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Martinez K, Agirre J, Akune Y, Aoki-Kinoshita KF, Arighi C, Axelsen KB, Bolton E, Bordeleau E, Edwards NJ, Fadda E, Feizi T, Hayes C, Ives CM, Joshi HJ, Krishna Prasad K, Kossida S, Lisacek F, Liu Y, Lütteke T, Ma J, Malik A, Martin M, Mehta AY, Neelamegham S, Panneerselvam K, Ranzinger R, Ricard-Blum S, Sanou G, Shanker V, Thomas PD, Tiemeyer M, Urban J, Vita R, Vora J, Yamamoto Y, Mazumder R. Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy. Database (Oxford) 2024; 2024:baae073. [PMID: 39137905 PMCID: PMC11321244 DOI: 10.1093/database/baae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/24/2024] [Accepted: 07/10/2024] [Indexed: 08/15/2024]
Abstract
Dynamic changes in protein glycosylation impact human health and disease progression. However, current resources that capture disease and phenotype information focus primarily on the macromolecules within the central dogma of molecular biology (DNA, RNA, proteins). To gain a better understanding of organisms, there is a need to capture the functional impact of glycans and glycosylation on biological processes. A workshop titled "Functional impact of glycans and their curation" was held in conjunction with the 16th Annual International Biocuration Conference to discuss ongoing worldwide activities related to glycan function curation. This workshop brought together subject matter experts, tool developers, and biocurators from over 20 projects and bioinformatics resources. Participants discussed four key topics for each of their resources: (i) how they curate glycan function-related data from publications and other sources, (ii) what type of data they would like to acquire, (iii) what data they currently have, and (iv) what standards they use. Their answers contributed input that provided a comprehensive overview of state-of-the-art glycan function curation and annotations. This report summarizes the outcome of discussions, including potential solutions and areas where curators, data wranglers, and text mining experts can collaborate to address current gaps in glycan and glycosylation annotations, leveraging each other's work to improve their respective resources and encourage impactful data sharing among resources. Database URL: https://wiki.glygen.org/Glycan_Function_Workshop_2023.
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Affiliation(s)
- Karina Martinez
- Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 I St. NW, Washington, DC 20052, United States
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, Wentworth Way, York YO10 5DD, United Kingdom
| | - Yukie Akune
- The Glycosciences Laboratory, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, United Kingdom
| | - Kiyoko F Aoki-Kinoshita
- Glycan and Life Systems Integration Center (GaLSIC), Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Cecilia Arighi
- Department of Computer and Information Sciences, University of Delaware, 18 Amstel Ave, Newark, DE 19716, United States
| | - Kristian B Axelsen
- Swiss-Prot Group, Swiss Institute of Bioinformatics (SIB), CMU, 1 rue Michel Servet, Geneva 4 1211, Switzerland
| | - Evan Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, United States
| | - Emily Bordeleau
- Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Nathan J Edwards
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, 2115 Wisconsin Ave NW, Washington, DC 20007, United States
| | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Kilcock Road, Maynooth, Co. Kildare W23 AH3Y, Ireland
| | - Ten Feizi
- The Glycosciences Laboratory, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, United Kingdom
| | - Catherine Hayes
- Proteome Informatics Group, Swiss Institute of Bioinformatics (SIB), route de Drize 7, Geneva CH-1227, Switzerland
| | - Callum M Ives
- Department of Chemistry and Hamilton Institute, Maynooth University, Kilcock Road, Maynooth, Co. Kildare W23 AH3Y, Ireland
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
| | - Khakurel Krishna Prasad
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, Dolní Břežany 25241, Czech Republic
| | - Sofia Kossida
- IMGT, The International ImMunoGeneTics Information System, National Center for Scientific Research (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), 141 rue de la Cardonille, Montpellier 34 090, France
| | - Frederique Lisacek
- Proteome Informatics Group, Swiss Institute of Bioinformatics (SIB), route de Drize 7, Geneva CH-1227, Switzerland
| | - Yan Liu
- The Glycosciences Laboratory, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, United Kingdom
| | - Thomas Lütteke
- Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Gießen, Frankfurter Str. 100, Gießen 35392, Germany
| | - Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3900 Reservior Road NW, Washington, DC 20007, United States
| | - Adnan Malik
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Maria Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Akul Y Mehta
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, United States
| | - Sriram Neelamegham
- Departments of Chemical & Biological Engineering, Biomedical Engineering and Medicine, University at Buffalo, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, United States
| | - Kalpana Panneerselvam
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - René Ranzinger
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States
| | - Sylvie Ricard-Blum
- Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, University Lyon 1, CNRS, 43 Boulevard du 11 novembre 1918, Villeurbanne cedex F-69622, France
| | - Gaoussou Sanou
- IMGT, The International ImMunoGeneTics Information System, National Center for Scientific Research (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), 141 rue de la Cardonille, Montpellier 34 090, France
| | - Vijay Shanker
- Department of Computer and Information Sciences, University of Delaware, 18 Amstel Ave, Newark, DE 19716, United States
| | - Paul D Thomas
- Department of Population and Public Health Sciences, University of Southern California, 2001 N Soto Street, Los Angeles, CA 90032, United States
| | - Michael Tiemeyer
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States
| | - James Urban
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 7 B, Gothenburg 41390, Sweden
| | - Randi Vita
- Immune Epitope Database and Analysis Project, La Jolla Institute for Allergy & Immunology, 9420 Athena Circle, La Jolla, CA 92037, United States
| | - Jeet Vora
- Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 I St. NW, Washington, DC 20052, United States
| | - Yasunori Yamamoto
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Raja Mazumder
- Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 I St. NW, Washington, DC 20052, United States
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2
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Wardman JF, Withers SG. Carbohydrate-active enzyme (CAZyme) discovery and engineering via (Ultra)high-throughput screening. RSC Chem Biol 2024; 5:595-616. [PMID: 38966674 PMCID: PMC11221537 DOI: 10.1039/d4cb00024b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/16/2024] [Indexed: 07/06/2024] Open
Abstract
Carbohydrate-active enzymes (CAZymes) constitute a diverse set of enzymes that catalyze the assembly, degradation, and modification of carbohydrates. These enzymes have been fashioned into potent, selective catalysts by millennia of evolution, and yet are also highly adaptable and readily evolved in the laboratory. To identify and engineer CAZymes for different purposes, (ultra)high-throughput screening campaigns have been frequently utilized with great success. This review provides an overview of the different approaches taken in screening for CAZymes and how mechanistic understandings of CAZymes can enable new approaches to screening. Within, we also cover how cutting-edge techniques such as microfluidics, advances in computational approaches and synthetic biology, as well as novel assay designs are leading the field towards more informative and effective screening approaches.
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Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia Vancouver BC V6T 1Z1 Canada
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3
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Freitas R, Ferreira E, Miranda A, Ferreira D, Relvas-Santos M, Castro F, Santos B, Gonçalves M, Quintas S, Peixoto A, Palmeira C, Silva AMN, Santos LL, Oliveira MJ, Sarmento B, Ferreira JA. Targeted and Self-Adjuvated Nanoglycovaccine Candidate for Cancer Immunotherapy. ACS NANO 2024; 18:10088-10103. [PMID: 38535625 DOI: 10.1021/acsnano.3c12487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Advanced-stage solid primary tumors and metastases often express mucin 16 (MUC16), carrying immature glycans such as the Tn antigen, resulting in specific glycoproteoforms not found in healthy human tissues. This presents a valuable approach for designing targeted therapeutics, including cancer glycovaccines, which could potentially promote antigen recognition and foster the immune response to control disease spread and prevent relapse. In this study, we describe an adjuvant-free poly(lactic-co-glycolic acid) (PLGA)-based nanoglycoantigen delivery approach that outperforms conventional methods by eliminating the need for protein carriers while exhibiting targeted and adjuvant properties. To achieve this, we synthesized a library of MUC16-Tn glycoepitopes through single-pot enzymatic glycosylation, which were then stably engrafted onto the surface of PLGA nanoparticles, generating multivalent constructs that better represent cancer molecular heterogeneity. These glycoconstructs demonstrated affinity for Macrophage Galactose-type Lectin (MGL) receptor, known to be highly expressed by immature antigen-presenting cells, enabling precise targeting of immune cells. Moreover, the glycopeptide-grafted nanovaccine candidate displayed minimal cytotoxicity and induced the activation of dendritic cells in vitro, even in the absence of an adjuvant. In vivo, the formulated nanovaccine candidate was also nontoxic and elicited the production of IgG specifically targeting MUC16 and MUC16-Tn glycoproteoforms in cancer cells and tumors, offering potential for precise cancer targeting, including targeted immunotherapies.
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Affiliation(s)
- Rui Freitas
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal
- RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
- ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
| | - Eduardo Ferreira
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal
- RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
| | - Andreia Miranda
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal
- RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
- ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
| | - Dylan Ferreira
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal
- RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
- ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal
- RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
- ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Flávia Castro
- i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
| | - Beatriz Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal
- RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
- ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
| | - Martina Gonçalves
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal
- RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
- ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
| | - Sofia Quintas
- ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal
- RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
- i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
| | - Carlos Palmeira
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal
- RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
- Immunology Department, Portuguese Oncology Institute of Porto (IPO-Porto), 4200-072 Porto, Portugal
- Health School of University Fernando Pessoa, 4249-004 Porto, Portugal
| | - André M N Silva
- ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
- GlycoMatters Biotech, 4500-162 Espinho, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal
- RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
- GlycoMatters Biotech, 4500-162 Espinho, Portugal
- Department of Surgical Oncology, Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal
| | - Maria José Oliveira
- ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
| | - Bruno Sarmento
- i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
- IUCS-CESPU, 4585-116 Gandra, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal
- RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
- ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- GlycoMatters Biotech, 4500-162 Espinho, Portugal
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4
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Freitas R, Miranda A, Ferreira D, Relvas-Santos M, Castro F, Ferreira E, Gaiteiro C, Soares J, Cotton S, Gonçalves M, Eiras M, Santos B, Palmeira C, Correia MP, Oliveira MJ, Sarmento B, Peixoto A, Santos LL, Silva AMN, Ferreira JA. A multivalent CD44 glycoconjugate vaccine candidate for cancer immunotherapy. J Control Release 2024; 367:540-556. [PMID: 38301927 DOI: 10.1016/j.jconrel.2024.01.065] [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: 12/17/2023] [Revised: 01/18/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
Cancer presents a high mortality rate due to ineffective treatments and tumour relapse with progression. Cancer vaccines hold tremendous potential due to their capability to eradicate tumour and prevent relapse. In this study, we present a novel glycovaccine for precise targeting and immunotherapy of aggressive solid tumours that overexpress CD44 standard isoform (CD44s) carrying immature Tn and sialyl-Tn (sTn) O-glycans. We describe an enzymatic method and an enrichment strategy to generate libraries of well-characterized cancer-specific CD44s-Tn and/or sTn glycoproteoforms, which mimic the heterogeneity found in tumours. We conjugated CD44-Tn-derived glycopeptides with carrier proteins making them more immunogenic, with further demonstration of the importance of this conjugation to overcome the glycopeptides' intrinsic toxicity. We have optimized the glycopeptide-protein maleimide-thiol conjugation chemistry to avoid undesirable cross-linking between carrier proteins and CD44s glycopeptides. The resulting glycovaccines candidates were well-tolerated in vivo, inducing both humoral and cellular immunity, including immunological memory. The generated antibodies exhibited specific reactivity against synthetic CD44s-Tn glycopeptides, CD44s-Tn glycoengineered cells, and human tumours. In summary, we present a promising prototype of a cancer glycovaccine for future therapeutical pre-clinical efficacy validation.
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Affiliation(s)
- Rui Freitas
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal; RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal; i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal / INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
| | - Andreia Miranda
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal; RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal; i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal / INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
| | - Dylan Ferreira
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal; RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal; i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal / INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal; RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal; i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal / INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal; REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Flávia Castro
- i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal / INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
| | - Eduardo Ferreira
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal; RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
| | - Cristiana Gaiteiro
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal; RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
| | - Janine Soares
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal; RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; REQUIMTE-LAQV, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Sofia Cotton
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal; RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
| | - Martina Gonçalves
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal; RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
| | - Mariana Eiras
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal; RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; REQUIMTE-LAQV, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Beatriz Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal; RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
| | - Carlos Palmeira
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal; RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; Immunology Department, Portuguese Oncology Institute of Porto (IPO-Porto), 4200-072 Porto, Portugal; Health School of University Fernando Pessoa, 4249-004 Porto, Portugal
| | - Margareta P Correia
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP), 4200-072 Porto, Portugal
| | - Maria José Oliveira
- ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal; i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal / INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal
| | - Bruno Sarmento
- i3S - Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal / INEB - Institute for Biomedical Engineering, University of Porto, 4200-135 Porto, Portugal; IUCS-CESPU, 4585-116 Gandra, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal; RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal; RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal; Health School of University Fernando Pessoa, 4249-004 Porto, Portugal; GlycoMatters Biotech, 4500-162 Espinho, Portugal; Department of Surgical Oncology, Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal
| | - André M N Silva
- ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal; REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal; GlycoMatters Biotech, 4500-162 Espinho, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Research Center of IPO-Porto (CI-IPOP), 4200-072 Porto, Portugal; RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC Raquel Seruca), 4200-072 Porto, Portugal; ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal; GlycoMatters Biotech, 4500-162 Espinho, Portugal.
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5
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Yang Y, Ding M, Yin H, Chen W, Shen H, Diao W, Yang L, Qin H, Gan W, Qiu X, Guo H. GALNT12 suppresses the bone-specific prostate cancer metastasis by activating BMP pathway via the O-glycosylation of BMPR1A. Int J Biol Sci 2024; 20:1297-1313. [PMID: 38385080 PMCID: PMC10878148 DOI: 10.7150/ijbs.91925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/24/2024] [Indexed: 02/23/2024] Open
Abstract
Bone metastasis caused the majority death of prostate cancer (PCa) but the mechanism remains poorly understood. In this present study, we show that polypeptide N-acetylgalactosaminyltransferase 12 (GALNT12) suppresses bone-specific metastasis of PCa. GALNT12 suppresses proliferation, migration, invasion and cell division ability of PCa cells by activating the BMP pathway. Mechanistic investigations showed that GALNT12 augments the O-glycosylation of BMPR1A then actives the BMP pathway. Activated BMP signaling inhibits the expression of integrin αVβ3 to reduce the bone-specific seeding of PCa cells. Furthermore, activated BMP signaling remolds the immune microenvironment by suppressing the STAT3 pathway. Our results of this study illustrate the role and mechanism of GALNT12 in the process of bone metastasis of PCa and identify GALNT12 as a potential therapeutic target for metastatic PCa.
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Affiliation(s)
- Yang Yang
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, China
| | - Meng Ding
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, China
| | - Haoli Yin
- Department of Urology, The Third Affiliated Hospital of Kunming Medical University, Tumor Hospital of Yunnan Province, Kunming, China
| | - Wei Chen
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, China
| | - Hongwei Shen
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, China
| | - Wenli Diao
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, China
| | - Lin Yang
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, China
| | - Haixiang Qin
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, China
| | - Weidong Gan
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, China
| | - Xuefeng Qiu
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, China
| | - Hongqian Guo
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, China
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6
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Mazuca LG, Mohl JE. ISOGlyP: O-Glycosylation Site Prediction Using Peptide Sequences and GALNTs. Methods Mol Biol 2024; 2763:237-247. [PMID: 38347415 DOI: 10.1007/978-1-0716-3670-1_20] [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] [Indexed: 02/15/2024]
Abstract
Mucin-type O-glycosylation is one of the most common posttranslational modifications of proteins. The abnormal expression of various polypeptide GalNAc-transferases (GALNTs) which initiate and define sites of O-glycosylation is linked to many cancers and other diseases. Many current O-glycosylation prediction programs utilize O-glycoproteomics data obtained without using the transferase isoform(s) responsible for the glycosylation. With 20 different GALNTs in humans, having the ability to predict and interpret O-glycosylation sites in terms of specific GALNT isoforms is invaluable.To fill this gap, ISOGlyP (isoform-specific O-glycosylation prediction) has been developed. Using position-specific enhancement values generated based on GalNAc-T isoform-specific amino acid preferences, ISOGlyP predicts the propensity that a site would be glycosylated by a specific transferase. ISOGlyP gave an overall prediction accuracy of 70% against in vivo data, which is comparable to that of the NetOGlyc4.0 predictor. Additionally, ISOGlyP can identify the known effects of long- and short-range prior glycosylation and can generate potential peptide sequences selectively glycosylated by specific isoforms. ISOGlyP is freely available for use at https://ISOGlyP.utep.edu . The code is also available on GitHub ( https://github.com/jonmohl/ISOGlyP ).
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7
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Pokharel S, Pratyush P, Ismail HD, Ma J, KC DB. Integrating Embeddings from Multiple Protein Language Models to Improve Protein O-GlcNAc Site Prediction. Int J Mol Sci 2023; 24:16000. [PMID: 37958983 PMCID: PMC10650050 DOI: 10.3390/ijms242116000] [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: 08/17/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 11/15/2023] Open
Abstract
O-linked β-N-acetylglucosamine (O-GlcNAc) is a distinct monosaccharide modification of serine (S) or threonine (T) residues of nucleocytoplasmic and mitochondrial proteins. O-GlcNAc modification (i.e., O-GlcNAcylation) is involved in the regulation of diverse cellular processes, including transcription, epigenetic modifications, and cell signaling. Despite the great progress in experimentally mapping O-GlcNAc sites, there is an unmet need to develop robust prediction tools that can effectively locate the presence of O-GlcNAc sites in protein sequences of interest. In this work, we performed a comprehensive evaluation of a framework for prediction of protein O-GlcNAc sites using embeddings from pre-trained protein language models. In particular, we compared the performance of three protein sequence-based large protein language models (pLMs), Ankh, ESM-2, and ProtT5, for prediction of O-GlcNAc sites and also evaluated various ensemble strategies to integrate embeddings from these protein language models. Upon investigation, the decision-level fusion approach that integrates the decisions of the three embedding models, which we call LM-OGlcNAc-Site, outperformed the models trained on these individual language models as well as other fusion approaches and other existing predictors in almost all of the parameters evaluated. The precise prediction of O-GlcNAc sites will facilitate the probing of O-GlcNAc site-specific functions of proteins in physiology and diseases. Moreover, these findings also indicate the effectiveness of combined uses of multiple protein language models in post-translational modification prediction and open exciting avenues for further research and exploration in other protein downstream tasks. LM-OGlcNAc-Site's web server and source code are publicly available to the community.
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Affiliation(s)
- Suresh Pokharel
- Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA; (S.P.); (P.P.); (H.D.I.)
| | - Pawel Pratyush
- Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA; (S.P.); (P.P.); (H.D.I.)
| | - Hamid D. Ismail
- Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA; (S.P.); (P.P.); (H.D.I.)
| | - Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, DC 20057, USA;
| | - Dukka B. KC
- Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA; (S.P.); (P.P.); (H.D.I.)
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8
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Ballard CJ, Paserba MR, Paul Daniel EJ, Hurtado-Guerrero R, Gerken TA. Polypeptide N-acetylgalactosaminyltransferase (GalNAc-T) isozyme surface charge governs charge substrate preferences to modulate mucin type O-glycosylation. Glycobiology 2023; 33:817-836. [PMID: 37555669 PMCID: PMC10629720 DOI: 10.1093/glycob/cwad066] [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: 05/31/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023] Open
Abstract
A large family of polypeptide N-acetylgalactosaminyltransferases (GalNAc-Ts) initiate mucin type O-glycosylation transferring α-GalNAc from a UDP-GalNAc donor to the hydroxyl groups of Ser and Thr residues of peptides and proteins, thereby defining sites of O-glycosylation. Mutations and differential expression of several GalNAc-Ts are associated with many disease states including cancers. The mechanisms by which these isozymes choose their targets and their roles in disease are not fully understood. We previously showed that the GalNAc-Ts possess common and unique specificities for acceptor type, peptide sequence and prior neighboring, and/or remote substrate GalNAc glycosylation. In the present study, the role of flanking charged residues was investigated using a library of charged peptide substrates containing the central -YAVTPGP- acceptor sequence. Eleven human and one bird GalNAc-T were initially characterized revealing a range of preferences for net positive, net negative, or unique combinations of flanking N- and/or C-terminal charge, correlating to each isozyme's different electrostatic surface potential. It was further found that isoforms with high sequence identity (>70%) within a subfamily can possess vastly different charge specificities. Enzyme kinetics, activities obtained at elevated ionic strength, and molecular dynamics simulations confirm that the GalNAc-Ts differently recognize substrate charge outside the common +/-3 residue binding site. These electrostatic interactions impact how charged peptide substrates bind/orient on the transferase surface, thus modulating their activities. In summary, we show the GalNAc-Ts utilize more extended surfaces than initially thought for binding substrates based on electrostatic, and likely other hydrophobic/hydrophilic interactions, furthering our understanding of how these transferases select their target.
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Affiliation(s)
- Collin J Ballard
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Miya R Paserba
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Ramón Hurtado-Guerrero
- Department of Biomedical Engineering, The Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
- Fundación ARAID, Zaragoza 50018, Spain
| | - Thomas A Gerken
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
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9
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Yang W, Tian E, Chernish A, McCluggage P, Dalal K, Lara A, Ten Hagen KG, Tabak LA. Quantitative mapping of the in vivo O-GalNAc glycoproteome in mouse tissues identifies GalNAc-T2 O-glycosites in metabolic disorder. Proc Natl Acad Sci U S A 2023; 120:e2303703120. [PMID: 37862385 PMCID: PMC10614836 DOI: 10.1073/pnas.2303703120] [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: 03/05/2023] [Accepted: 09/03/2023] [Indexed: 10/22/2023] Open
Abstract
The family of GalNAc-Ts (GalNAcpolypeptide:N-Acetylgalactosaminyl transferases) catalyzes the first committed step in the synthesis of O-glycans, which is an abundant and biologically important protein modification. Abnormalities in the activity of individual GalNAc-Ts can result in congenital disorders of O-glycosylation (CDG) and influence a broad array of biological functions. How site-specific O-glycans regulate biology is unclear. Compiling in vivo O-glycosites would be an invaluable step in determining the function of site-specific O-glycans. We integrated chemical and enzymatic conditions that cleave O-glycosites, a higher-energy dissociation product ions-triggered electron-transfer/higher-energy collision dissociation mass spectrometry (MS) workflow and software to study nine mouse tissues and whole blood. We identified 2,154 O-glycosites from 595 glycoproteins. The O-glycosites and glycoproteins displayed consensus motifs and shared functions as classified by Gene Ontology terms. Limited overlap of O-glycosites was observed with protein O-GlcNAcylation and phosphorylation sites. Quantitative glycoproteomics and proteomics revealed a tissue-specific regulation of O-glycosites that the differential expression of Galnt isoenzymes in tissues partly contributes to. We examined the Galnt2-null mouse model, which phenocopies congenital disorder of glycosylation involving GALNT2 and revealed a network of glycoproteins that lack GalNAc-T2-specific O-glycans. The known direct and indirect functions of these glycoproteins appear consistent with the complex metabolic phenotypes observed in the Galnt2-null animals. Through this study and interrogation of databases and the literature, we have compiled an atlas of experimentally identified mouse O-glycosites consisting of 2,925 O-glycosites from 758 glycoproteins.
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Affiliation(s)
- Weiming Yang
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
| | - E. Tian
- Developmental Glycobiology Section, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
| | - Aliona Chernish
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
| | - Peggy McCluggage
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
| | - Kruti Dalal
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
| | - Alexander Lara
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
| | - Kelly G. Ten Hagen
- Developmental Glycobiology Section, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
| | - Lawrence A. Tabak
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
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10
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Wardman JF, Sim L, Liu J, Howard TA, Geissner A, Danby PM, Boraston AB, Wakarchuk WW, Withers SG. A high-throughput screening platform for enzymes active on mucin-type O-glycoproteins. Nat Chem Biol 2023; 19:1246-1255. [PMID: 37592157 DOI: 10.1038/s41589-023-01405-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/12/2023] [Indexed: 08/19/2023]
Abstract
Mucin-type O-glycosylation is a post-translational modification present at the interface between cells where it has important roles in cellular communication. However, deciphering the function of O-glycoproteins and O-glycans can be challenging, especially as few enzymes are available for their assembly or selective degradation. Here, to address this deficiency, we developed a genetically encoded screening methodology for the discovery and engineering of the diverse classes of enzymes that act on O-glycoproteins. The method uses Escherichia coli that have been engineered to produce an O-glycosylated fluorescence resonance energy transfer probe that can be used to screen for O-glycopeptidase activity. Subsequent cleavage of the substrate by O-glycopeptidases provides a read-out of the glycosylation state of the probe, allowing the method to also be used to assay glycosidases and glycosyltransferases. We further show the potential of this methodology in the first ultrahigh-throughput-directed evolution of an O-glycopeptidase.
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Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Lyann Sim
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer Liu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Teresa A Howard
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andreas Geissner
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Phillip M Danby
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alisdair B Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Warren W Wakarchuk
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
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11
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Freitas R, Peixoto A, Ferreira E, Miranda A, Santos LL, Ferreira JA. Immunomodulatory glycomedicine: Introducing next generation cancer glycovaccines. Biotechnol Adv 2023; 65:108144. [PMID: 37028466 DOI: 10.1016/j.biotechadv.2023.108144] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 03/17/2023] [Accepted: 03/30/2023] [Indexed: 04/09/2023]
Abstract
Cancer remains a leading cause of death worldwide due to the lack of safer and more effective therapies. Cancer vaccines developed from neoantigens are an emerging strategy to promote protective and therapeutic anti-cancer immune responses. Advances in glycomics and glycoproteomics have unveiled several cancer-specific glycosignatures, holding tremendous potential to foster effective cancer glycovaccines. However, the immunosuppressive nature of tumours poses a major obstacle to vaccine-based immunotherapy. Chemical modification of tumour associated glycans, conjugation with immunogenic carriers and administration in combination with potent immune adjuvants constitute emerging strategies to address this bottleneck. Moreover, novel vaccine vehicles have been optimized to enhance immune responses against otherwise poorly immunogenic cancer epitopes. Nanovehicles have shown increased affinity for antigen presenting cells (APCs) in lymph nodes and tumours, while reducing treatment toxicity. Designs exploiting glycans recognized by APCs have further enhanced the delivery of antigenic payloads, improving glycovaccine's capacity to elicit innate and acquired immune responses. These solutions show potential to reduce tumour burden, while generating immunological memory. Building on this rationale, we provide a comprehensive overview on emerging cancer glycovaccines, emphasizing the potential of nanotechnology in this context. A roadmap towards clinical implementation is also delivered foreseeing advances in glycan-based immunomodulatory cancer medicine.
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Affiliation(s)
- Rui Freitas
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal; Porto Comprehensive Cancer Center (P.ccc), 4200-072 Porto, Portugal; Abel Salazar Biomedical Sciences Institute - University of Porto (ICBAS), 4050-313 Porto, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal; Porto Comprehensive Cancer Center (P.ccc), 4200-072 Porto, Portugal
| | - Eduardo Ferreira
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal
| | - Andreia Miranda
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; Abel Salazar Biomedical Sciences Institute - University of Porto (ICBAS), 4050-313 Porto, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; Porto Comprehensive Cancer Center (P.ccc), 4200-072 Porto, Portugal; Abel Salazar Biomedical Sciences Institute - University of Porto (ICBAS), 4050-313 Porto, Portugal; Health School of University Fernando Pessoa, 4249-004 Porto, Portugal; GlycoMatters Biotech, 4500-162 Espinho, Portugal; Department of Surgical Oncology, Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; Porto Comprehensive Cancer Center (P.ccc), 4200-072 Porto, Portugal; GlycoMatters Biotech, 4500-162 Espinho, Portugal.
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12
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Park S, Chin-Hun Kuo J, Reesink HL, Paszek MJ. Recombinant mucin biotechnology and engineering. Adv Drug Deliv Rev 2023; 193:114618. [PMID: 36375719 PMCID: PMC10253230 DOI: 10.1016/j.addr.2022.114618] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/14/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022]
Abstract
Mucins represent a largely untapped class of polymeric building block for biomaterials, therapeutics, and other biotechnology. Because the mucin polymer backbone is genetically encoded, sequence-specific mucins with defined physical and biochemical properties can be fabricated using recombinant technologies. The pendent O-glycans of mucins are increasingly implicated in immunomodulation, suppression of pathogen virulence, and other biochemical activities. Recent advances in engineered cell production systems are enabling the scalable synthesis of recombinant mucins with precisely tuned glycan side chains, offering exciting possibilities to tune the biological functionality of mucin-based products. New metabolic and chemoenzymatic strategies enable further tuning and functionalization of mucin O-glycans, opening new possibilities to expand the chemical diversity and functionality of mucin building blocks. In this review, we discuss these advances, and the opportunities for engineered mucins in biomedical applications ranging from in vitro models to therapeutics.
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Affiliation(s)
- Sangwoo Park
- Field of Biophysics, Cornell University, Ithaca, NY 14853, USA
| | - Joe Chin-Hun Kuo
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Heidi L Reesink
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Matthew J Paszek
- Field of Biophysics, Cornell University, Ithaca, NY 14853, USA; Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA.
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13
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Li J, Guo B, Zhang W, Yue S, Huang S, Gao S, Ma J, Cipollo JF, Yang S. Recent advances in demystifying O-glycosylation in health and disease. Proteomics 2022; 22:e2200156. [PMID: 36088641 DOI: 10.1002/pmic.202200156] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/09/2022]
Abstract
O-Glycosylation is one of the most common protein post-translational modifications (PTM) and plays an essential role in the pathophysiology of diseases. However, the complexity of O-glycosylation and the lack of specific enzymes for the processing of O-glycans and their O-glycopeptides make O-glycosylation analysis challenging. Recently, research on O-glycosylation has received attention owing to technological innovation and emerging O-glycoproteases. Several serine/threonine endoproteases have been found to specifically cleave O-glycosylated serine or threonine, allowing for the systematic analysis of O-glycoproteins. In this review, we first assessed the field of protein O-glycosylation over the past decade and used bibliometric analysis to identify keywords and emerging trends. We then summarized recent advances in O-glycosylation, covering several aspects: O-glycan release, site-specific elucidation of intact O-glycopeptides, identification of O-glycosites, characterization of different O-glycoproteases, mass spectrometry (MS) fragmentation methods for site-specific O-glycosylation assignment, and O-glycosylation data analysis. Finally, the role of O-glycosylation in health and disease was discussed.
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Affiliation(s)
- Jiajia Li
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Bo Guo
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Wenqi Zhang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Shuang Yue
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Shan Huang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Song Gao
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, DC, USA
| | - John F Cipollo
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
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14
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Algrain M, Hennebert E, Bertemes P, Wattiez R, Flammang P, Lengerer B. In the footsteps of sea stars: deciphering the catalogue of proteins involved in underwater temporary adhesion. Open Biol 2022; 12:220103. [PMID: 35975651 PMCID: PMC9382459 DOI: 10.1098/rsob.220103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Sea stars adhere strongly but temporarily to underwater substrata via the secretion of a blend of proteins, forming an adhesive footprint that they leave on the surface after detachment. Their tube feet enclose a duo-gland adhesive system comprising two types of adhesive cells, contributing different layers of the footprint and de-adhesive cells. In this study, we characterized the catalogue of sea star footprint proteins (Sfps) in the species Asterias rubens to gain insights in their potential function. We identified 16 Sfps and mapped their expression to type 1 and/or type 2 adhesive cells or to de-adhesive cells by double fluorescent in situ hybridization. Based on their cellular expression pattern and their conserved functional domains, we propose that the identified Sfps serve different functions during attachment, with two Sfps coupling to the surface, six providing cohesive strength and the rest forming a binding matrix. Immunolabelling of footprints with antibodies directed against one protein of each category confirmed these roles. A de-adhesive gland cell-specific astacin-like proteinase presumably weakens the bond between the adhesive material and the tube foot surface during detachment. Overall, we provide a model for temporary adhesion in sea stars, including a comprehensive list of the proteins involved.
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Affiliation(s)
- Morgane Algrain
- Laboratory of Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons 7000, Belgium
| | - Elise Hennebert
- Laboratory of Cell Biology, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons 7000, Belgium
| | - Philip Bertemes
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Technikerstr. 25, Innsbruck 6020, Austria
| | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons 7000, Belgium
| | - Patrick Flammang
- Laboratory of Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences, University of Mons, Place du Parc 23, Mons 7000, Belgium
| | - Birgit Lengerer
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Technikerstr. 25, Innsbruck 6020, Austria
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15
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Abstract
Mucin domains are densely O-glycosylated modular protein domains found in various extracellular and transmembrane proteins. Mucin-domain glycoproteins play important roles in many human diseases, such as cancer and cystic fibrosis, but the scope of the mucinome remains poorly defined. Recently, we characterized a bacterial O-glycoprotease, StcE, and demonstrated that an inactive point mutant retains binding selectivity for mucin-domain glycoproteins. In this work, we leverage inactive StcE to selectively enrich and identify mucin-domain glycoproteins from complex samples like cell lysate and crude ovarian cancer patient ascites fluid. Our enrichment strategy is further aided by an algorithm to assign confidence to mucin-domain glycoprotein identifications. This mucinomics platform facilitates detection of hundreds of glycopeptides from mucin domains and highly overlapping populations of mucin-domain glycoproteins from ovarian cancer patients. Ultimately, we demonstrate our mucinomics approach can reveal key molecular signatures of cancer from in vitro and ex vivo sources. Mucin-domain glycoproteins are densely O-glycosylated proteins with unique secondary structure that imparts a large influence on cellular environments. Here, the authors develop a technique to selectively enrich and characterize mucin-domain glycoproteins from cell lysate and patient biofluids.
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16
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Konstantinidi A, Nason R, Čaval T, Sun L, Sørensen DM, Furukawa S, Ye Z, Vincentelli R, Narimatsu Y, Vakhrushev SY, Clausen H. Exploring the glycosylation of mucins by use of O-glycodomain reporters recombinantly expressed in glycoengineered HEK293 cells. J Biol Chem 2022; 298:101784. [PMID: 35247390 PMCID: PMC8980628 DOI: 10.1016/j.jbc.2022.101784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 12/18/2022] Open
Abstract
Mucins and glycoproteins with mucin-like regions contain densely O-glycosylated domains often found in tandem repeat (TR) sequences. These O-glycodomains have traditionally been difficult to characterize because of their resistance to proteolytic digestion, and knowledge of the precise positions of O-glycans is particularly limited for these regions. Here, we took advantage of a recently developed glycoengineered cell-based platform for the display and production of mucin TR reporters with custom-designed O-glycosylation to characterize O-glycodomains derived from mucins and mucin-like glycoproteins. We combined intact mass and bottom–up site-specific analysis for mapping O-glycosites in the mucins, MUC2, MUC20, MUC21, protein P-selectin-glycoprotein ligand 1, and proteoglycan syndecan-3. We found that all the potential Ser/Thr positions in these O-glycodomains were O-glycosylated when expressed in human embryonic kidney 293 SimpleCells (Tn-glycoform). Interestingly, we found that all potential Ser/Thr O-glycosites in TRs derived from secreted mucins and most glycosites from transmembrane mucins were almost fully occupied, whereas TRs from a subset of transmembrane mucins were less efficiently processed. We further used the mucin TR reporters to characterize cleavage sites of glycoproteases StcE (secreted protease of C1 esterase inhibitor from EHEC) and BT4244, revealing more restricted substrate specificities than previously reported. Finally, we conducted a bottom–up analysis of isolated ovine submaxillary mucin, which supported our findings that mucin TRs in general are efficiently O-glycosylated at all potential glycosites. This study provides insight into O-glycosylation of mucins and mucin-like domains, and the strategies developed open the field for wider analysis of native mucins.
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Affiliation(s)
- Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rebecca Nason
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tomislav Čaval
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lingbo Sun
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Daniel M Sørensen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sanae Furukawa
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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17
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Thompson NK, LeClaire LTN, Rodriguez Perez S, Wakarchuk WW. Investigation of sequon engineering for improved O-glycosylation by the human polypeptide N-acetylgalactosaminyl transferase T2 isozyme and two orthologues. Biochem J 2021; 478:3527-3537. [PMID: 34523671 DOI: 10.1042/bcj20210382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022]
Abstract
We have been developing bacterial expression systems for human mucin-type O-glycosylation on therapeutic proteins, which is initiated by the addition of α-linked GalNAc to serine or threonine residues by enzymes in the GT-27 family of glycosyltransferases. Substrate preference across different isoforms of this enzyme is influenced by isoform-specific amino acid sequences at the site of glycosylation, which we have exploited to engineer production of Core 1 glycan structures in bacteria on human therapeutic proteins. Using RP-HPLC with a novel phenyl bonded phase to resolve intact protein glycoforms, the effect of sequon mutation on O-glycosylation initiation was examined through in vitro modification of the naturally O-glycosylated human interferon α-2b, and a sequon engineered human growth hormone. As part of the development of our glycan engineering in the bacterial expression system we are surveying various orthologues of critical enzymes to ensure complete glycosylation. Here we present an in vitro enzyme kinetic profile of three related GT-27 orthologues on natural and engineered sequons in recombinant human interferon α2b and human growth hormone where we show a significant change in kinetic properties with the amino acid changes. It was found that optimizing the protein substrate amino acid sequence using Isoform Specific O-Glycosylation Prediction (ISOGlyP, http://isoglyp.utep.edu/index.php) resulted in a measurable increase in kcat/KM, thus improving glycosylation efficiency. We showed that the Drosophila orthologue showed superior activity with our human growth hormone designed sequons compared with the human enzyme.
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Affiliation(s)
- Nicole K Thompson
- Department of Biological Sciences, University of Alberta, Edmonton AB T6G2E9, Canada
| | - Leif T N LeClaire
- Department of Biological Sciences, University of Alberta, Edmonton AB T6G2E9, Canada
| | | | - Warren W Wakarchuk
- Department of Biological Sciences, University of Alberta, Edmonton AB T6G2E9, Canada
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18
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Abstract
Mucin-domain glycoproteins comprise a class of proteins whose densely O-glycosylated mucin domains adopt a secondary structure with unique biophysical and biochemical properties. The canonical family of mucins is well-known to be involved in various diseases, especially cancer. Despite this, very little is known about the site-specific molecular structures and biological activities of mucins, in part because they are extremely challenging to study by mass spectrometry (MS). Here, we summarize recent advancements toward this goal, with a particular focus on mucin-domain glycoproteins as opposed to general O-glycoproteins. We summarize proteolytic digestion techniques, enrichment strategies, MS fragmentation, and intact analysis, as well as new bioinformatic platforms. In particular, we highlight mucin directed technologies such as mucin-selective proteases, tunable mucin platforms, and a mucinomics strategy to enrich mucin-domain glycoproteins from complex samples. Finally, we provide examples of targeted mucin-domain glycoproteomics that combine these techniques in comprehensive site-specific analyses of proteins. Overall, this Review summarizes the methods, challenges, and new opportunities associated with studying enigmatic mucin domains.
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Affiliation(s)
- Valentina Rangel-Angarita
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States
| | - Stacy A. Malaker
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States
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19
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Wang Y, Wu Z, Hu W, Hao P, Yang S. Impact of Expressing Cells on Glycosylation and Glycan of the SARS-CoV-2 Spike Glycoprotein. ACS OMEGA 2021; 6:15988-15999. [PMID: 34179644 PMCID: PMC8204757 DOI: 10.1021/acsomega.1c01785] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 06/02/2021] [Indexed: 05/09/2023]
Abstract
The spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the first point of contact for the virus to recognize and bind to host receptors, is the focus of biomedical research seeking to effectively prevent and treat coronavirus disease (COVID-19). The mass production of spike glycoproteins is usually carried out in different cell systems. Studies have been shown that different expression cell systems alter protein glycosylation of hemagglutinin and neuraminidase in the influenza virus. However, it is not clear whether the cellular system affects the spike protein glycosylation. In this work, we investigated the effect of an expression system on the glycosylation of the spike glycoprotein and its receptor-binding domain. We found that there are significant differences in the glycosylation and glycans attached at each glycosite of the spike glycoprotein obtained from different expression cells. Since glycosylation at the binding site and adjacent amino acids affects the interaction between the spike glycoprotein and the host cell receptor, we recognize that caution should be taken when selecting an expression system to develop inhibitors, antibodies, and vaccines.
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Affiliation(s)
- Yan Wang
- Mass
Spectrometry Facility, National Institute
of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Zhen Wu
- State
Key Laboratory of Genetic Engineering, Department of Biochemistry,
School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Wenhua Hu
- Center
for Clinical Mass Spectrometry, Department of Pharmaceutical Analysis, Soochow University, Suzhou, Jiangsu 215123, China
| | - Piliang Hao
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
| | - Shuang Yang
- Center
for Clinical Mass Spectrometry, Department of Pharmaceutical Analysis, Soochow University, Suzhou, Jiangsu 215123, China
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20
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Cotton S, Ferreira D, Soares J, Peixoto A, Relvas-Santos M, Azevedo R, Piairo P, Diéguez L, Palmeira C, Lima L, Silva AMN, Lara Santos L, Ferreira JA. Target Score-A Proteomics Data Selection Tool Applied to Esophageal Cancer Identifies GLUT1-Sialyl Tn Glycoforms as Biomarkers of Cancer Aggressiveness. Int J Mol Sci 2021; 22:ijms22041664. [PMID: 33562270 PMCID: PMC7915893 DOI: 10.3390/ijms22041664] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
Esophageal cancer (EC) is a life-threatening disease, demanding the discovery of new biomarkers and molecular targets for precision oncology. Aberrantly glycosylated proteins hold tremendous potential towards this objective. In the current study, a series of esophageal squamous cell carcinomas (ESCC) and EC-derived circulating tumor cells (CTCs) were screened by immunoassays for the sialyl-Tn (STn) antigen, a glycan rarely expressed in healthy tissues and widely observed in aggressive gastrointestinal cancers. An ESCC cell model was glycoengineered to express STn and characterized in relation to cell proliferation and invasion in vitro. STn was found to be widely present in ESCC (70% of tumors) and in CTCs in 20% of patients, being associated with general recurrence and reduced survival. Furthermore, STn expression in ESCC cells increased invasion in vitro, while reducing cancer cells proliferation. In parallel, an ESCC mass spectrometry-based proteomics dataset, obtained from the PRIDE database, was comprehensively interrogated for abnormally glycosylated proteins. Data integration with the Target Score, an algorithm developed in-house, pinpointed the glucose transporter type 1 (GLUT1) as a biomarker of poor prognosis. GLUT1-STn glycoproteoforms were latter identified in tumor tissues in patients facing worst prognosis. Furthermore, healthy human tissues analysis suggested that STn glycosylation provided cancer specificity to GLUT1. In conclusion, STn is a biomarker of worst prognosis in EC and GLUT1-STn glycoforms may be used to increase its specificity on the stratification and targeting of aggressive ESCC forms.
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Affiliation(s)
- Sofia Cotton
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; (S.C.); (D.F.); (J.S.); (A.P.); (M.R.-S.); (C.P.); (L.L.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute for Biomedical Engineering (INEB), 4200-135 Porto, Portugal
| | - Dylan Ferreira
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; (S.C.); (D.F.); (J.S.); (A.P.); (M.R.-S.); (C.P.); (L.L.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute for Biomedical Engineering (INEB), 4200-135 Porto, Portugal
| | - Janine Soares
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; (S.C.); (D.F.); (J.S.); (A.P.); (M.R.-S.); (C.P.); (L.L.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- QOPNA/LAQV, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; (S.C.); (D.F.); (J.S.); (A.P.); (M.R.-S.); (C.P.); (L.L.); (L.L.S.)
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute for Biomedical Engineering (INEB), 4200-135 Porto, Portugal
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; (S.C.); (D.F.); (J.S.); (A.P.); (M.R.-S.); (C.P.); (L.L.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- Institute for Biomedical Engineering (INEB), 4200-135 Porto, Portugal
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal;
| | - Rita Azevedo
- Institute of Biomedicine, University of Turku, FI-20014 Turku, Finland;
| | - Paulina Piairo
- Medical Devices Research Group, International Iberian Nanotechnology Laboratory (INL), 4715-330 Braga, Portugal; (P.P.); (L.D.)
| | - Lorena Diéguez
- Medical Devices Research Group, International Iberian Nanotechnology Laboratory (INL), 4715-330 Braga, Portugal; (P.P.); (L.D.)
| | - Carlos Palmeira
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; (S.C.); (D.F.); (J.S.); (A.P.); (M.R.-S.); (C.P.); (L.L.); (L.L.S.)
- Department of Immunology, Portuguese Institute of Oncology of Porto, 4200-072 Porto, Portugal
- Health Science Faculty, University of Fernando Pessoa, 4249-004 Porto, Portugal
| | - Luís Lima
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; (S.C.); (D.F.); (J.S.); (A.P.); (M.R.-S.); (C.P.); (L.L.); (L.L.S.)
- Porto Comprehensive Cancer Center (P.ccc), 4200-072 Porto, Portugal
| | - André M. N. Silva
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal;
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; (S.C.); (D.F.); (J.S.); (A.P.); (M.R.-S.); (C.P.); (L.L.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Health Science Faculty, University of Fernando Pessoa, 4249-004 Porto, Portugal
- Porto Comprehensive Cancer Center (P.ccc), 4200-072 Porto, Portugal
- Department of Surgical Oncology, Portuguese Institute of Oncology, 4200-072 Porto, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute (IPO Porto), 4200-072 Porto, Portugal; (S.C.); (D.F.); (J.S.); (A.P.); (M.R.-S.); (C.P.); (L.L.); (L.L.S.)
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Porto Comprehensive Cancer Center (P.ccc), 4200-072 Porto, Portugal
- Correspondence: ; Tel.: +351-225-084-000 (ext. 5111)
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21
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Ferreira JA, Relvas-Santos M, Peixoto A, M N Silva A, Lara Santos L. Glycoproteogenomics: Setting the Course for Next-generation Cancer Neoantigen Discovery for Cancer Vaccines. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:25-43. [PMID: 34118464 PMCID: PMC8498922 DOI: 10.1016/j.gpb.2021.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/25/2021] [Accepted: 03/01/2021] [Indexed: 12/24/2022]
Abstract
Molecular-assisted precision oncology gained tremendous ground with high-throughput next-generation sequencing (NGS), supported by robust bioinformatics. The quest for genomics-based cancer medicine set the foundations for improved patient stratification, while unveiling a wide array of neoantigens for immunotherapy. Upfront pre-clinical and clinical studies have successfully used tumor-specific peptides in vaccines with minimal off-target effects. However, the low mutational burden presented by many lesions challenges the generalization of these solutions, requiring the diversification of neoantigen sources. Oncoproteogenomics utilizing customized databases for protein annotation by mass spectrometry (MS) is a powerful tool toward this end. Expanding the concept toward exploring proteoforms originated from post-translational modifications (PTMs) will be decisive to improve molecular subtyping and provide potentially targetable functional nodes with increased cancer specificity. Walking through the path of systems biology, we highlight that alterations in protein glycosylation at the cell surface not only have functional impact on cancer progression and dissemination but also originate unique molecular fingerprints for targeted therapeutics. Moreover, we discuss the outstanding challenges required to accommodate glycoproteomics in oncoproteogenomics platforms. We envisage that such rationale may flag a rather neglected research field, generating novel paradigms for precision oncology and immunotherapy.
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Affiliation(s)
- José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal.
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal
| | - André M N Silva
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, Porto 4169-007, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto 4200-072, Portugal; Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto 4050-313, Portugal; Porto Comprehensive Cancer Center (P.ccc), Porto 4200-072, Portugal
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22
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Freitas R, Relvas-Santos M, Azevedo R, Soares J, Fernandes E, Teixeira B, Santos LL, Silva AMN, Ferreira JA. Single-pot enzymatic synthesis of cancer-associated MUC16 O-glycopeptide libraries and multivalent protein glycoconjugates: a step towards cancer glycovaccines. NEW J CHEM 2021. [DOI: 10.1039/d0nj06021f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Glycosyltransferases and nucleotide sugars are combined in single-pot settings to synthesize a library of cancer-associated MUC16 O-glycopeptides and multivalent protein glycoconjugates foreseeing future development of cancer glycovaccines.
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Affiliation(s)
- Rui Freitas
- Experimental Pathology and Therapeutics Group
- Portuguese Oncology Institute of Porto
- 4200-072 Porto
- Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS)
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group
- Portuguese Oncology Institute of Porto
- 4200-072 Porto
- Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS)
| | - Rita Azevedo
- Experimental Pathology and Therapeutics Group
- Portuguese Oncology Institute of Porto
- 4200-072 Porto
- Portugal
| | - Janine Soares
- Experimental Pathology and Therapeutics Group
- Portuguese Oncology Institute of Porto
- 4200-072 Porto
- Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS)
| | - Elisabete Fernandes
- Experimental Pathology and Therapeutics Group
- Portuguese Oncology Institute of Porto
- 4200-072 Porto
- Portugal
- Institute for Research and Innovation in Health (i3S)
| | - Beatriz Teixeira
- Experimental Pathology and Therapeutics Group
- Portuguese Oncology Institute of Porto
- 4200-072 Porto
- Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS)
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group
- Portuguese Oncology Institute of Porto
- 4200-072 Porto
- Portugal
- REQUIMTE-LAQV
| | - André M. N. Silva
- REQUIMTE-LAQV
- Department of Chemistry and Biochemistry
- Faculty of Sciences
- University of Porto
- 4169-007 Porto
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group
- Portuguese Oncology Institute of Porto
- 4200-072 Porto
- Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS)
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23
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Mucin-Type O-GalNAc Glycosylation in Health and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1325:25-60. [PMID: 34495529 DOI: 10.1007/978-3-030-70115-4_2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mucin-type GalNAc O-glycosylation is one of the most abundant and unique post-translational modifications. The combination of proteome-wide mapping of GalNAc O-glycosylation sites and genetic studies with knockout animals and genome-wide analyses in humans have been instrumental in our understanding of GalNAc O-glycosylation. Combined, such studies have revealed well-defined functions of O-glycans at single sites in proteins, including the regulation of pro-protein processing and proteolytic cleavage, as well as modulation of receptor functions and ligand binding. In addition to isolated O-glycans, multiple clustered O-glycans have an important function in mammalian biology by providing structural support and stability of mucins essential for protecting our inner epithelial surfaces, especially in the airways and gastrointestinal tract. Here the many O-glycans also provide binding sites for both endogenous and pathogen-derived carbohydrate-binding proteins regulating critical developmental programs and helping maintain epithelial homeostasis with commensal organisms. Finally, O-glycan changes have been identified in several diseases, most notably in cancer and inflammation, where the disease-specific changes can be used for glycan-targeted therapies. This chapter will review the biosynthesis, the biology, and the translational perspectives of GalNAc O-glycans.
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