grand Rapids, MI;
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29
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Tang H, Hsueh P, Kletter D, Bern M, Haab B. The detection and discovery of glycan motifs in biological samples using lectins and antibodies: new methods and opportunities. Adv Cancer Res 2015; 126:167-202. [PMID: 25727148 DOI: 10.1016/bs.acr.2014.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recent research has uncovered unexpected ways that glycans contribute to biology, as well as new strategies for combatting disease using approaches involving glycans. To make full use of glycans for clinical applications, we need more detailed information on the location, nature, and dynamics of glycan expression in vivo. Such studies require the use of specimens acquired directly from patients. Effective studies of clinical specimens require low-volume assays, high precision measurements, and the ability to process many samples. Assays using affinity reagents-lectins and glycan-binding antibodies-can meet these requirements, but further developments are needed to make the methods routine and effective. Recent advances in the use of glycan-binding proteins involve improved determination of specificity using glycan arrays; the availability of databases for mining and analyzing glycan array data; lectin engineering methods; and the ability to quantitatively interpret lectin measurements. Here, we describe many of the challenges and opportunities involved in the application of these new approaches to the study of biological samples. The new tools hold promise for developing methods to improve the outcomes of patients afflicted with diseases characterized by aberrant glycan expression.
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Affiliation(s)
- Huiyuan Tang
- Van Andel Research Institute, Grand Rapids, MI, USA
| | - Peter Hsueh
- Van Andel Research Institute, Grand Rapids, MI, USA
| | | | | | - Brian Haab
- Van Andel Research Institute, Grand Rapids, MI, USA.
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30
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Biophysical characterization of lectin–glycan interactions for therapeutics, vaccines and targeted drug-delivery. Future Med Chem 2014; 6:2113-29. [DOI: 10.4155/fmc.14.130] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lectin–glycan interactions play a role in biological processes, host–pathogen interactions and in disease. A more detailed understanding of these interactions is not only useful for the elucidation of their biological function but can also be applied in immunology, drug development and delivery and diagnostics. We review some commonly used biophysical techniques for studying lectin–glycan interactions; namely: frontal affinity chromatography, glycan/lectin microarray, surface plasmon resonance, electrochemical impedance spectroscopy, isothermal titration calorimetry, fluorescent assays, enzyme linked lectin sorbent assay and saturation transfer difference nuclear magnetic resonance spectroscopy. Each method is evaluated on efficiency, cost and throughput. We also consider the advantages and limitations of each technique and provide examples of their application in biology, drug discovery and delivery, immunology, glycoprofiling and biosensing.
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31
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Cummings RD, Pierce JM. The challenge and promise of glycomics. CHEMISTRY & BIOLOGY 2014; 21:1-15. [PMID: 24439204 PMCID: PMC3955176 DOI: 10.1016/j.chembiol.2013.12.010] [Citation(s) in RCA: 280] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 12/27/2013] [Accepted: 12/30/2013] [Indexed: 01/22/2023]
Abstract
Glycomics is a broad and emerging scientific discipline focused on defining the structures and functional roles of glycans in biological systems. The staggering complexity of the glycome, minimally defined as the repertoire of glycans expressed in a cell or organism, has resulted in many challenges that must be overcome; these are being addressed by new advances in mass spectrometry as well as by the expansion of genetic and cell biology studies. Conversely, identifying the specific glycan recognition determinants of glycan-binding proteins by employing the new technology of glycan microarrays is providing insights into how glycans function in recognition and signaling within an organism and with microbes and pathogens. The promises of a more complete knowledge of glycomes are immense in that glycan modifications of intracellular and extracellular proteins have critical functions in almost all biological pathways.
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Affiliation(s)
- Richard D Cummings
- Department of Biochemistry, Emory Glycomics Center, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta, GA 30322, USA.
| | - J Michael Pierce
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA.
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32
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Geissner A, Anish C, Seeberger PH. Glycan arrays as tools for infectious disease research. Curr Opin Chem Biol 2013; 18:38-45. [PMID: 24534751 DOI: 10.1016/j.cbpa.2013.11.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 11/15/2013] [Accepted: 11/27/2013] [Indexed: 10/25/2022]
Abstract
Infectious diseases cause millions of deaths worldwide each year and are a major burden for economies, especially in underdeveloped countries. Glycans and their interactions with other biomolecules are involved in all major steps of infection. Glycan arrays enable the rapid and sensitive detection of those interactions and are among the most powerful techniques to study the molecular biology of infectious diseases. This review will focus on recent developments and discuss the applications of glycan arrays to the elucidation of host-pathogen and pathogen-pathogen interactions, the development of tools for infection diagnosis and the use of glycan arrays in modern vaccine design.
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Affiliation(s)
- Andreas Geissner
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany; Institute for Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Chakkumkal Anish
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany.
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany; Institute for Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany.
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33
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Deng L, Chen X, Varki A. Exploration of sialic acid diversity and biology using sialoglycan microarrays. Biopolymers 2013; 99:650-65. [PMID: 23765393 PMCID: PMC7161822 DOI: 10.1002/bip.22314] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 06/04/2013] [Indexed: 12/13/2022]
Abstract
Sialic acids (Sias) are a group of α-keto acids with a nine-carbon backbone, which display many types of modifications in nature. The diversity of natural Sia presentations is magnified by a variety of glycosidic linkages to underlying glycans, the sequences and classes of such glycans, as well as the spatial organization of Sias with their surroundings. This diversity is closely linked to the numerous and varied biological functions of Sias. Relatively large libraries of natural and unnatural Sias have recently been chemically/chemoenzymatically synthesized and/or isolated from natural sources. The resulting sialoglycan microarrays have proved to be valuable tools for the exploration of diversity and biology of Sias. Here we provide an overview of Sia diversity in nature, the approaches used to generate sialoglycan microarrays, and the achievements and challenges arising.
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Affiliation(s)
- Lingquan Deng
- Departments of Medicine and Cellular & Molecular MedicineGlycobiology Research and Training Center, University of CaliforniaSan Diego, La JollaCA92093‐0687
| | - Xi Chen
- Department of ChemistryUniversity of CaliforniaDavisCA95616
| | - Ajit Varki
- Departments of Medicine and Cellular & Molecular MedicineGlycobiology Research and Training Center, University of CaliforniaSan Diego, La JollaCA92093‐0687
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34
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Haab BB, Partyka K, Cao Z. Using antibody arrays to measure protein abundance and glycosylation: considerations for optimal performance. ACTA ACUST UNITED AC 2013; 73:27.6.1-27.6.16. [PMID: 24510592 DOI: 10.1002/0471140864.ps2706s73] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Antibody arrays provide a valuable method for obtaining multiple protein measurements from small volumes of biological samples. Antibody arrays can be designed to target not only core protein abundances (relative or absolute abundances, depending on the availability of standards for calibration), but also posttranslational modifications, provided antibodies or other affinity reagents are available to detect them. Glycosylation is a common modification that has important and diverse functions in both normal and disease biology. Significant progress has been made in developing methods for measuring glycan levels on multiple specific proteins using antibody arrays and glycan-binding reagents. This unit describes practical approaches for developing, optimizing, and using antibody array assays to determine both protein abundance and glycosylation state. Low-volume arrays can be used to reduce sample consumption, and a new way to improve the binding strength of particular glycan-binding reagents through multimerization is discussed. These methods can be useful for a wide range of biological studies in which glycosylation may change and/or affect protein function.
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Affiliation(s)
- Brian B Haab
- Van Andel Research Institute, Grand Rapids, Michigan
| | - Katie Partyka
- Van Andel Research Institute, Grand Rapids, Michigan
| | - Zheng Cao
- Van Andel Research Institute, Grand Rapids, Michigan
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35
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McCarter C, Kletter D, Tang H, Partyka K, Ma Y, Singh S, Yadav J, Bern M, Haab BB. Prediction of glycan motifs using quantitative analysis of multi-lectin binding: Motifs on MUC1 produced by cultured pancreatic cancer cells. Proteomics Clin Appl 2013; 7:632-41. [PMID: 23956151 DOI: 10.1002/prca.201300069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 01/05/2023]
Abstract
PURPOSE Lectins are valuable tools for detecting specific glycans in biological samples, but the interpretation of the measurements can be ambiguous due to the complexities of lectin specificities. Here, we present an approach to improve the accuracy of interpretation by converting lectin measurements into quantitative predictions of the presence of various glycan motifs. EXPERIMENTAL DESIGN The conversion relies on a database of analyzed glycan array data that provides information on the specificities of the lectins for each of the motifs. We tested the method using measurements of lectin binding to glycans on glycan arrays and then applied the method to predicting motifs on the protein mucin 1 (MUC1) expressed in eight different pancreatic cancer cell lines. RESULTS The combined measurements from several lectins were more accurate than individual measurements for predicting the presence or absence of motifs on arrayed glycans. The analysis of MUC1 revealed that each cell line expressed a unique pattern of glycoforms, and that the glycoforms significantly differed between MUC1 collected from conditioned media and MUC1 collected from cell lysates. CONCLUSIONS AND CLINICAL RELEVANCE This new method could provide more accurate analyses of glycans in biological sample and make the use of lectins more practical and effective for a broad range of researchers.
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Affiliation(s)
| | | | - Huiyuan Tang
- Van Andel Research Institute, Grand Rapids, MI, USA
| | | | - Yinjiao Ma
- Van Andel Research Institute, Grand Rapids, MI, USA.,Genetics Program, Michigan State University, East Lansing MI, USA
| | - Sudhir Singh
- Van Andel Research Institute, Grand Rapids, MI, USA
| | | | | | - Brian B Haab
- Van Andel Research Institute, Grand Rapids, MI, USA
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36
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Dallas DC, Lee H, Parc AL, de Moura Bell JMLN, Barile D. Coupling Mass Spectrometry-Based "Omic" Sciences with Bioguided Processing to Unravel Milk's Hidden Bioactivities. JOURNAL OF ADVANCES IN DAIRY RESEARCH 2013; 1:104. [PMID: 24818172 PMCID: PMC4012335 DOI: 10.4172/2329-888x.1000104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Many of milk's functional molecules could not be discovered until the right concordance of novel separation and analytical technologies were developed and applied. Many health-promoting components still await discovery due to technical challenges in their identification, isolation and testing. As new analytical technologies are assembled, new functional milk molecules will be discovered. Bovine milk is a source of a wide array of known bioactive compounds from a variety of molecular classes, including free glycans, lipids, glycolipids, peptides, proteins, glycoproteins, stem cells and microRNA. Because milk is such a complex mixture, when analyzed without fractionation or purification, many components mask the analytical signal of others, so some components cannot be detected. Modern analytics allow for the discovery and characterization of hundreds of novel milk compounds with high-resolution and high-accuracy. Liquid chromatography paired with electrospray ionization allows the separation of peptides, glycans and glycolipids for improved mass spectrometric detection. Target proteins and glycoproteins can now be purified from intact milk or other dairy streams by chromatography in order to better characterize these proteins for new bioactivities. The combination of advanced analytics with the new engineering capabilities will allow for high molecular resolution and separation techniques that can be scaled-up to semi-industrial and industrial scale for translation of lab-based discoveries. Bioguided analysis and design of dairy processing side streams will result in the transformation of waste into isolated functional ingredients to add value to dietary products.
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Affiliation(s)
- David C Dallas
- Department of Food Science & Technology, University of California, One Shields Avenue, Davis, CA 95616, USA ; Foods for Health Institute, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Hyeyoung Lee
- Department of Food Science & Technology, University of California, One Shields Avenue, Davis, CA 95616, USA ; Foods for Health Institute, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Annabelle Le Parc
- Department of Food Science & Technology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | | | - Daniela Barile
- Department of Food Science & Technology, University of California, One Shields Avenue, Davis, CA 95616, USA ; Foods for Health Institute, University of California, One Shields Avenue, Davis, CA 95616, USA
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