1
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Mach N. The forecasting power of the mucin-microbiome interplay in livestock respiratory diseases. Vet Q 2024; 44:1-18. [PMID: 38606662 PMCID: PMC11018052 DOI: 10.1080/01652176.2024.2340003] [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: 05/23/2023] [Accepted: 03/31/2024] [Indexed: 04/13/2024] Open
Abstract
Complex respiratory diseases are a significant challenge for the livestock industry worldwide. These diseases considerably impact animal health and welfare and cause severe economic losses. One of the first lines of pathogen defense combines the respiratory tract mucus, a highly viscous material primarily composed of mucins, and a thriving multi-kingdom microbial ecosystem. The microbiome-mucin interplay protects from unwanted substances and organisms, but its dysfunction may enable pathogenic infections and the onset of respiratory disease. Emerging evidence also shows that noncoding regulatory RNAs might modulate the structure and function of the microbiome-mucin relationship. This opinion paper unearths the current understanding of the triangular relationship between mucins, the microbiome, and noncoding RNAs in the context of respiratory infections in animals of veterinary interest. There is a need to look at these molecular underpinnings that dictate distinct health and disease outcomes to implement effective prevention, surveillance, and timely intervention strategies tailored to the different epidemiological contexts.
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Affiliation(s)
- Núria Mach
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
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2
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Peng W, Giesbers KC, Šiborová M, Beugelink JW, Pronker MF, Schulte D, Hilkens J, Janssen BJ, Strijbis K, Snijder J. Reverse-engineering the anti-MUC1 antibody 139H2 by mass spectrometry-based de novo sequencing. Life Sci Alliance 2024; 7:e202302366. [PMID: 38508723 PMCID: PMC10955041 DOI: 10.26508/lsa.202302366] [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: 09/12/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/22/2024] Open
Abstract
Mucin 1 (MUC1) is a transmembrane mucin expressed at the apical surface of epithelial cells at mucosal surfaces. MUC1 has a barrier function against bacterial invasion and is well known for its aberrant expression and glycosylation in adenocarcinomas. The MUC1 extracellular domain contains a variable number of tandem repeats (VNTR) of 20 amino acids, which are heavily O-linked glycosylated. Monoclonal antibodies against the MUC1 VNTR are powerful research tools with applications in the diagnosis and treatment of MUC1-expressing cancers. Here, we report direct mass spectrometry-based sequencing of anti-MUC1 hybridoma-derived 139H2 IgG, enabling reverse-engineering of the functional recombinant monoclonal antibody. The crystal structure of the 139H2 Fab fragment in complex with the MUC1 epitope was solved, revealing the molecular basis of 139H2 binding specificity to MUC1 and its tolerance to O-glycosylation of the VNTR. The available sequence of 139H2 will allow further development of MUC1-related diagnostic, targeting, and treatment strategies.
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Affiliation(s)
- Weiwei Peng
- https://ror.org/04pp8hn57 Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Koen Cap Giesbers
- https://ror.org/04pp8hn57 Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Marta Šiborová
- https://ror.org/04pp8hn57 Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - J Wouter Beugelink
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Matti F Pronker
- https://ror.org/04pp8hn57 Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Douwe Schulte
- https://ror.org/04pp8hn57 Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - John Hilkens
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Bert Jc Janssen
- https://ror.org/04pp8hn57 Structural Biochemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Karin Strijbis
- https://ror.org/04pp8hn57 Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Joost Snijder
- https://ror.org/04pp8hn57 Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
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3
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Elzinga J, Narimatsu Y, de Haan N, Clausen H, de Vos WM, Tytgat HLP. Binding of Akkermansia muciniphila to mucin is O-glycan specific. Nat Commun 2024; 15:4582. [PMID: 38811534 PMCID: PMC11137150 DOI: 10.1038/s41467-024-48770-8] [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: 11/05/2023] [Accepted: 05/09/2024] [Indexed: 05/31/2024] Open
Abstract
The intestinal anaerobic bacterium Akkermansia muciniphila is specialized in the degradation of mucins, which are heavily O-glycosylated proteins that constitute the major components of the mucus lining the intestine. Despite that adhesion to mucins is considered critical for the persistence of A. muciniphila in the human intestinal tract, our knowledge of how this intestinal symbiont recognizes and binds to mucins is still limited. Here, we first show that the mucin-binding properties of A. muciniphila are independent of environmental oxygen concentrations and not abolished by pasteurization. We then dissected the mucin-binding properties of pasteurized A. muciniphila by use of a recently developed cell-based mucin array that enables display of the tandem repeats of human mucins with distinct O-glycan patterns and structures. We found that A. muciniphila recognizes the unsialylated LacNAc (Galβ1-4GlcNAcβ1-R) disaccharide selectively on core2 and core3 O-glycans. This disaccharide epitope is abundantly found on human colonic mucins capped by sialic acids, and we demonstrated that endogenous A. muciniphila neuraminidase activity can uncover the epitope and promote binding. In summary, our study provides insights into the mucin-binding properties important for colonization of a key mucin-foraging bacterium.
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Affiliation(s)
- Janneke Elzinga
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- GlycoDisplay ApS, Copenhagen, Denmark
| | - Noortje de Haan
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland.
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4
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Zhang SZ, Lobo A, Li PF, Zhang YF. Sialylated glycoproteins and sialyltransferases in digestive cancers: Mechanisms, diagnostic biomarkers, and therapeutic targets. Crit Rev Oncol Hematol 2024; 197:104330. [PMID: 38556071 DOI: 10.1016/j.critrevonc.2024.104330] [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: 10/11/2023] [Revised: 03/12/2024] [Accepted: 03/19/2024] [Indexed: 04/02/2024] Open
Abstract
Sialic acid (SA), as the ultimate epitope of polysaccharides, can act as a cap at the end of polysaccharide chains to prevent their overextension. Sialylation is the enzymatic process of transferring SA residues onto polysaccharides and is catalyzed by a group of enzymes known as sialyltransferases (SiaTs). It is noteworthy that the sialylation level of glycoproteins is significantly altered when digestive cancer occurs. And this alteration exhibits a close correlation with the progression of these cancers. In this review, from the perspective of altered SiaTs expression levels and changed glycoprotein sialylation patterns, we summarize the pathogenesis of gastric cancer (GC), colorectal cancer (CRC), pancreatic ductal adenocarcinoma (PDAC), and hepatocellular carcinoma (HCC). Furthermore, we propose potential early diagnostic biomarkers and prognostic indicators for different digestive cancers. Finally, we summarize the therapeutic value of sialylation in digestive system cancers.
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Affiliation(s)
- Shao-Ze Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Amara Lobo
- Department of Critical Care Medicine Holy Family Hospital, St Andrew's Road, Bandra (West), Mumbai 400050, India
| | - Pei-Feng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.
| | - Yin-Feng Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.
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5
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Touhara KK, Rossen ND, Deng F, Chu T, Harrington AM, Garcia Caraballo S, Brizuela M, O'Donnell T, Cil O, Brierley SM, Li Y, Julius D. Crypt and Villus Enterochromaffin Cells are Distinct Stress Sensors in the Gut. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579180. [PMID: 38370814 PMCID: PMC10871270 DOI: 10.1101/2024.02.06.579180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The crypt-villus structure of the small intestine serves as an essential protective barrier, with its integrity monitored by the gut's sensory system. Enterochromaffin (EC) cells, which are rare sensory epithelial cells that release serotonin (5-HT), surveil the mucosal environment and signal both within and outside the gut. However, it remains unclear whether EC cells in intestinal crypts and villi respond to different stimuli and elicit distinct responses. In this study, we introduce a new reporter mouse model to observe the release and propagation of serotonin in live intestines. Using this system, we show that crypt EC cells exhibit two modes of serotonin release: transient receptor potential A1 (TRPA1)-dependent tonic serotonin release that controls basal ionic secretion, and irritant-evoked serotonin release that activates gut sensory neurons. Furthermore, we find that a thick protective mucus layer prevents TRPA1 receptors on crypt EC cells from responding to luminal irritants such as reactive electrophiles; if this mucus layer is compromised, then crypt EC cells become susceptible to activation by luminal irritants. On the other hand, villus EC cells detect oxidative stress through TRPM2 channels and co-release serotonin and ATP to activate nearby gut sensory fibers. Our work highlights the physiological importance of intestinal architecture and differential TRP channel expression in sensing noxious stimuli that elicit nausea and/or pain sensations in the gut.
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6
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Mahoney KE, Chang V, Lucas TM, Maruszko K, Malaker SA. Mass Spectrometry-Compatible Elution Technique Enables an Improved Mucin-Selective Enrichment Strategy to Probe the Mucinome. Anal Chem 2024; 96:5242-5250. [PMID: 38512228 DOI: 10.1021/acs.analchem.3c05762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of healthy and disease-driven biological functions. Previously, we developed a mucin-selective enrichment strategy by employing a catalytically inactive mucinase (StcE) conjugated to a solid support. While this method was effective, it suffered from low throughput and high sample requirements. Further, the elution step required boiling in SDS, thus necessitating an in-gel digest with trypsin. Here, we introduce innovative elution conditions amenable to mucinase digestion and downstream analysis using mass spectrometry. This increased throughput and lowered sample input while maintaining mucin selectivity and enhancing the glycopeptide signal. We then benchmarked this technique against different O-glycan binding moieties for their ability to enrich mucins from various cell lines and human serum. Overall, the new method outperformed our previous procedure and all of the other enrichment techniques tested. This allowed for the effective isolation of more mucin-domain glycoproteins, resulting in a high number of O-glycopeptides, thus enhancing our ability to analyze the mucinome.
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Affiliation(s)
- Keira E Mahoney
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Vincent Chang
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Taryn M Lucas
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Krystyna Maruszko
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Stacy A Malaker
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
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7
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Pedram K, Shon DJ, Tender GS, Mantuano NR, Northey JJ, Metcalf KJ, Wisnovsky SP, Riley NM, Forcina GC, Malaker SA, Kuo A, George BM, Miller CL, Casey KM, Vilches-Moure JG, Ferracane MJ, Weaver VM, Läubli H, Bertozzi CR. Design of a mucin-selective protease for targeted degradation of cancer-associated mucins. Nat Biotechnol 2024; 42:597-607. [PMID: 37537499 PMCID: PMC11018308 DOI: 10.1038/s41587-023-01840-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 05/22/2023] [Indexed: 08/05/2023]
Abstract
Targeted protein degradation is an emerging strategy for the elimination of classically undruggable proteins. Here, to expand the landscape of targetable substrates, we designed degraders that achieve substrate selectivity via recognition of a discrete peptide and glycan motif and achieve cell-type selectivity via antigen-driven cell-surface binding. We applied this approach to mucins, O-glycosylated proteins that drive cancer progression through biophysical and immunological mechanisms. Engineering of a bacterial mucin-selective protease yielded a variant for fusion to a cancer antigen-binding nanobody. The resulting conjugate selectively degraded mucins on cancer cells, promoted cell death in culture models of mucin-driven growth and survival, and reduced tumor growth in mouse models of breast cancer progression. This work establishes a blueprint for the development of biologics that degrade specific protein glycoforms on target cells.
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Affiliation(s)
- Kayvon Pedram
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - D Judy Shon
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Gabrielle S Tender
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Natalia R Mantuano
- Cancer Immunotherapy Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Oncology, Department of Theragnostics, University Hospital, Basel, Switzerland
| | - Jason J Northey
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Kevin J Metcalf
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Simon P Wisnovsky
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Giovanni C Forcina
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Stacy A Malaker
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Angel Kuo
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Benson M George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Caitlyn L Miller
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Kerriann M Casey
- Department of Comparative Medicine, Stanford University, Stanford, CA, USA
| | | | | | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
- Departments of Radiation Oncology and Bioengineering and Therapeutic Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Heinz Läubli
- Cancer Immunotherapy Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Oncology, Department of Theragnostics, University Hospital, Basel, Switzerland
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford, CA, USA.
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8
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Ayyalasomayajula R, Cudic M. Targeting Siglec-Sialylated MUC1 Immune Axis in Cancer. Cancers (Basel) 2024; 16:1334. [PMID: 38611013 PMCID: PMC11011055 DOI: 10.3390/cancers16071334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Siglecs play a key role in mediating cell-cell interactions via the recognition of different sialylated glycoconjugates, including tumor-associated MUC1, which can lead to the activation or inhibition of the immune response. The activation occurs through the signaling of Siglecs with the cytoplasmic immunoreceptor tyrosine-based activation motif (ITAM)-containing proteins, while the inhibition signal is a result of the interaction of intracellular immunoreceptor tyrosine-based inhibition motif (ITIM)-bearing receptors. The interaction of tumor-associated MUC1 sialylated glycans with Siglecs via ITIM motifs decreases antitumor immunity. Consequently, these interactions are expected to play a key role in tumor evasion. Efforts to modulate the response of immune cells by blocking the immune-suppressive effects of inhibitory Siglecs, driving immune-activating Siglecs, and/or altering the synthesis and expression of the sialic acid glycocalyx are new therapeutic strategies deserving further investigation. We will highlight the role of Siglec's family receptors in immune evasion through interactions with glycan ligands in their natural context, presented on the protein such as MUC1, factors affecting their fine binding specificities, such as the role of multivalency either at the ligand or receptor side, their spatial organization, and finally the current and future therapeutic interventions targeting the Siglec-sialylated MUC1 immune axis in cancer.
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Affiliation(s)
| | - Mare Cudic
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Rd., Boca Raton, FL 33431, USA;
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9
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Park S, Colville MJ, Paek JH, Shurer CR, Singh A, Secor EJ, Sailer CJ, Huang LT, Kuo JCH, Goudge MC, Su J, Kim M, DeLisa MP, Neelamegham S, Lammerding J, Zipfel WR, Fischbach C, Reesink HL, Paszek MJ. Immunoengineering can overcome the glycocalyx armour of cancer cells. NATURE MATERIALS 2024; 23:429-438. [PMID: 38361041 DOI: 10.1038/s41563-024-01808-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 01/03/2024] [Indexed: 02/17/2024]
Abstract
Cancer cell glycocalyx is a major line of defence against immune surveillance. However, how specific physical properties of the glycocalyx are regulated on a molecular level, contribute to immune evasion and may be overcome through immunoengineering must be resolved. Here we report how cancer-associated mucins and their glycosylation contribute to the nanoscale material thickness of the glycocalyx and consequently modulate the functional interactions with cytotoxic immune cells. Natural-killer-cell-mediated cytotoxicity is inversely correlated with the glycocalyx thickness of the target cells. Changes in glycocalyx thickness of approximately 10 nm can alter the susceptibility to immune cell attack. Enhanced stimulation of natural killer and T cells through equipment with chimeric antigen receptors can improve the cytotoxicity against mucin-bearing target cells. Alternatively, cytotoxicity can be enhanced through engineering effector cells to display glycocalyx-editing enzymes, including mucinases and sialidases. Together, our results motivate the development of immunoengineering strategies that overcome the glycocalyx armour of cancer cells.
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Affiliation(s)
- Sangwoo Park
- Field of Biophysics, Cornell University, Ithaca, NY, USA
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Marshall J Colville
- Field of Biophysics, Cornell University, Ithaca, NY, USA
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Justin H Paek
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Carolyn R Shurer
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Arun Singh
- State University of New York, Buffalo, NY, USA
| | - Erica J Secor
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Cooper J Sailer
- Department of Pathology, University of Rochester Medical Center, Rochester, NY, USA
| | - Ling-Ting Huang
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Joe Chin-Hun Kuo
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Marc C Goudge
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Jin Su
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Minsoo Kim
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | | | - Jan Lammerding
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Warren R Zipfel
- Field of Biophysics, Cornell University, Ithaca, NY, USA
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Claudia Fischbach
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 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, USA.
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA.
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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10
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Park S, Choi S, Shimpi AA, Estroff LA, Fischbach C, Paszek MJ. COLLAGEN MINERALIZATION DECREASES NK CELL-MEDIATED CYTOTOXICITY OF BREAST CANCER CELLS VIA INCREASED GLYCOCALYX THICKNESS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576377. [PMID: 38328161 PMCID: PMC10849468 DOI: 10.1101/2024.01.20.576377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Skeletal metastasis is common in patients with advanced breast cancer, and often caused by immune evasion of disseminated tumor cells (DTCs). In the skeleton, tumor cells not only disseminate to the bone marrow, but also to osteogenic niches in which they interact with newly mineralizing bone extracellular matrix (ECM). However, it remains unclear how mineralization of collagen type I, the primary component of bone ECM, regulates tumor-immune cell interactions. Here, we have utilized a combination of synthetic bone matrix models with controlled mineral content, nanoscale optical imaging, and flow cytometry to evaluate how collagen type I mineralization affects the biochemical and biophysical properties of the tumor cell glycocalyx, a dense layer of glycosylated proteins and lipids decorating their cell surface. Our results suggest that collagen mineralization upregulates mucin-type O-glycosylation and sialylation by tumor cells, which increased their glycocalyx thickness while enhancing resistance to attack by Natural Killer (NK) cells. These changes were functionally linked as treatment with a sialylation inhibitor decreased mineralization-dependent glycocalyx thickness and made tumor cells more susceptible to NK cell attack. Together, our results suggest that interference with glycocalyx sialylation may represent a therapeutic strategy to enhance cancer immunotherapies targeting bone-metastatic breast cancer.
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Affiliation(s)
- Sangwoo Park
- Graduate Field of Biophysics, Cornell University, Ithaca, NY 14853, USA
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Siyoung Choi
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Adrian A. Shimpi
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Lara A. Estroff
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, 14853, USA
| | - Claudia Fischbach
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew J. Paszek
- Graduate Field of Biophysics, Cornell University, Ithaca, NY 14853, USA
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, 14853, USA
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11
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Chernykh A, Abrahams JL, Grant OC, Kambanis L, Sumer-Bayraktar Z, Ugonotti J, Kawahara R, Corcilius L, Payne RJ, Woods RJ, Thaysen-Andersen M. Position-specific N- and O-glycosylation of the reactive center loop impacts neutrophil elastase-mediated proteolysis of corticosteroid-binding globulin. J Biol Chem 2024; 300:105519. [PMID: 38042488 PMCID: PMC10784704 DOI: 10.1016/j.jbc.2023.105519] [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: 03/21/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/04/2023] Open
Abstract
Corticosteroid-binding globulin (CBG) delivers anti-inflammatory cortisol to inflamed tissues through proteolysis of an exposed reactive center loop (RCL) by neutrophil elastase (NE). We previously demonstrated that RCL-localized Asn347-linked N-glycans impact NE proteolysis, but a comprehensive structure-function characterization of the RCL glycosylation is still required to better understand CBG glycobiology. Herein, we first performed RCL-centric glycoprofiling of serum-derived CBG to elucidate the Asn347-glycans and then used molecular dynamics simulations to study their impact on NE proteolysis. Importantly, we also identified O-glycosylation (di/sialyl T) across four RCL sites (Thr338/Thr342/Thr345/Ser350) of serum CBG close to the NE-targeted Val344-Thr345 cleavage site. A restricted N- and O-glycan co-occurrence pattern on the RCL involving exclusively Asn347 and Thr338 glycosylation was experimentally observed and supported in silico by modeling of a CBG-GalNAc-transferase (GalNAc-T) complex with various RCL glycans. GalNAc-T2 and GalNAc-T3 abundantly expressed by liver and gall bladder, respectively, showed in vitro a capacity to transfer GalNAc (Tn) to multiple RCL sites suggesting their involvement in RCL O-glycosylation. Recombinant CBG was then used to determine roles of RCL O-glycosylation through longitudinal NE-centric proteolysis experiments, which demonstrated that both sialoglycans (disialyl T) and asialoglycans (T) decorating Thr345 inhibit NE proteolysis. Synthetic RCL O-glycopeptides expanded on these findings by showing that Thr345-Tn and Thr342-Tn confer strong and moderate protection against NE cleavage, respectively. Molecular dynamics substantiated that short Thr345-linked O-glycans abrogate NE interactions. In conclusion, we report on biologically relevant CBG RCL glycosylation events, which improve our understanding of mechanisms governing cortisol delivery to inflamed tissues.
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Affiliation(s)
- Anastasia Chernykh
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Jodie L Abrahams
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Lucas Kambanis
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Zeynep Sumer-Bayraktar
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Glycometabolic Biochemistry Team, Cluster of Pioneering Research, RIKEN, Wako, Saitama, Japan
| | - Julian Ugonotti
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Rebeca Kawahara
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| | - Leo Corcilius
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan.
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12
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Huang LT, Colville MJ, Paszek M. Recombinant Production of Glycoengineered Mucins in HEK293-F Cells. Methods Mol Biol 2024; 2763:281-308. [PMID: 38347419 DOI: 10.1007/978-1-0716-3670-1_24] [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
Recombinant mucins are attractive polymeric building blocks for new biomaterials, biolubricants, and therapeutics. Advances in glycoengineered host cell systems now enable the recombinant production of mucins with tailored O-glycan side chains, offering new opportunities to tune the functionality of mucins and investigate the biology of specific O-glycan structures. Here, we provide a protocol for the scalable production of glycoengineered mucins and mucin-like glycoproteins in suspension-adapted HEK293-F cells. The protocol includes the preparation of engineered cell lines with homozygous knockout (KO) of glycosyltransferases using CRISPR/Cas9 and homology-directed repair (HDR) templates designed for efficient screening of clones. Strategies are provided for the stable introduction of mucin expression cassettes into the HEK293-F genome and the subsequent isolation of high-expressing cell populations. The high-titer production of recombinant mucins in conventional shaker flasks is described as an example production strategy using these cell lines.
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Affiliation(s)
- Ling-Ting Huang
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Marshall J Colville
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Matthew Paszek
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, USA
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13
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Mahoney KE, Chang V, Lucas TM, Maruszko K, Malaker SA. Optimized mucin-selective enrichment strategy to probe the mucinome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572204. [PMID: 38187615 PMCID: PMC10769219 DOI: 10.1101/2023.12.18.572204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of healthy and disease-driven biological functions. Previously, we developed a mucin-selective enrichment strategy by employing a catalytically inactive mucinase (StcE) conjugated to solid support. While this method was effective, it suffered from low throughput and high sample requirements. Further, the elution step required boiling in SDS, thus necessitating an in-gel digest with trypsin. Here, we optimized our previous enrichment method to include elution conditions amenable to mucinase digestion and downstream analysis with mass spectrometry. This increased throughput and lowered sample input while maintaining mucin selectivity and enhancing glycopeptide signal. We then benchmarked this technique against different O-glycan binding moieties for their ability to enrich mucins from various cell lines and human serum. Overall, the new method outperformed our previous procedure and all other enrichment techniques tested. This allowed for effective isolation of more mucin-domain glycoproteins, resulting in a high number of O-glycopeptides, thus enhancing our ability to analyze the mucinome.
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Affiliation(s)
- Keira E. Mahoney
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Vincent Chang
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Taryn M. Lucas
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | | | - Stacy A. Malaker
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
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14
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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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15
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Anggara K, Sršan L, Jaroentomeechai T, Wu X, Rauschenbach S, Narimatsu Y, Clausen H, Ziegler T, Miller RL, Kern K. Direct observation of glycans bonded to proteins and lipids at the single-molecule level. Science 2023; 382:219-223. [PMID: 37824645 PMCID: PMC7615228 DOI: 10.1126/science.adh3856] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/31/2023] [Indexed: 10/14/2023]
Abstract
Proteins and lipids decorated with glycans are found throughout biological entities, playing roles in biological functions and dysfunctions. Current analytical strategies for these glycan-decorated biomolecules, termed glycoconjugates, rely on ensemble-averaged methods that do not provide a full view of positions and structures of glycans attached at individual sites in a given molecule, especially for glycoproteins. We show single-molecule analysis of glycoconjugates by direct imaging of individual glycoconjugate molecules using low-temperature scanning tunneling microscopy. Intact glycoconjugate ions from electrospray are soft-landed on a surface for their direct single-molecule imaging. The submolecular imaging resolution corroborated by quantum mechanical modeling unveils whole structures and attachment sites of glycans in glycopeptides, glycolipids, N-glycoproteins, and O-glycoproteins densely decorated with glycans.
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Affiliation(s)
- Kelvin Anggara
- Max-Planck Institute for Solid-State Research; Stuttgart, DE-70569, Germany
| | - Laura Sršan
- Institute of Organic Chemistry, University of Tübingen; Tübingen, DE-72076, Germany
| | - Thapakorn Jaroentomeechai
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen; Copenhagen, DK-2200, Denmark
| | - Xu Wu
- Max-Planck Institute for Solid-State Research; Stuttgart, DE-70569, Germany
| | - Stephan Rauschenbach
- Max-Planck Institute for Solid-State Research; Stuttgart, DE-70569, Germany
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford; Oxford, OX1 3TA, United Kingdom
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen; Copenhagen, DK-2200, Denmark
- GlycoDisplay ApS, Copenhagen, DK-2200, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen; Copenhagen, DK-2200, Denmark
| | - Thomas Ziegler
- Institute of Organic Chemistry, University of Tübingen; Tübingen, DE-72076, Germany
| | - Rebecca L. Miller
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen; Copenhagen, DK-2200, Denmark
| | - Klaus Kern
- Max-Planck Institute for Solid-State Research; Stuttgart, DE-70569, Germany
- Institut de Physique, École Polytechnique Fédérale de Lausanne; Lausanne, CH-1015, Switzerland
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16
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Chongsaritsinsuk J, Steigmeyer AD, Mahoney KE, Rosenfeld MA, Lucas TM, Smith CM, Li A, Ince D, Kearns FL, Battison AS, Hollenhorst MA, Judy Shon D, Tiemeyer KH, Attah V, Kwon C, Bertozzi CR, Ferracane MJ, Lemmon MA, Amaro RE, Malaker SA. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. Nat Commun 2023; 14:6169. [PMID: 37794035 PMCID: PMC10550946 DOI: 10.1038/s41467-023-41756-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 09/11/2023] [Indexed: 10/06/2023] Open
Abstract
Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of biological functions. In particular, the T cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, -3, -4) decorate immune cells and act as key regulators in cellular immunity. However, their dense O-glycosylation remains enigmatic, primarily due to the challenges associated with studying mucin domains. Here, we demonstrate that the mucinase SmE has a unique ability to cleave at residues bearing very complex glycans. SmE enables improved mass spectrometric analysis of several mucins, including the entire TIM family. With this information in-hand, we perform molecular dynamics (MD) simulations of TIM-3 and -4 to understand how glycosylation affects structural features of these proteins. Finally, we use these models to investigate the functional relevance of glycosylation for TIM-3 function and ligand binding. Overall, we present a powerful workflow to better understand the detailed molecular structures and functions of the mucinome.
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Affiliation(s)
| | | | - Keira E Mahoney
- Department of Chemistry, Yale University, New Haven, CT, 06511, USA
| | - Mia A Rosenfeld
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Taryn M Lucas
- Department of Chemistry, Yale University, New Haven, CT, 06511, USA
| | - Courtney M Smith
- Yale Cancer Biology Institute and Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Alice Li
- Yale Cancer Biology Institute and Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Deniz Ince
- Department of Chemistry, Yale University, New Haven, CT, 06511, USA
| | - Fiona L Kearns
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Marie A Hollenhorst
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, 94305, USA
| | - D Judy Shon
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Katherine H Tiemeyer
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Victor Attah
- Department of Chemistry, Yale University, New Haven, CT, 06511, USA
| | - Catherine Kwon
- Department of Chemistry, Yale University, New Haven, CT, 06511, USA
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA
| | | | - Mark A Lemmon
- Yale Cancer Biology Institute and Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Stacy A Malaker
- Department of Chemistry, Yale University, New Haven, CT, 06511, USA.
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17
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Strasser R. Plant glycoengineering for designing next-generation vaccines and therapeutic proteins. Biotechnol Adv 2023; 67:108197. [PMID: 37315875 DOI: 10.1016/j.biotechadv.2023.108197] [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: 01/18/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/16/2023]
Abstract
Protein glycosylation has a huge impact on biological processes in all domains of life. The type of glycan present on a recombinant glycoprotein depends on protein intrinsic features and the glycosylation repertoire of the cell type used for expression. Glycoengineering approaches are used to eliminate unwanted glycan modifications and to facilitate the coordinated expression of glycosylation enzymes or whole metabolic pathways to furnish glycans with distinct modifications. The formation of tailored glycans enables structure-function studies and optimization of therapeutic proteins used in different applications. While recombinant proteins or proteins from natural sources can be in vitro glycoengineered using glycosyltransferases or chemoenzymatic synthesis, many approaches use genetic engineering involving the elimination of endogenous genes and introduction of heterologous genes to cell-based production systems. Plant glycoengineering enables the in planta production of recombinant glycoproteins with human or animal-type glycans that resemble natural glycosylation or contain novel glycan structures. This review summarizes key achievements in glycoengineering of plants and highlights current developments aiming to make plants more suitable for the production of a diverse range of recombinant glycoproteins for innovative therapies.
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Affiliation(s)
- Richard Strasser
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
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18
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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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19
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Mo J, Zou Y, Li BH, Li G, Zheng XJ, Liu Y, Ye XS. Tumor-Associated Extracellular Microvesicles with Fluorine-Modified Carbohydrate Antigens Trigger a Stronger Antitumor Immune Response. ACS APPLIED MATERIALS & INTERFACES 2023; 15:40201-40212. [PMID: 37589474 DOI: 10.1021/acsami.3c06399] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Abnormal glycosylation is a hallmark of tumor development, and tumor-associated carbohydrate antigens are potential immune targets for tumor therapy. Tumor-associated extracellular microvesicles are subcellular vesicles released from cell membranes that have immunogenicity similar to that of precursor cells. However, unmodified tumor-derived microvesicles have weaknesses, such as low immunogenicity, poor biostability, and short half-life in vivo. For the first time, we herein generated extracellular microvesicles containing modified tumor-associated carbohydrate antigens by constructing a cell line with highly expressed antigen-processing enzymes utilizing fluorine-modified monosaccharide substrates via a metabolic oligosaccharide engineering strategy. The microvesicles were applied to tumor immunity, achieving enhanced immunoprophylaxis and immunotherapy effects. Furthermore, the mechanisms of antitumor immunity were explored. Our findings may provide new insights into the adhibition of suitably modified extracellular microvesicles and the development of more effective carbohydrate-based anticancer vaccines.
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Affiliation(s)
- Juan Mo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, and Chemical Biology Center, Peking University, Beijing 100191, People's Republic of China
| | - You Zou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, and Chemical Biology Center, Peking University, Beijing 100191, People's Republic of China
| | - Bo-Han Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, and Chemical Biology Center, Peking University, Beijing 100191, People's Republic of China
| | - Gefei Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, and Chemical Biology Center, Peking University, Beijing 100191, People's Republic of China
- College of Science, Nanjing Forestry University, Nanjing, Jiangsu 210037, People's Republic of China
| | - Xiu-Jing Zheng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, and Chemical Biology Center, Peking University, Beijing 100191, People's Republic of China
| | - Yang Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, and Chemical Biology Center, Peking University, Beijing 100191, People's Republic of China
| | - Xin-Shan Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, and Chemical Biology Center, Peking University, Beijing 100191, People's Republic of China
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20
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Chatterjee M, Huang LZX, Mykytyn AZ, Wang C, Lamers MM, Westendorp B, Wubbolts RW, van Putten JPM, Bosch BJ, Haagmans BL, Strijbis K. Glycosylated extracellular mucin domains protect against SARS-CoV-2 infection at the respiratory surface. PLoS Pathog 2023; 19:e1011571. [PMID: 37561789 PMCID: PMC10464970 DOI: 10.1371/journal.ppat.1011571] [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: 02/09/2023] [Revised: 08/29/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Mucins play an essential role in protecting the respiratory tract against microbial infections while also acting as binding sites for bacterial and viral adhesins. The heavily O-glycosylated gel-forming mucins MUC5AC and MUC5B eliminate pathogens by mucociliary clearance. Transmembrane mucins MUC1, MUC4, and MUC16 can restrict microbial invasion at the apical surface of the epithelium. In this study, we determined the impact of host mucins and mucin glycans on epithelial entry of SARS-CoV-2. Human lung epithelial Calu-3 cells express the SARS-CoV-2 entry receptor ACE2 and high levels of glycosylated MUC1, but not MUC4 and MUC16, on their cell surface. The O-glycan-specific mucinase StcE specifically removed the glycosylated part of the MUC1 extracellular domain while leaving the underlying SEA domain and cytoplasmic tail intact. StcE treatment of Calu-3 cells significantly enhanced infection with SARS-CoV-2 pseudovirus and authentic virus, while removal of terminal mucin glycans sialic acid and fucose from the epithelial surface did not impact viral entry. In Calu-3 cells, the transmembrane mucin MUC1 and ACE2 are located to the apical surface in close proximity and StcE treatment results in enhanced binding of purified spike protein. Both MUC1 and MUC16 are expressed on the surface of human organoid-derived air-liquid interface (ALI) differentiated airway cultures and StcE treatment led to mucin removal and increased levels of SARS-CoV-2 replication. In these cultures, MUC1 was highly expressed in non-ciliated cells while MUC16 was enriched in goblet cells. In conclusion, the glycosylated extracellular domains of different transmembrane mucins might have similar protective functions in different respiratory cell types by restricting SARS-CoV-2 binding and entry.
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Affiliation(s)
- Maitrayee Chatterjee
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Liane Z. X. Huang
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Anna Z. Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Chunyan Wang
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Mart M. Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bart Westendorp
- Department of Biomolecular Health Sciences, Division Cell Biology, Metabolism and Cancer, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - Jos P. M. van Putten
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Berend-Jan Bosch
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Bart L. Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Karin Strijbis
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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21
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Liu M, Bakker AS, Narimatsu Y, van Kuppeveld FJM, Clausen H, de Haan CAM, de Vries E. H3N2 influenza A virus gradually adapts to human-type receptor binding and entry specificity after the start of the 1968 pandemic. Proc Natl Acad Sci U S A 2023; 120:e2304992120. [PMID: 37467282 PMCID: PMC10401031 DOI: 10.1073/pnas.2304992120] [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: 03/27/2023] [Accepted: 06/01/2023] [Indexed: 07/21/2023] Open
Abstract
To become established upon zoonotic transfer, influenza A viruses (IAV) need to switch binding from "avian-type" α2-3-linked sialic acid receptors (2-3Sia) to "human-type" Siaα2-6-linked sialic acid receptors (2-6Sia). For the 1968 H3N2 pandemic virus, this was accomplished by two canonical amino acid substitutions in its hemagglutinin (HA) although a full specificity shift had not occurred. The receptor repertoire on epithelial cells is highly diverse and simultaneous interaction of a virus particle with a range of low- to very low-affinity receptors results in tight heteromultivalent binding. How this range of affinities determines binding selectivity and virus motility remains largely unknown as the analysis of low-affinity monovalent HA-receptor interactions is technically challenging. Here, a biolayer interferometry assay enabled a comprehensive analysis of receptor-binding kinetics evolution upon host-switching. Virus-binding kinetics of H3N2 virus isolates slowly evolved from 1968 to 1979 from mixed 2-3/2-6Sia specificity to high 2-6Sia specificity, surprisingly followed by a decline in selectivity after 1992. By using genetically tuned HEK293 cells, presenting either a simplified 2-3Sia- or 2-6Sia-specific receptor repertoire, receptor-specific binding was shown to correlate strongly with receptor-specific entry. In conclusion, the slow and continuous evolution of entry and receptor-binding specificity of seasonal H3N2 viruses contrasts with the paradigm that human IAVs need to rapidly acquire and maintain a high specificity for 2-6Sia. Analysis of the kinetic parameters of receptor binding provides a basis for understanding virus-binding specificity, motility, and HA/neuraminidase balance at the molecular level.
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Affiliation(s)
- Mengying Liu
- Virology section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584CLUtrecht, the Netherlands
| | - A. Sophie Bakker
- Virology section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584CLUtrecht, the Netherlands
| | - Yoshiki Narimatsu
- Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200Copenhagen, Denmark
| | - Frank J. M. van Kuppeveld
- Virology section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584CLUtrecht, the Netherlands
| | - Henrik Clausen
- Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200Copenhagen, Denmark
| | - Cornelis A. M. de Haan
- Virology section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584CLUtrecht, the Netherlands
| | - Erik de Vries
- Virology section, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584CLUtrecht, the Netherlands
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22
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Huang X, Nero T, Weerasekera R, Matej KH, Hinbest A, Jiang Z, Lee RF, Wu L, Chak C, Nijjer J, Gibaldi I, Yang H, Gamble N, Ng WL, Malaker SA, Sumigray K, Olson R, Yan J. Vibrio cholerae biofilms use modular adhesins with glycan-targeting and nonspecific surface binding domains for colonization. Nat Commun 2023; 14:2104. [PMID: 37055389 PMCID: PMC10102183 DOI: 10.1038/s41467-023-37660-0] [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: 01/23/2023] [Accepted: 03/24/2023] [Indexed: 04/15/2023] Open
Abstract
Bacterial biofilms are formed on environmental surfaces and host tissues, and facilitate host colonization and antibiotic resistance by human pathogens. Bacteria often express multiple adhesive proteins (adhesins), but it is often unclear whether adhesins have specialized or redundant roles. Here, we show how the model biofilm-forming organism Vibrio cholerae uses two adhesins with overlapping but distinct functions to achieve robust adhesion to diverse surfaces. Both biofilm-specific adhesins Bap1 and RbmC function as a "double-sided tape": they share a β-propeller domain that binds to the biofilm matrix exopolysaccharide, but have distinct environment-facing domains. Bap1 adheres to lipids and abiotic surfaces, while RbmC mainly mediates binding to host surfaces. Furthermore, both adhesins contribute to adhesion in an enteroid monolayer colonization model. We expect that similar modular domains may be utilized by other pathogens, and this line of research can potentially lead to new biofilm-removal strategies and biofilm-inspired adhesives.
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Affiliation(s)
- Xin Huang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Thomas Nero
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Ranjuna Weerasekera
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Katherine H Matej
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Alex Hinbest
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Zhaowei Jiang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Rebecca F Lee
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Longjun Wu
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong SAR, Guangzhou, Hong Kong SAR
| | - Cecilia Chak
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Japinder Nijjer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Isabella Gibaldi
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Hang Yang
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Nathan Gamble
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Wai-Leung Ng
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Stacy A Malaker
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Kaelyn Sumigray
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Rich Olson
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA.
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- Quantitative Biology Institute, Yale University, New Haven, CT, USA.
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23
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Chandler KB, Pavan CH, Cotto Aparicio HG, Sackstein R. Enrichment and nLC-MS/MS Analysis of Head and Neck Cancer Mucinome Glycoproteins. J Proteome Res 2023; 22:1231-1244. [PMID: 36971183 DOI: 10.1021/acs.jproteome.2c00746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Mucin-domain glycoproteins expressed on cancer cell surfaces play central roles in cell adhesion, cancer progression, stem cell renewal, and immune evasion. Despite abundant evidence that mucin-domain glycoproteins are critical to the pathobiology of head and neck squamous cell carcinoma (HNSCC), our knowledge of the composition of that mucinome is grossly incomplete. Here, we utilized a catalytically inactive point mutant of the enzyme StcE (StcEE447D) to capture mucin-domain glycoproteins in head and neck cancer cell line lysates followed by their characterization using sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE), in-gel digestion, nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS), and enrichment analyses. We demonstrate the feasibility of this workflow for the study of mucin-domain glycoproteins in HNSCC, identify a set of mucin-domain glycoproteins common to multiple HNSCC cell lines, and report a subset of mucin-domain glycoproteins that are uniquely expressed in HSC-3 cells, a cell line derived from a highly aggressive metastatic tongue squamous cell carcinoma. This effort represents the first attempt to identify mucin-domain glycoproteins in HNSCC in an untargeted, unbiased analysis, paving the way for a more comprehensive characterization of the mucinome components that mediate aggressive tumor cell phenotypes. Data associated with this study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD029420.
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24
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O-Mucin-degrading carbohydrate-active enzymes and their possible implication in inflammatory bowel diseases. Essays Biochem 2023; 67:331-344. [PMID: 36912232 PMCID: PMC10154620 DOI: 10.1042/ebc20220153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 03/14/2023]
Abstract
Inflammatory bowel diseases (IBD) are modern diseases, with incidence rising around the world. They are associated with perturbation of the intestinal microbiota, and with alteration and crossing of the mucus barrier by the commensal bacteria that feed on it. In the process of mucus catabolism and invasion by gut bacteria, carbohydrate-active enzymes (CAZymes) play a critical role since mucus is mainly made up by O- and N-glycans. Moreover, the occurrence of IBD seems to be associated with low-fiber diets. Conversely, supplementation with oligosaccharides, such as human milk oligosaccharides (HMOs), which are structurally similar to intestinal mucins and could thus compete with them towards bacterial mucus-degrading CAZymes, has been suggested to prevent inflammation. In this mini-review, we will establish the current state of knowledge regarding the identification and characterization of mucus-degrading enzymes from both cultured and uncultured species of gut commensals and enteropathogens, with a particular focus on the present technological opportunities available to further the discovery of mucus-degrading CAZymes within the entire gut microbiome, by coupling microfluidics with metagenomics and culturomics. Finally, we will discuss the challenges to overcome to better assess how CAZymes targeting specific functional oligosaccharides could be involved in the modulation of the mucus-driven cross-talk between gut bacteria and their host in the context of IBD.
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25
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Sanz-Martinez I, Pereira S, Merino P, Corzana F, Hurtado-Guerrero R. Molecular Recognition of GalNAc in Mucin-Type O-Glycosylation. Acc Chem Res 2023; 56:548-560. [PMID: 36815693 PMCID: PMC9996832 DOI: 10.1021/acs.accounts.2c00723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
ConspectusN-Acetylgalactosamine (GalNAc)-type O-glycosylation is an essential posttranslational modification (PTM) that plays fundamental roles in biology. Malfunction of this PTM is exemplified by the presence of truncated O-glycans in cancer. For instance, the glycoprotein MUC1 is overexpressed in many tumor tissues and tends to carry simple oligosaccharides that allow for the presentation of different tumor-associated antigens, such as the Tn or sTn antigens (GalNAc-α-1-O-Thr/Ser and Neu5Acα2-6GalNAcα1-O-Ser/Thr, respectively). In other cases, such as tumoral calcinosis associated with O-glycosylation of the fibroblast growth factor 23, O-glycans are absent or less abundant. Significant progress has been made in determining the three-dimensional structures of biomolecules that recognize GalNAc, such as antibodies, lectins, mucinases, GalNAc-transferases, and other glycosyltransferases. Analysis of the complexes between these entities and GalNAc-containing glycopeptides, in most cases derived from crystallographic or NMR analysis, provides an understanding of the key structural elements that control molecular recognition of these glycopeptides. Here, we describe and compare the binding sites of these proteins in detail, focusing on how the GalNAc moieties interact selectively with them. We also summarize the differences and similarities in GalNAc recognition. In general, the recognition of GalNAc-containing glycopeptides is determined by hydrogen bonds between hydroxyl groups and the N-acetyl group of GalNAc with proteins, as well as CH-π contacts in which the hydrophobic α-face of the sugar and the methyl group of NHAc can be involved. The latter interaction usually provides the basis for selectivity. It is worth noting that binding of these glycopeptides depends primarily on recognition of the sugar moiety, with some exceptions such as a few anti-MUC1 antibodies that primarily recognize the peptide backbone and use the sugar to facilitate shape complementarity or to establish a limited number of interactions with the protein. Focusing specifically on the GalNAc moiety, we can observe that there is some degeneracy of interactions within the same protein families, likely due to substrate flexibility. However, when all studied proteins are considered together, despite the commonalities within each protein family, no pattern can be discerned between the different families, apart from the presence of common residues such as Tyr, His, or Asp, which are responsible for hydrogen bonds. The lack of a pattern can be anticipated, given the diverse functions of mucinases, glycosyltransferases, antibodies, and lectins. Finally, it is important to point out that the conformational differences observed in solution in glycopeptides bearing GalNAc-α-1-O-Ser or GalNAc-α-1-O-Thr also can be found in the bound state. This unique characteristic is exploited, for instance, by the enzyme C1GalT1 to broadly glycosylate both acceptor substrates. The findings summarized in this review may contribute to the rational structure-guided development of therapeutic vaccines, novel diagnostic tools for early cancer detection, and new cancer treatments for cancer with tailored anti-Tn or anti-STn antibodies or new drugs to inhibit GalNAc-T isoenzymes.
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Affiliation(s)
- Ignacio Sanz-Martinez
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Glycobiology Unit, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain.,Department of Organic Chemistry, Faculty of Sciences, University of Zaragoza, Campus San Francisco, 50009 Zaragoza, Spain
| | - Sandra Pereira
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Glycobiology Unit, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain.,Department of Organic Chemistry, Faculty of Sciences, University of Zaragoza, Campus San Francisco, 50009 Zaragoza, Spain
| | - Pedro Merino
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Glycobiology Unit, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain.,Department of Organic Chemistry, Faculty of Sciences, University of Zaragoza, Campus San Francisco, 50009 Zaragoza, Spain
| | - Francisco Corzana
- Department of Chemistry, Centro de Investigación en Síntesis Química, University of La Rioja, Madre de Dios 53, 26006 Logroño, Spain
| | - Ramon Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Glycobiology Unit, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain.,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark.,Fundación ARAID, 50018 Zaragoza, Spain
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26
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Sørensen DM, Büll C, Madsen TD, Lira-Navarrete E, Clausen TM, Clark AE, Garretson AF, Karlsson R, Pijnenborg JFA, Yin X, Miller RL, Chanda SK, Boltje TJ, Schjoldager KT, Vakhrushev SY, Halim A, Esko JD, Carlin AF, Hurtado-Guerrero R, Weigert R, Clausen H, Narimatsu Y. Identification of global inhibitors of cellular glycosylation. Nat Commun 2023; 14:948. [PMID: 36804936 PMCID: PMC9941569 DOI: 10.1038/s41467-023-36598-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
Small molecule inhibitors of glycosylation enzymes are valuable tools for dissecting glycan functions and potential drug candidates. Screening for inhibitors of glycosyltransferases are mainly performed by in vitro enzyme assays with difficulties moving candidates to cells and animals. Here, we circumvent this by employing a cell-based screening assay using glycoengineered cells expressing tailored reporter glycoproteins. We focused on GalNAc-type O-glycosylation and selected the GalNAc-T11 isoenzyme that selectively glycosylates endocytic low-density lipoprotein receptor (LDLR)-related proteins as targets. Our screen of a limited small molecule compound library did not identify selective inhibitors of GalNAc-T11, however, we identify two compounds that broadly inhibited Golgi-localized glycosylation processes. These compounds mediate the reversible fragmentation of the Golgi system without affecting secretion. We demonstrate how these inhibitors can be used to manipulate glycosylation in cells to induce expression of truncated O-glycans and augment binding of cancer-specific Tn-glycoprotein antibodies and to inhibit expression of heparan sulfate and binding and infection of SARS-CoV-2.
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Affiliation(s)
- Daniel Madriz Sørensen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Christian Büll
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Thomas D Madsen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Erandi Lira-Navarrete
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- The Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, 50018, Zaragoza, Spain
- Fundación ARAID, 50018, Zaragoza, Spain
| | - Thomas Mandel Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alex E Clark
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Aaron F Garretson
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Richard Karlsson
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Johan F A Pijnenborg
- Institute for Molecules and Materials, Department of Synthetic Organic Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Xin Yin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Rebecca L Miller
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Sumit K Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Thomas J Boltje
- Institute for Molecules and Materials, Department of Synthetic Organic Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Aaron F Carlin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ramon Hurtado-Guerrero
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- The Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, 50018, Zaragoza, Spain
- Fundación ARAID, 50018, Zaragoza, Spain
| | - Roberto Weigert
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark.
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark.
- GlycoDisplay ApS, Copenhagen, Denmark.
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27
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Chongsaritsinsuk J, Steigmeyer AD, Mahoney KE, Rosenfeld MA, Lucas TM, Ince D, Kearns FL, Battison AS, Hollenhorst MA, Shon DJ, Tiemeyer KH, Attah V, Kwon C, Bertozzi CR, Ferracane MJ, Amaro RE, Malaker SA. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526488. [PMID: 36778266 PMCID: PMC9915616 DOI: 10.1101/2023.02.01.526488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of biological functions. In particular, the T cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, -3, -4) decorate immune cells and act as key checkpoint inhibitors in cancer. However, their dense O-glycosylation remains enigmatic both in terms of glycoproteomic landscape and structural dynamics, primarily due to the challenges associated with studying mucin domains. Here, we present a mucinase (SmE) and demonstrate its ability to selectively cleave along the mucin glycoprotein backbone, similar to others of its kind. Unlike other mucinases, though, SmE harbors the unique ability to cleave at residues bearing extremely complex glycans which enabled improved mass spectrometric analysis of several mucins, including the entire TIM family. With this information in-hand, we performed molecular dynamics (MD) simulations of TIM-3 and -4 to demonstrate how glycosylation affects structural features of these proteins. Overall, we present a powerful workflow to better understand the detailed molecular structures of the mucinome.
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Affiliation(s)
| | | | - Keira E. Mahoney
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Mia A. Rosenfeld
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Taryn M. Lucas
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Deniz Ince
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Fiona L. Kearns
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Marie A. Hollenhorst
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA 94305, USA
| | - D. Judy Shon
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Katherine H. Tiemeyer
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Victor Attah
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Catherine Kwon
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Carolyn R. Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | | | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stacy A. Malaker
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
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28
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Riley NM, Bertozzi CR. Deciphering O-glycoprotease substrate preferences with O-Pair Search. Mol Omics 2022; 18:908-922. [PMID: 36373229 PMCID: PMC10010678 DOI: 10.1039/d2mo00244b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
O-Glycoproteases are an emerging class of enzymes that selectively digest glycoproteins at positions decorated with specific O-linked glycans. O-Glycoprotease substrates range from any O-glycoprotein (albeit with specific O-glycan modifications) to only glycoproteins harboring specific O-glycosylated sequence motifs, such as those found in mucin domains. Their utility for multiple glycoproteomic applications is driving the search to both discover new O-glycoproteases and to understand how structural features of characterized O-glycoproteases influence their substrate specificities. One challenge of defining O-glycoprotease specificity restraints is the need to characterize O-glycopeptides with site-specific analysis of O-glycosites. Here, we demonstrate how O-Pair Search, a recently developed O-glycopeptide-centric identification platform that enables rapid searches and confident O-glycosite localization, can be used to determine substrate specificities of various O-glycoproteases de novo from LC-MS/MS data of O-glycopeptides. Using secreted protease of C1 esterase inhibitor (StcE) from enterohemorrhagic Escherichia coli and O-endoprotease OgpA from Akkermansia mucinophila, we explore numerous settings that effect O-glycopeptide identification and show how non-specific and semi-tryptic searches of O-glycopeptide data can produce candidate cleavage motifs. These putative motifs can be further used to define new protease cleavage settings that lower search times and improve O-glycopeptide identifications. We use this platform to generate a consensus motif for the recently characterized immunomodulating metalloprotease (IMPa) from Pseudomonas aeruginosa and show that IMPa is a favorable O-glycoprotease for characterizing densely O-glycosylated mucin-domain glycoproteins.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Sarafan ChEM-H, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Sarafan ChEM-H, Stanford University, Stanford, California, USA. .,Howard Hughes Medical Institute, Stanford, California, USA
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29
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Lang T, Pelaseyed T. Discovery of a MUC3B gene reconstructs the membrane mucin gene cluster on human chromosome 7. PLoS One 2022; 17:e0275671. [PMID: 36256656 PMCID: PMC9578598 DOI: 10.1371/journal.pone.0275671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 09/21/2022] [Indexed: 11/12/2022] Open
Abstract
Human tissue surfaces are coated with mucins, a family of macromolecular sugar-laden proteins serving diverse functions from lubrication to the formation of selective biochemical barriers against harmful microorganisms and molecules. Membrane mucins are a distinct group of mucins that are attached to epithelial cell surfaces where they create a dense glycocalyx facing the extracellular environment. All mucin proteins carry long stretches of tandemly repeated sequences that undergo extensive O-linked glycosylation to form linear mucin domains. However, the repetitive nature of mucin domains makes them prone to recombination and renders their genetic sequences particularly difficult to read with standard sequencing technologies. As a result, human mucin genes suffer from significant sequence gaps that have hampered the investigation of gene function in health and disease. Here we leveraged a recent human genome assembly to characterize a previously unmapped MUC3B gene located at the q22 locus on chromosome 7, within a cluster of four structurally related membrane mucin genes that we name the MUC3 cluster. We found that MUC3B shares high sequence identity with the known MUC3A gene and that the two genes are governed by evolutionarily conserved regulatory elements. Furthermore, we show that MUC3A, MUC3B, MUC12, and MUC17 in the human MUC3 cluster are expressed in intestinal epithelial cells (IECs). Our results complete existing genetic gaps in the MUC3 cluster which is a conserved genetic unit in vertebrates. We anticipate our results to be the starting point for the detection of disease-associated polymorphisms in the human MUC3 cluster. Moreover, our study provides the basis for the exploration of intestinal mucin gene function in widely used experimental models such as human intestinal organoids and genetic mouse models.
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Affiliation(s)
- Tiange Lang
- Big Data Decision Institution, Jinan University, Tianhe, Guangzhou, China
| | - Thaher Pelaseyed
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
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30
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Riley NM, Wen RM, Bertozzi CR, Brooks JD, Pitteri SJ. Measuring the multifaceted roles of mucin-domain glycoproteins in cancer. Adv Cancer Res 2022; 157:83-121. [PMID: 36725114 PMCID: PMC10582998 DOI: 10.1016/bs.acr.2022.09.001] [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] [Indexed: 11/05/2022]
Abstract
Mucin-domain glycoproteins are highly O-glycosylated cell surface and secreted proteins that serve as both biochemical and biophysical modulators. Aberrant expression and glycosylation of mucins are known hallmarks in numerous malignancies, yet mucin-domain glycoproteins remain enigmatic in the broad landscape of cancer glycobiology. Here we review the multifaceted roles of mucins in cancer through the lens of the analytical and biochemical methods used to study them. We also describe a collection of emerging tools that are specifically equipped to characterize mucin-domain glycoproteins in complex biological backgrounds. These approaches are poised to further elucidate how mucin biology can be understood and subsequently targeted for the next generation of cancer therapeutics.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States.
| | - Ru M Wen
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States; Howard Hughes Medical Institute, Stanford, CA, United States
| | - James D Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States; Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States.
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31
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Reeves AE, Huang ML. Mucopedia 101: capturing and assigning mucin-domain glycoproteins. Trends Microbiol 2022; 31:428-429. [PMID: 36153262 DOI: 10.1016/j.tim.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/30/2022] [Accepted: 09/06/2022] [Indexed: 11/19/2022]
Abstract
Glycoproteins bearing mucin domains serve important biological functions, yet they are understudied due to their dense glycosylation. Malaker et al. describe a new tool that will advance the capture, identification, and prediction of new members of the 'mucinome'.
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Affiliation(s)
- Abigail E Reeves
- Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd, La Jolla, CA 92037, USA; Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 N. Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Mia L Huang
- Department of Molecular Medicine, Scripps Research, 10550 N. Torrey Pines Rd, La Jolla, CA 92037, USA.
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32
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Srivastava S, Verhagen A, Sasmal A, Wasik BR, Diaz S, Yu H, Bensing BA, Khan N, Khedri Z, Secrest P, Sullam P, Varki N, Chen X, Parrish CR, Varki A. Development and applications of sialoglycan-recognizing probes (SGRPs) with defined specificities: exploring the dynamic mammalian sialoglycome. Glycobiology 2022; 32:1116-1136. [PMID: 35926090 PMCID: PMC9680117 DOI: 10.1093/glycob/cwac050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/20/2022] [Accepted: 07/14/2022] [Indexed: 01/07/2023] Open
Abstract
Glycans that are abundantly displayed on vertebrate cell surface and secreted molecules are often capped with terminal sialic acids (Sias). These diverse 9-carbon-backbone monosaccharides are involved in numerous intrinsic biological processes. They also interact with commensals and pathogens, while undergoing dynamic changes in time and space, often influenced by environmental conditions. However, most of this sialoglycan complexity and variation remains poorly characterized by conventional techniques, which often tend to destroy or overlook crucial aspects of Sia diversity and/or fail to elucidate native structures in biological systems, i.e. in the intact sialome. To date, in situ detection and analysis of sialoglycans has largely relied on the use of plant lectins, sialidases, or antibodies, whose preferences (with certain exceptions) are limited and/or uncertain. We took advantage of naturally evolved microbial molecules (bacterial adhesins, toxin subunits, and viral hemagglutinin-esterases) that recognize sialoglycans with defined specificity to delineate 9 classes of sialoglycan recognizing probes (SGRPs: SGRP1-SGRP9) that can be used to explore mammalian sialome changes in a simple and systematic manner, using techniques common in most laboratories. SGRP candidates with specificity defined by sialoglycan microarray studies were engineered as tagged probes, each with a corresponding nonbinding mutant probe as a simple and reliable negative control. The optimized panel of SGRPs can be used in methods commonly available in most bioscience labs, such as ELISA, western blot, flow cytometry, and histochemistry. To demonstrate the utility of this approach, we provide examples of sialoglycome differences in tissues from C57BL/6 wild-type mice and human-like Cmah-/- mice.
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Affiliation(s)
- Saurabh Srivastava
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Andrea Verhagen
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Aniruddha Sasmal
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Brian R Wasik
- College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Sandra Diaz
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Hai Yu
- Department of Chemistry, University of California at Davis, Davis, CA, USA
| | - Barbara A Bensing
- Department of Medicine, University of California, San Francisco, CA, USA,VA Medical Center, San Francisco, CA, USA
| | - Naazneen Khan
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Zahra Khedri
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Patrick Secrest
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Paul Sullam
- Department of Medicine, University of California, San Francisco, CA, USA,VA Medical Center, San Francisco, CA, USA
| | - Nissi Varki
- Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, San Diego, CA, USA,Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
| | - Xi Chen
- Department of Chemistry, University of California at Davis, Davis, CA, USA
| | - Colin R Parrish
- College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Ajit Varki
- Corresponding author: UCSD School of Medicine, La Jolla, CA 92093-0687, USA.
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33
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Wisnovsky S, Bertozzi CR. Reading the glyco-code: New approaches to studying protein-carbohydrate interactions. Curr Opin Struct Biol 2022; 75:102395. [PMID: 35653954 PMCID: PMC9811956 DOI: 10.1016/j.sbi.2022.102395] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/06/2022] [Accepted: 04/16/2022] [Indexed: 01/07/2023]
Abstract
The surface of all living cells is decorated with carbohydrate molecules. Hundreds of functional proteins bind to these glycosylated ligands; such binding events subsequently modulate many aspects of protein and cell function. Identifying ligands for glycan-binding proteins (GBPs) is a defining challenge of glycoscience research. Here, we review recent advances that are allowing protein-carbohydrate interactions to be dissected with an unprecedented level of precision. We specifically highlight how cell-based glycan arrays and glyco-genomic profiling are being used to define the structural determinants of glycan-protein interactions in living cells. Going forward, these methods create exciting new opportunities for the study of glycans in physiology and disease.
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Affiliation(s)
- Simon Wisnovsky
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA,Howard Hughes Medical Institute, Stanford, CA, 94305, USA
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34
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Taleb V, Liao Q, Narimatsu Y, García-García A, Compañón I, Borges RJ, González-Ramírez AM, Corzana F, Clausen H, Rovira C, Hurtado-Guerrero R. Structural and mechanistic insights into the cleavage of clustered O-glycan patches-containing glycoproteins by mucinases of the human gut. Nat Commun 2022; 13:4324. [PMID: 35882872 PMCID: PMC9325726 DOI: 10.1038/s41467-022-32021-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/13/2022] [Indexed: 11/09/2022] Open
Abstract
Mucinases of human gut bacteria cleave peptide bonds in mucins strictly depending on the presence of neighboring O-glycans. The Akkermansia muciniphila AM0627 mucinase cleaves specifically in between contiguous (bis) O-glycans of defined truncated structures, suggesting that this enzyme may recognize clustered O-glycan patches. Here, we report the structure and molecular mechanism of AM0627 in complex with a glycopeptide containing a bis-T (Galβ1-3GalNAcα1-O-Ser/Thr) O-glycan, revealing that AM0627 recognizes both the sugar moieties and the peptide sequence. AM0627 exhibits preference for bis-T over bis-Tn (GalNAcα1-O-Ser/Thr) O-glycopeptide substrates, with the first GalNAc residue being essential for cleavage. AM0627 follows a mechanism relying on a nucleophilic water molecule and a catalytic base Glu residue. Structural comparison among mucinases identifies a conserved Tyr engaged in sugar-π interactions in both AM0627 and the Bacteroides thetaiotaomicron BT4244 mucinase as responsible for the common activity of these two mucinases with bis-T/Tn substrates. Our work illustrates how mucinases through tremendous flexibility adapt to the diversity in distribution and patterns of O-glycans on mucins. AM0627 is a bis-O-glycan mucinase that might work in the final steps of mucus degradation, thereby providing a carbon and nitrogen source for Akkermansia muciniphila. Here, the authors provide molecular insights into AM0627 function from X-ray crystallography and computer simulations.
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Affiliation(s)
- Víctor Taleb
- Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
| | - Qinghua Liao
- Departament de Química Inorgánica i Orgánica (Secció de Química Orgánica) and Institut de Química Teorica i Computacional (IQTCUB), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ana García-García
- Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
| | - Ismael Compañón
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006, Logroño, Spain
| | - Rafael Junqueira Borges
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, Brazil
| | - Andrés Manuel González-Ramírez
- Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006, Logroño, Spain
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Carme Rovira
- Departament de Química Inorgánica i Orgánica (Secció de Química Orgánica) and Institut de Química Teorica i Computacional (IQTCUB), Universitat de Barcelona, 08028, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avancats (ICREA), 08010, Barcelona, Spain.
| | - Ramon Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain. .,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark. .,Fundación ARAID, 50018, Zaragoza, Spain.
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35
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Griffin ME, Hsieh-Wilson LC. Tools for mammalian glycoscience research. Cell 2022; 185:2657-2677. [PMID: 35809571 PMCID: PMC9339253 DOI: 10.1016/j.cell.2022.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 10/17/2022]
Abstract
Cellular carbohydrates or glycans are critical mediators of biological function. Their remarkably diverse structures and varied activities present exciting opportunities for understanding many areas of biology. In this primer, we discuss key methods and recent breakthrough technologies for identifying, monitoring, and manipulating glycans in mammalian systems.
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Affiliation(s)
- Matthew E. Griffin
- Department of Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Linda C. Hsieh-Wilson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 92115, USA,Correspondence: (L.C.H.W.)
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36
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Noborn F, Nilsson J, Larson G. Site-specific glycosylation of proteoglycans: a revisited frontier in proteoglycan research. Matrix Biol 2022; 111:289-306. [PMID: 35840015 DOI: 10.1016/j.matbio.2022.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/11/2022] [Accepted: 07/11/2022] [Indexed: 11/29/2022]
Abstract
Proteoglycans (PGs), a class of carbohydrate-modified proteins, are present in essentially all metazoan organisms investigated to date. PGs are composed of glycosaminoglycan (GAG) chains attached to various core proteins and are important for embryogenesis and normal homeostasis. PGs exert many of their functions via their GAG chains and understanding the details of GAG-ligand interactions has been an essential part of PG research. Although PGs are also involved in many diseases, the number of GAG-related drugs used in the clinic is yet very limited, indicating a lack of detailed structure-function understanding. Structural analysis of PGs has traditionally been obtained by first separating the GAG chains from the core proteins, after which the two components are analyzed separately. While this strategy greatly facilitates the analysis, it precludes site-specific information and introduces either a "GAG" or a "core protein" perspective on the data interpretation. Mass-spectrometric (MS) glycoproteomic approaches have recently been introduced, providing site-specific information on PGs. Such methods have revealed a previously unknown structural complexity of the GAG linkage regions and resulted in identification of several novel CSPGs and HSPGs in humans and in model organisms, thereby expanding our view on PG complexity. In light of these findings, we discuss here if the use of such MS-based techniques, in combination with various functional assays, can also be used to expand our functional understanding of PGs. We have also summarized the site-specific information of all human PGs known to date, providing a theoretical framework for future studies on site-specific functional analysis of PGs in human pathophysiology.
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Affiliation(s)
- Fredrik Noborn
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Department of Laboratory Medicine, Sundsvall County Hospital, Sweden.
| | - Jonas Nilsson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Proteomics Core Facility, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Göran Larson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
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37
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Ince D, Lucas TM, Malaker SA. Current strategies for characterization of mucin-domain glycoproteins. Curr Opin Chem Biol 2022; 69:102174. [PMID: 35752002 DOI: 10.1016/j.cbpa.2022.102174] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/02/2022] [Accepted: 05/19/2022] [Indexed: 11/18/2022]
Abstract
Glycosylation, and especially O-linked glycosylation, remains a critical blind spot in the understanding of post-translational modifications. Due to their nature as proteins defined by a large density and abundance of O-glycosylation, mucins present extra challenges in the analysis of their structure and function. However, recent breakthroughs in multiple areas of research have rendered mucin-domain glycoproteins more accessible to current characterization techniques. In particular, the adaptation of mucinases to glycoproteomic workflows, the manipulation of cellular glycosylation pathways, and the advances in synthetic methods to more closely mimic mucin domains have introduced new and exciting avenues to study mucin glycoproteins. Here, we summarize recent developments in understanding the structure and biological function of mucin domains and their associated glycans, from glycoproteomic tools and visualization methods to synthetic glycopeptide mimetics.
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Affiliation(s)
- Deniz Ince
- Department of Chemistry, Yale University, 275 Prospect St, New Haven, CT 06511, United States
| | - Taryn M Lucas
- Department of Chemistry, Yale University, 275 Prospect St, New Haven, CT 06511, United States
| | - Stacy A Malaker
- Department of Chemistry, Yale University, 275 Prospect St, New Haven, CT 06511, United States.
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38
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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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39
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Dworkin LA, Clausen H, Joshi HJ. Applying transcriptomics to studyglycosylation at the cell type level. iScience 2022; 25:104419. [PMID: 35663018 PMCID: PMC9156939 DOI: 10.1016/j.isci.2022.104419] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/30/2022] [Accepted: 05/12/2022] [Indexed: 11/22/2022] Open
Abstract
The complex multi-step process of glycosylation occurs in a single cell, yet current analytics generally cannot measure the output (the glycome) of a single cell. Here, we addressed this discordance by investigating how single cell RNA-seq data can be used to characterize the state of the glycosylation machinery and metabolic network in a single cell. The metabolic network involves 214 glycosylation and modification enzymes outlined in our previously built atlas of cellular glycosylation pathways. We studied differential mRNA regulation of enzymes at the organ and single cell level, finding that most of the general protein and lipid oligosaccharide scaffolds are produced by enzymes exhibiting limited transcriptional regulation among cells. We predict key enzymes within different glycosylation pathways to be highly transcriptionally regulated as regulatable hotspots of the cellular glycome. We designed the Glycopacity software that enables investigators to extract and interpret glycosylation information from transcriptome data and define hotspots of regulation. RNA-seq can provide information on the glycosylation metabolic network state It is possible to readout glycosylation capacity from single cell RNA-seq data Genes regulating the biosynthesis of common glycan scaffolds show little regulation Key enzymes in the glycosylation network are predicted to be regulatable hotspots
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Affiliation(s)
- Leo Alexander Dworkin
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Hiren Jitendra Joshi
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
- Corresponding author
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40
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Bensing BA, Stubbs HE, Agarwal R, Yamakawa I, Luong K, Solakyildirim K, Yu H, Hadadianpour A, Castro MA, Fialkowski KP, Morrison KM, Wawrzak Z, Chen X, Lebrilla CB, Baudry J, Smith JC, Sullam PM, Iverson TM. Origins of glycan selectivity in streptococcal Siglec-like adhesins suggest mechanisms of receptor adaptation. Nat Commun 2022; 13:2753. [PMID: 35585145 PMCID: PMC9117288 DOI: 10.1038/s41467-022-30509-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 04/26/2022] [Indexed: 11/22/2022] Open
Abstract
Bacterial binding to host receptors underlies both commensalism and pathogenesis. Many streptococci adhere to protein-attached carbohydrates expressed on cell surfaces using Siglec-like binding regions (SLBRs). The precise glycan repertoire recognized may dictate whether the organism is a strict commensal versus a pathogen. However, it is currently not clear what drives receptor selectivity. Here, we use five representative SLBRs and identify regions of the receptor binding site that are hypervariable in sequence and structure. We show that these regions control the identity of the preferred carbohydrate ligand using chimeragenesis and single amino acid substitutions. We further evaluate how the identity of the preferred ligand affects the interaction with glycoprotein receptors in human saliva and plasma samples. As point mutations can change the preferred human receptor, these studies suggest how streptococci may adapt to changes in the environmental glycan repertoire.
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Affiliation(s)
- Barbara A Bensing
- Division of Infectious Diseases, Veterans Affairs Medical Center, Department of Medicine, University of California, San Francisco, CA, USA
- the Northern California Institute for Research and Education, San Francisco, CA, 94121, USA
| | - Haley E Stubbs
- Graduate Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Rupesh Agarwal
- University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6309, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Izumi Yamakawa
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
- School of Nursing, Belmont University, Nashville, TN, 37212, USA
| | - Kelvin Luong
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Kemal Solakyildirim
- Department of Chemistry, Erzincan Binali Yildirim University, Erzincan, 24100, Turkey
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Hai Yu
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Azadeh Hadadianpour
- Department of Microbiology, Pathology, and Immunology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Manuel A Castro
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Kevin P Fialkowski
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
- College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - KeAndreya M Morrison
- Department of Pharmacology, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN, 37208, USA
| | - Zdzislaw Wawrzak
- LS-CAT Synchrotron Research Center, Northwestern University, Argonne, IL, 60439, USA
| | - Xi Chen
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Jerome Baudry
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Jeremy C Smith
- University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6309, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Paul M Sullam
- Division of Infectious Diseases, Veterans Affairs Medical Center, Department of Medicine, University of California, San Francisco, CA, USA
- the Northern California Institute for Research and Education, San Francisco, CA, 94121, USA
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA.
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA.
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41
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Wei X, Du W, Duca M, Yu G, de Vries E, de Haan CAM, Pieters RJ. Preventing Influenza A Virus Infection by Mixed Inhibition of Neuraminidase and Hemagglutinin by Divalent Inhibitors. J Med Chem 2022; 65:7312-7323. [PMID: 35549211 PMCID: PMC9150099 DOI: 10.1021/acs.jmedchem.2c00319] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Divalent inhibitors
of the neuraminidase enzyme (NA) of the Influenza
A virus were synthesized with vastly different spacers. The spacers
varied from 14 to 56 atoms and were relatively rigid by way of the
building blocks and their connection by CuAAC. As the ligand for these
constructs, a Δ4-β-d-glucoronide was
used, which can be prepared form N-acetyl glucosamine.
This ligand showed good NA inhibitory potency but with room for improvement
by multivalency enhancement. The synthesized compounds showed modest
potency enhancement in NA activity assays but a sizeable potency increase
in a 4-day cytopathic effect assay. The demonstration that the compounds
can also inhibit hemagglutinin in addition to NA may be the cause
of the enhancement.
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Affiliation(s)
- Xuan Wei
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, Utrecht NL-3508 TB, The Netherlands
| | - Wenjuan Du
- Section Virology, Division Infectious Diseases and Immunology, Faculty Veterinary Medicine, Utrecht University, Utrecht NL-3508 TB, The Netherlands
| | - Margherita Duca
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, Utrecht NL-3508 TB, The Netherlands
| | - Guangyun Yu
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, Utrecht NL-3508 TB, The Netherlands
| | - Erik de Vries
- Section Virology, Division Infectious Diseases and Immunology, Faculty Veterinary Medicine, Utrecht University, Utrecht NL-3508 TB, The Netherlands
| | - Cornelis A M de Haan
- Section Virology, Division Infectious Diseases and Immunology, Faculty Veterinary Medicine, Utrecht University, Utrecht NL-3508 TB, The Netherlands
| | - Roland J Pieters
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, Utrecht NL-3508 TB, The Netherlands
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42
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González-Ramírez AM, Grosso AS, Yang Z, Compañón I, Coelho H, Narimatsu Y, Clausen H, Marcelo F, Corzana F, Hurtado-Guerrero R. Structural basis for the synthesis of the core 1 structure by C1GalT1. Nat Commun 2022; 13:2398. [PMID: 35504880 PMCID: PMC9065035 DOI: 10.1038/s41467-022-29833-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/31/2022] [Indexed: 12/18/2022] Open
Abstract
C1GalT1 is an essential inverting glycosyltransferase responsible for synthesizing the core 1 structure, a common precursor for mucin-type O-glycans found in many glycoproteins. To date, the structure of C1GalT1 and the details of substrate recognition and catalysis remain unknown. Through biophysical and cellular studies, including X-ray crystallography of C1GalT1 complexed to a glycopeptide, we report that C1GalT1 is an obligate GT-A fold dimer that follows a SN2 mechanism. The binding of the glycopeptides to the enzyme is mainly driven by the GalNAc moiety while the peptide sequence provides optimal kinetic and binding parameters. Interestingly, to achieve glycosylation, C1GalT1 recognizes a high-energy conformation of the α-GalNAc-Thr linkage, negligibly populated in solution. By imposing this 3D-arrangement on that fragment, characteristic of α-GalNAc-Ser peptides, C1GalT1 ensures broad glycosylation of both acceptor substrates. These findings illustrate a structural and mechanistic blueprint to explain glycosylation of multiple acceptor substrates, extending the repertoire of mechanisms adopted by glycosyltransferases. The glycosyltransferase C1GalT1 directs a key step in protein O-glycosylation important for the expression of the cancer-associated Tn and T antigens. Here, the authors provide molecular insights into the function of C1GalT1 by solving the crystal structure of the Drosophila enzyme-substrate complex.
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Affiliation(s)
- Andrés Manuel González-Ramírez
- Institute of Biocompuation and Physics of Complex Systems, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018, Zaragoza, Spain
| | - Ana Sofia Grosso
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, 2829-516, Caparica, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, 2829-516, Caparica, Portugal
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Ismael Compañón
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006, Logroño, Spain
| | - Helena Coelho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, 2829-516, Caparica, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, 2829-516, Caparica, Portugal
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
| | - Filipa Marcelo
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, 2829-516, Caparica, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, 2829-516, Caparica, Portugal
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006, Logroño, Spain.
| | - Ramon Hurtado-Guerrero
- Institute of Biocompuation and Physics of Complex Systems, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018, Zaragoza, Spain. .,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark. .,Fundación ARAID, 50018, Zaragoza, Spain.
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43
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Yao Y, Kim G, Shafer S, Chen Z, Kubo S, Ji Y, Luo J, Yang W, Perner SP, Kanellopoulou C, Park AY, Jiang P, Li J, Baris S, Aydiner EK, Ertem D, Mulder DJ, Warner N, Griffiths AM, Topf-Olivestone C, Kori M, Werner L, Ouahed J, Field M, Liu C, Schwarz B, Bosio CM, Ganesan S, Song J, Urlaub H, Oellerich T, Malaker SA, Zheng L, Bertozzi CR, Zhang Y, Matthews H, Montgomery W, Shih HY, Jiang J, Jones M, Baras A, Shuldiner A, Gonzaga-Jauregui C, Snapper SB, Muise AM, Shouval DS, Ozen A, Pan KT, Wu C, Lenardo MJ. Mucus sialylation determines intestinal host-commensal homeostasis. Cell 2022; 185:1172-1188.e28. [PMID: 35303419 PMCID: PMC9088855 DOI: 10.1016/j.cell.2022.02.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/18/2021] [Accepted: 02/09/2022] [Indexed: 02/07/2023]
Abstract
Intestinal mucus forms the first line of defense against bacterial invasion while providing nutrition to support microbial symbiosis. How the host controls mucus barrier integrity and commensalism is unclear. We show that terminal sialylation of glycans on intestinal mucus by ST6GALNAC1 (ST6), the dominant sialyltransferase specifically expressed in goblet cells and induced by microbial pathogen-associated molecular patterns, is essential for mucus integrity and protecting against excessive bacterial proteolytic degradation. Glycoproteomic profiling and biochemical analysis of ST6 mutations identified in patients show that decreased sialylation causes defective mucus proteins and congenital inflammatory bowel disease (IBD). Mice harboring a patient ST6 mutation have compromised mucus barriers, dysbiosis, and susceptibility to intestinal inflammation. Based on our understanding of the ST6 regulatory network, we show that treatment with sialylated mucin or a Foxo3 inhibitor can ameliorate IBD.
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Affiliation(s)
- Yikun Yao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, and Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, MD 20892, USA
| | - Girak Kim
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Samantha Shafer
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, and Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zuojia Chen
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Satoshi Kubo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, and Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yanlong Ji
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany; Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Jialie Luo
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Weiming Yang
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD 20892, USA
| | - Sebastian P Perner
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Chrysi Kanellopoulou
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, and Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ann Y Park
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, and Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ping Jiang
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, and Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jian Li
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Safa Baris
- Division of Allergy and Immunology, Department of Pediatrics, School of Medicine, Marmara University, 34722 Istanbul, Turkey; The Isil Berat Barlan Center for Translational Medicine, Marmara University, 34722 Istanbul, Turkey
| | - Elif Karakoc Aydiner
- Division of Allergy and Immunology, Department of Pediatrics, School of Medicine, Marmara University, 34722 Istanbul, Turkey; The Isil Berat Barlan Center for Translational Medicine, Marmara University, 34722 Istanbul, Turkey
| | - Deniz Ertem
- Marmara University School of Medicine, Division of Pediatric Gastroenterology Hepatology and Nutrition, 34854 Istanbul, Turkey
| | - Daniel J Mulder
- Departments of Pediatrics, Medicine, and Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Neil Warner
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Anne M Griffiths
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Chani Topf-Olivestone
- Pediatric Gastroenterology, Kaplan Medical Center, Pasternak St., POB 1, Rehovot 76100, Israel
| | - Michal Kori
- Pediatric Gastroenterology, Kaplan Medical Center, Pasternak St., POB 1, Rehovot 76100, Israel
| | - Lael Werner
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petach Tikva 4920235, Israel
| | - Jodie Ouahed
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Michael Field
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Chengyu Liu
- Transgenic Core Facility, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Benjamin Schwarz
- Immunity to Pulmonary Pathogens Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Catharine M Bosio
- Immunity to Pulmonary Pathogens Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jian Song
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, MD 20892, USA
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Thomas Oellerich
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany; German Cancer Consortium/German Cancer Research Center, 69120 Heidelberg, Germany
| | - Stacy A Malaker
- Yale University, Department of Chemistry, New Haven, CT 06511, USA
| | - Lixin Zheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, and Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Helen Matthews
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Will Montgomery
- Neuro-Immune Regulome Unit, National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Han-Yu Shih
- Neuro-Immune Regulome Unit, National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Marcus Jones
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Aris Baras
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Alan Shuldiner
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Claudia Gonzaga-Jauregui
- Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA; International Laboratory for Human Genome Research, Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro 04510, Mexico
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Aleixo M Muise
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Pediatrics, IMS, and Biochemistry, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Dror S Shouval
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petach Tikva 4920235, Israel
| | - Ahmet Ozen
- The Isil Berat Barlan Center for Translational Medicine, Marmara University, 34722 Istanbul, Turkey; Marmara University School of Medicine, Division of Pediatric Gastroenterology Hepatology and Nutrition, 34854 Istanbul, Turkey
| | - Kuan-Ting Pan
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, and Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, MD 20892, USA.
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44
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Coelho H, Rivas MDL, Grosso AS, Diniz A, Soares CO, Francisco RA, Dias JS, Compañon I, Sun L, Narimatsu Y, Vakhrushev SY, Clausen H, Cabrita EJ, Jiménez-Barbero J, Corzana F, Hurtado-Guerrero R, Marcelo F. Atomic and Specificity Details of Mucin 1 O-Glycosylation Process by Multiple Polypeptide GalNAc-Transferase Isoforms Unveiled by NMR and Molecular Modeling. JACS AU 2022; 2:631-645. [PMID: 35373202 PMCID: PMC8969996 DOI: 10.1021/jacsau.1c00529] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Indexed: 05/10/2023]
Abstract
The large family of polypeptide GalNAc-transferases (GalNAc-Ts) controls with precision how GalNAc O-glycans are added in the tandem repeat regions of mucins (e.g., MUC1). However, the structural features behind the creation of well-defined and clustered patterns of O-glycans in mucins are poorly understood. In this context, herein, we disclose the full process of MUC1 O-glycosylation by GalNAc-T2/T3/T4 isoforms by NMR spectroscopy assisted by molecular modeling protocols. By using MUC1, with four tandem repeat domains as a substrate, we confirmed the glycosylation preferences of different GalNAc-Ts isoforms and highlighted the importance of the lectin domain in the glycosylation site selection after the addition of the first GalNAc residue. In a glycosylated substrate, with yet multiple acceptor sites, the lectin domain contributes to orientate acceptor sites to the catalytic domain. Our experiments suggest that during this process, neighboring tandem repeats are critical for further glycosylation of acceptor sites by GalNAc-T2/T4 in a lectin-assisted manner. Our studies also show local conformational changes in the peptide backbone during incorporation of GalNAc residues, which might explain GalNAc-T2/T3/T4 fine specificities toward the MUC1 substrate. Interestingly, we postulate that a specific salt-bridge and the inverse γ-turn conformation of the PDTRP sequence in MUC1 are the main structural motifs behind the GalNAc-T4 specificity toward this region. In addition, in-cell analysis shows that the GalNAc-T4 isoform is the only isoform glycosylating the Thr of the immunogenic epitope PDTRP in vivo, which highlights the relevance of GalNAc-T4 in the glycosylation of this epitope. Finally, the NMR methodology established herein can be extended to other glycosyltransferases, such as C1GalT1 and ST6GalNAc-I, to determine the specificity toward complex mucin acceptor substrates.
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Affiliation(s)
- Helena Coelho
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- CIC
bioGUNE, Basque Research and Technology
Alliance (BRTA), Bizkaia
Technology Park, Building 801A, 48170 Derio, Spain
- Department
of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, Leioa 48940, Bizkaia, Spain
| | - Matilde de las Rivas
- Institute
for Biocomputation and Physics of Complex Systems (BIFI), Laboratorio
de Microscopias Avanzadas (LMA), University
of Zaragoza, Mariano
Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain
| | - Ana S. Grosso
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Diniz
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Cátia O. Soares
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Rodrigo A. Francisco
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Jorge S. Dias
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ismael Compañon
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, E-26006 Logroño, Spain
| | - Lingbo Sun
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Yoshiki Narimatsu
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Sergey Y. Vakhrushev
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Henrik Clausen
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Eurico J. Cabrita
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Basque Research and Technology
Alliance (BRTA), Bizkaia
Technology Park, Building 801A, 48170 Derio, Spain
- Department
of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, Leioa 48940, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain
- Centro de Investigacion
Biomedica En Red de Enfermedades Respiratorias, 28029 Madrid, Spain
| | - Francisco Corzana
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, E-26006 Logroño, Spain
| | - Ramon Hurtado-Guerrero
- Institute
for Biocomputation and Physics of Complex Systems (BIFI), Laboratorio
de Microscopias Avanzadas (LMA), University
of Zaragoza, Mariano
Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
- Fundación
ARAID, 50018 Zaragoza, Spain
| | - Filipa Marcelo
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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45
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de Haan N, Narimatsu Y, Koed Møller Aasted M, Larsen ISB, Marinova IN, Dabelsteen S, Vakhrushev SY, Wandall HH. In-Depth Profiling of O-Glycan Isomers in Human Cells Using C18 Nanoliquid Chromatography-Mass Spectrometry and Glycogenomics. Anal Chem 2022; 94:4343-4351. [PMID: 35245040 PMCID: PMC8928149 DOI: 10.1021/acs.analchem.1c05068] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
O-Glycosylation is an omnipresent modification
of the human proteome affecting many cellular functions, including
protein cleavage, protein folding, and cellular signaling, interactions,
and trafficking. The functions are governed by differentially regulated O-glycan types and terminal structures. It is therefore
essential to develop analytical methods that facilitate the annotation
of O-glycans in biological material. While various
successful strategies for the in-depth profiling of released O-glycans have been reported, these methods are often limitedly
accessible to the nonspecialist or challenged by the high abundance
of O-glycan structural isomers. Here, we developed
a high-throughput sample preparation approach for the nonreductive
release and characterization of O-glycans from human
cell material. Reducing-end labeling allowed efficient isomer separation
and detection using C18 nanoliquid chromatography coupled to Orbitrap
mass spectrometry. Using the method in combination with a library
of genetically glycoengineered cells displaying defined O-glycan types and structures, we were able to annotate individual O-glycan structural isomers from a complex mixture. Applying
the method in a model system of human keratinocytes, we found a wide
variety of O-glycan structures, including O-fucose, O-glucose, O-GlcNAc, and O-GalNAc glycosylation, with the latter
carrying both elongated core1 and core2 structures and varying numbers
of fucoses and sialic acids. The method, including the now well-characterized
standards, provides the opportunity to study glycomic changes in human
tissue and disease models using rather mainstream analytical equipment.
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Affiliation(s)
- Noortje de Haan
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | | | - Ida S B Larsen
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Irina N Marinova
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Sally Dabelsteen
- Department of Odontology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
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46
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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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47
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Critcher M, Hassan AA, Huang ML. Seeing the forest through the trees: characterizing the glycoproteome. Trends Biochem Sci 2022; 47:492-505. [DOI: 10.1016/j.tibs.2022.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 12/14/2022]
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48
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Lundstrøm J, Bojar D. Structural insights into host-microbe glycointeractions. Curr Opin Struct Biol 2022; 73:102337. [PMID: 35182928 DOI: 10.1016/j.sbi.2022.102337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/30/2021] [Accepted: 01/14/2022] [Indexed: 11/03/2022]
Abstract
Despite their ubiquitous presence in biological systems, glycans have historically received less attention than they deserved. Investigations in recent years have featured important findings about the role of glycans in regulating the human gut microbiota. Here, we present a brief overview of current trends that shape future directions of computational and experimental research approaches and add to our understanding of host-microbe glycointeractions.
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Affiliation(s)
- Jon Lundstrøm
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden. https://twitter.com/jonlundstrm
| | - Daniel Bojar
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.
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Klamer ZL, Harris CM, Beirne JM, Kelly JE, Zhang J, Haab BB. OUP accepted manuscript. Glycobiology 2022; 32:679-690. [PMID: 35352123 PMCID: PMC9280547 DOI: 10.1093/glycob/cwac022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 11/12/2022] Open
Abstract
Glycan arrays continue to be the primary resource for determining the glycan-binding specificity of proteins. The volume and diversity of glycan-array data are increasing, but no common method and resource exist to analyze, integrate, and use the available data. To meet this need, we developed a resource of analyzed glycan-array data called CarboGrove. Using the ability to process and interpret data from any type of glycan array, we populated the database with the results from 35 types of glycan arrays, 13 glycan families, 5 experimental methods, and 19 laboratories or companies. In meta-analyses of glycan-binding proteins, we observed glycan-binding specificities that were not uncovered from single sources. In addition, we confirmed the ability to efficiently optimize selections of glycan-binding proteins to be used in experiments for discriminating between closely related motifs. Through descriptive reports and a programmatically accessible Application Programming Interface, CarboGrove yields unprecedented access to the wealth of glycan-array data being produced and powerful capabilities for both experimentalists and bioinformaticians.
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Affiliation(s)
- Zachary L Klamer
- Department of Cancer and Cell Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, United States
| | | | | | | | | | - Brian B Haab
- Corresponding author: Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49504, United States.
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50
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Sun L, Konstantinidi A, Ye Z, Nason R, Zhang Y, Büll C, Kahl-Knutson B, Hansen L, Leffler H, Vakhrushev SY, Yang Z, Clausen H, Narimatsu Y. Installation of O-glycan sulfation capacities in human HEK293 cells for display of sulfated mucins. J Biol Chem 2021; 298:101382. [PMID: 34954141 PMCID: PMC8789585 DOI: 10.1016/j.jbc.2021.101382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 11/25/2022] Open
Abstract
The human genome contains at least 35 genes that encode Golgi sulfotransferases that function in the secretory pathway, where they are involved in decorating glycosaminoglycans, glycolipids, and glycoproteins with sulfate groups. Although a number of important interactions by proteins such as selectins, galectins, and sialic acid–binding immunoglobulin-like lectins are thought to mainly rely on sulfated O-glycans, our insight into the sulfotransferases that modify these glycoproteins, and in particular GalNAc-type O-glycoproteins, is limited. Moreover, sulfated mucins appear to accumulate in respiratory diseases, arthritis, and cancer. To explore further the genetic and biosynthetic regulation of sulfated O-glycans, here we expanded a cell-based glycan array in the human embryonic kidney 293 (HEK293) cell line with sulfation capacities. We stably engineered O-glycan sulfation capacities in HEK293 cells by site-directed knockin of sulfotransferase genes in combination with knockout of genes to eliminate endogenous O-glycan branching (core2 synthase gene GCNT1) and/or sialylation capacities in order to provide simplified substrates (core1 Galβ1–3GalNAcα1–O-Ser/Thr) for the introduced sulfotransferases. Expression of the galactose 3-O-sulfotransferase 2 in HEK293 cells resulted in sulfation of core1 and core2 O-glycans, whereas expression of galactose 3-O-sulfotransferase 4 resulted in sulfation of core1 only. We used the engineered cell library to dissect the binding specificity of galectin-4 and confirmed binding to the 3-O-sulfo-core1 O-glycan. This is a first step toward expanding the emerging cell-based glycan arrays with the important sulfation modification for display and production of glycoconjugates with sulfated O-glycans.
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Affiliation(s)
- Lingbo Sun
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; Medical College of Yan'an University, Yan'an University, Yan'an, 716000, Shaanxi Province, China
| | - Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Rebecca Nason
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Yuecheng Zhang
- Department of Biomedical Sciences, Faculty of Health and Society, Malmö University, Jan Waldenströms gata 25, 205 06 Malmö, Sweden
| | - Christian Büll
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Barbro Kahl-Knutson
- Department of Laboratory Medicine, Section MIG, Lund University BMC-C1228b, Klinikgatan28, 221 84 Lund, Sweden
| | - Lars Hansen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Hakon Leffler
- Department of Laboratory Medicine, Section MIG, Lund University BMC-C1228b, Klinikgatan28, 221 84 Lund, Sweden
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Zhang Yang
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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