Glycoproteomics

Nature Reviews Methods Primers, Journal Year: 2022, Volume and Issue: 2(1)

Published: June 23, 2022

Language: Английский

---

Mucus sialylation determines intestinal host-commensal homeostasis

Cell, Journal Year: 2022, Volume and Issue: 185(7), P. 1172 - 1188.e28

Published: March 1, 2022

Language: Английский

---

Probing the binding specificities of human Siglecs by cell-based glycan arrays

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(17)

Published: April 23, 2021

Significance Siglecs are immunomodulatory receptors that recognize sialic acid–carrying glycans with important functions in immunity. However, many of their natural ligands poorly defined. We generated a cell-based glycan array comprised library isogenic human cells displaying the greater complexity acids on diverse structures and glycoconjugates context cell surface. applied this to reveal fine binding specificities for sialoglycans, informed underlying required glycosyltransferase genes, provided evidence selective by presentation distinct protein sequences. Insight into will advance understanding biological benefit therapeutic targeting autoimmunity, inflammation, cancer, Alzheimer’s disease.

Language: Английский

---

Revealing the human mucinome

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: June 20, 2022

Abstract Mucin domains are densely O-glycosylated modular protein found in various extracellular and transmembrane proteins. Mucin-domain glycoproteins play important roles many human diseases, such as cancer cystic fibrosis, but the scope of mucinome remains poorly defined. Recently, we characterized a bacterial O-glycoprotease, StcE, demonstrated that an inactive point mutant retains binding selectivity for mucin-domain glycoproteins. In this work, leverage StcE to selectively enrich identify from complex samples like cell lysate crude ovarian patient ascites fluid. Our enrichment strategy is further aided by algorithm assign confidence glycoprotein identifications. This mucinomics platform facilitates detection hundreds glycopeptides mucin highly overlapping populations patients. Ultimately, demonstrate our approach can reveal key molecular signatures vitro ex vivo sources.

Language: Английский

---

Design of a mucin-selective protease for targeted degradation of cancer-associated mucins

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 42(4), P. 597 - 607

Published: Aug. 3, 2023

Targeted protein degradation is an emerging strategy for the elimination of classically undruggable proteins. Here, to expand landscape targetable substrates, we designed degraders that achieve substrate selectivity via recognition a discrete peptide and glycan motif cell-type antigen-driven cell-surface binding. We applied this approach mucins, O-glycosylated proteins drive cancer progression through biophysical immunological mechanisms. Engineering bacterial mucin-selective protease yielded variant fusion antigen-binding nanobody. The resulting conjugate selectively degraded mucins on cells, promoted cell death in culture models mucin-driven growth survival, reduced tumor mouse breast progression. This work establishes blueprint development biologics degrade specific glycoforms target cells.

Language: Английский

---

Direct observation of glycans bonded to proteins and lipids at the single-molecule level

Science, Journal Year: 2023, Volume and Issue: 382(6667), P. 219 - 223

Published: Oct. 12, 2023

Proteins and lipids decorated with glycans are found throughout biological entities, playing roles in functions 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 structures attached at individual sites given molecule, especially glycoproteins. We show single-molecule analysis glycoconjugates by direct imaging glycoconjugate molecules using low-temperature scanning tunneling microscopy. Intact ions from electrospray soft-landed surface their imaging. The submolecular resolution corroborated quantum mechanical modeling unveils whole attachment glycopeptides, glycolipids, N-glycoproteins, O-glycoproteins densely glycans.

Language: Английский

---

Sialic acid O-acetylation: From biosynthesis to roles in health and disease

Journal of Biological Chemistry, Journal Year: 2021, Volume and Issue: 297(2), P. 100906 - 100906

Published: June 19, 2021

Sialic acids are nine-carbon sugars that frequently cap glycans at the cell surface in cells of vertebrates as well certain types invertebrates and bacteria. The backbone sialic can undergo extensive enzymatic modification nature O-acetylation C-4/7/8/9 position particular is widely observed. In recent years, detection analysis O-acetylated have advanced, acid-specific O-acetyltransferases (SOATs) O-acetylesterases (SIAEs) add remove O-acetyl groups, respectively, been identified characterized mammalian cells, invertebrates, bacteria, viruses. These advances now allow us to draw a more complete picture biosynthetic pathway diverse drive generation genetically biochemically engineered model lines organisms with altered expression for dissection their roles glycoprotein stability, development, immune recognition, discovery novel functions. Furthermore, growing number studies associate acid cancer, autoimmunity, infection, providing rationale development selective probes inhibitors SOATs SIAEs. Here, we discuss current insights into biosynthesis biological functions review evidence linking this disease. emerging strategies design, synthesis, potential application unnatural SIAEs may enable therapeutic targeting versatile modification. Sugars serve essential molecular building blocks assemble complex numerous (1Marth J.D. A unified vision life.Nat. Cell Biol. 2008; 10: 1015-1016Crossref PubMed Scopus (0) Google Scholar). Virtually every produces glycans; short, long, linear, branched structures composed different sugar molecules attached membrane secreted glycoproteins glycolipids. vast collection produced by or tissue referred “the glycome” (2Schjoldager K.T. Narimatsu Y. Joshi H.J. Clausen H. Global view human protein glycosylation pathways functions.Nat. Rev. Mol. 2020; 21: 729-749Crossref (59) vertebrate assembled inside endoplasmic reticulum, Golgi system, nucleus, cytoplasm, mitochondria where over 200 glycosyltransferase enzymes build glycome Scholar, 3Narimatsu Nason R. Van Coillie J. Karlsson Sun L. Ye Z. Chen Y.H. Schjoldager Steentoft C. Furukawa S. Bensing B.A. Sullam P.M. Thompson A.J. Paulson J.C. et al.An Atlas enables display gene cells.Mol. Cell. 2019; 75: 394-407Abstract Full Text PDF (65) regulates multitude processes, such functional biochemical properties proteins lipids, cellular adhesion, communication, recognition events (4Varki A. Biological glycans.Glycobiology. 2017; 27: 3-49Crossref (784) Important determinants (Sias) reside terminal some pathogens. family comprises >80 naturally occurring members related nonulosonic acids, α-keto found (5Varki Schnaar R.L. Schauer other acids.in: Essentials Glycobiology. 3rd Ed. Cold Spring Harbor Laboratory, Harbor, NY2015: 179-195Google 6Schauer Kamerling J.P. Exploration world.Adv. Carbohydr. Chem. Biochem. 2018; 1-213Crossref (67) 7Angata T. Varki Chemical diversity alpha-keto acids: An evolutionary perspective.Chem. 2002; 102: 439-469Crossref (974) Regarding large diversity, assembly acid-carrying (sialoglycans) forms subclass within glycome—the sialome (8Cohen M. sialome--far than sum its parts.OMICS. 2010; 14: 455-464Crossref include protection from proteases (9Aquino D. Wong Margolis R.U. R.K. residues inhibit proteolytic degradation dopamine beta-hydroxylase.FEBS Lett. 1980; 112: 195-198Crossref 10Gorog P. Pearson moieties on protect endothelial damage.J. Pathol. 1985; 146: 205-212Crossref Scholar); regulation serum half-life erythrocytes cleared liver upon desialylation (11Morell A.G. Gregoriadis G. Scheinberg I.H. Hickman Ashwell role determining survival circulation.J. 1971; 246: 1461-1467Abstract 12Sorensen A.L. Rumjantseva V. Nayeb-Hashemi Hartwig J.H. Wandall H.H. Hoffmeister K.M. Role platelet life span: Exposure beta-galactose results rapid clearance platelets circulation asialoglycoprotein receptor-expressing macrophages hepatocytes.Blood. 2009; 114: 1645-1654Crossref (137) 13Yang W.H. Aziz P.V. Heithoff D.M. Mahan M.J. Smith J.W. Marth intrinsic mechanism aging turnover.Proc. Natl. Acad. Sci. U. 2015; 13657-13662Crossref (60) likely formation blood vessel lumen (14Strilic B. Eglinger Krieg Zeeb Axnick Babal Muller D.J. Lammert E. Electrostatic cell-surface repulsion initiates developing vessels.Curr. 20: 2003-2009Abstract (89) sialoglycans sialyl Lewisx contribute trafficking via binding selectins endothelium (15McEver R.P. Moore K.L. Cummings R.D. Leukocyte mediated selectin-carbohydrate interactions.J. 1995; 270: 11025-11028Abstract (574) Scholar), they form ligands immunomodulatory Siglec receptors set threshold activation (16Macauley M.S. Crocker P.R. Siglec-mediated function disease.Nat. Immunol. 2014; 653-666Crossref (466) 17Büll Heise Adema G.J. Boltje T.J. mimetics target acid-siglec Axis.Trends 2016; 41: 519-531Abstract (70) also sites pathogens be utilized microorganisms mimicry (18Heise Langereis Rossing de Jonge M.I. Büll Selective inhibition acid-based Haemophilus influenzae abrogates resistance.Cell 25: 1279-1285.e1278Abstract (3) 19Stencel-Baerenwald J.E. Reiss K. Reiter Stehle Dermody T.S. sweet spot: Defining virus-sialic interactions.Nat. Microbiol. 12: 739-749Crossref (168) aberrant sialoglycan associated tumor growth, evasion, metastasis (20Büll Stoel M.A. den Brok M.H. sweeten tumor's life.Cancer Res. 74: 3199-3204Crossref (220) 21van Wall Santegoets K.C.M. van Houtum E.J.H. Sialoglycans Siglecs shape microenvironment.Trends 274-285Abstract (27) 22Pearce O.M. Laubli cancer biology immunity.Glycobiology. 26: 111-128Crossref (192) versatility reflected structural arises natural modifications (Fig. 1A) linkages (α2-3/6/8) underlying glycoconjugates (N-/O-glycans, glycolipids). most prevalent derivative humans N-acetylneuraminic (Neu5Ac), notable derivatives 2-keto-3-deoxynononic (KDN) N-glycolylneuraminic (Neu5Gc) Interestingly, lost ability biosynthesize Neu5Gc due mutation CMP-Neu5Ac hydroxylase (CMAH) (23Chou Takematsu Diaz Iber Nickerson Wright Muchmore E.A. Nelson D.L. Warren S.T. CMP-sialic occurred after Homo-Pan divergence.Proc. 1998; 95: 11751-11756Crossref (411) however, scavenged exogenous, dietary sources, low amounts incorporated (24Tangvoranuntakul Gagneux Bardor N. Human uptake incorporation an immunogenic nonhuman acid.Proc. 2003; 100: 12045-12050Crossref (434) Further any hydroxyl amine groups result distinct known date (6Schauer Analysis these samples challenging, often not fully understood. Presumably, Sia race between host exploit infection. line Red Queen hypothesis, concept which species must constantly adapt survive competition evolving pathogens, evolved abrogate pathogen interactions while preserving overall endogenous (25Varki Nothing glycobiology makes sense, except light evolution.Cell. 2006; 126: 841-845Abstract (180) Moreover, additional regulatory informational cues advantageous host. common addition one esters yielding about 20 O-Ac-Sias (26Mandal Schwartz-Albiez Vlasak Functions acids.Top. Curr. 366: 1-30PubMed Due identification viruses, many aspects regarding disease recently uncovered, anticipate pace will continue. understanding health implications applications inhibitors. Soon Blix Klenk (27Blix Über die Kohlenhydratgruppen des Submaxillarismucins.Z. Physiol. 1936; 240: 43-54Crossref 28Klenk Neuraminsäure, das Spaltprodukt eines neuen Gehirnlipoids.Z. 1941; 268: 50-58Crossref presence was noted, among others, succeeded verification using mass spectrometry 29Kamerling Vliegenthart J.F. Identification O-cetylated N-acylneuraminic spectrometry.Carbohydr. 1975; 7-17Crossref occur C-4, C-7, C-8, C-9 1A). denoted exemplified Neu5Ac (which carries N-acetyl group C-5) Neu4,5Ac2, Neu5,7Ac2, Neu5,8Ac2, Neu5,9Ac2, respectively (30Varki Aebi Packer N.H. Seeberger P.H. Esko Stanley Hart Darvill Kinoshita Prestegard J.J. Freeze Bertozzi C.R. al.Symbol nomenclature graphical representations 1323-1324Crossref (448) simultaneously multiple positions, giving rise di- tri-O-acetylated Sias Neu5,7,9Ac3 Neu5,7,8,9Ac4, respectively. overview provided Varki, Schauer, Kamerling, who made seminal contributions 31Varki Roland (1936-2019): tribute “Mr. acid”.Glycobiology. 30: 132-133Crossref static, spontaneous migration glycerol chain occur, but C-4 (32Kamerling Shukla A.K. Stoll Halbeek Migration N,O-acetylneuraminic acids.Eur. 1987; 162: 601-607Crossref At neutral slightly basic pH, bidirectional along tail observed 33Ji Sasmal Li W. Oh Srivastava Hargett A.A. Wasik B.R. Yu Choudhury Parrish Freedberg D.I. Wang L.P. X. Reversible side influence recognition.ACS 2021; https://doi.org/10.1021/acschembio.0c00998Crossref (1) addition, di-O-acetyl-Sia Neu5,8,9Ac3 has indicated 34Varki release purification glycoconjugates: Methods minimize loss groups.Anal. 1984; 137: 236-247Crossref proceeds intramolecularly through orthoester intermediates, mainly takes place mild pH it stabilizes mildly acidic <5 Recent sample preparation O-Ac-Sia provide opportunity address process acetyl (35Wu Zhang Q. Liu Zheng Characterization MALDI-MS combination methylamidation permethylation.Sci. Rep. 7: 46206Crossref (10) 36Khedri Xiao Landig C.S. chemical solution problems studying biologically important unstable 9-O-acetyl acids.ACS 214-224Crossref 37Li Battistel M.D. Reeves combined NMR, MD DFT conformational acid-containing GM3 ganglioside glycan 9-N-acetyl mimic.Glycobiology. 787-801Crossref starts novo cytoplasm several steps derived exogenous sources (e.g., dietary) (38Freeze G.W. Glycosylation precursors.in: 51-63Google 39Moons S.J. Derks M.T. glycoengineering N-acetylmannosamine analogs.Glycobiology. 29: 433-445PubMed activated nucleus conjugation cytidine 5′-monophosphate (CMP) transported system sialyltransferase isoenzymes use donor incorporate glycosidic 40Harduin-Lepers Vallejo-Ruiz Krzewinski-Recchi Samyn-Petit Julien Delannoy family.Biochimie. 2001; 83: 727-737Crossref (402) involves activity esterases Scholar) 1B). So far, single SOAT (CASD1, capsule structure1 domain containing 1) (41Arming Wipfler Mayr Merling Vilas Cas1 protein: O-acetyltransferase?.Glycobiology. 2011; 553-564Crossref (40) 42Baumann A.M. Bakkers Buettner F.F. Hartmann Grove Groot R.J. Muhlenhoff 9-O-Acetylation catalysed CASD1 covalent acetyl-enzyme intermediate.Nat. Commun. 6: 7673Crossref sialic-acid-specific esterase (SIAE) (43Guimaraes Bazan Castagnola Copeland N.G. Gilbert Jenkins N.A. Zlotnik Molecular cloning characterization lysosomal O-acetylesterase.J. 1996; 271: 13697-13705Abstract 44Orizio F. Damiati Giacopuzzi Benaglia Pianta Borsani Bresciani Monti esterase: Towards better puzzling enzyme.Glycobiology. 992-1006Crossref (8) 45Takematsu Stoddart Lysosomal cytosolic 9-O-acetylesterase activities Be encoded differential usage signal peptide-encoding exon N terminus.J. 1999; 274: 25623-25631Abstract (31) 46Stoddart Paige C.J. cDNA encoding murine RNA hematopoietic non-hematopoietic origin.Nucleic Acids 24: 4003-4008Crossref 47Butor Higa Structural, immunological, O-acetylesterase rat liver.J. 1993; 10207-10213Abstract (Table 1). Especially remained challenging decades lability intact enzyme during (48Butor High level N-linked oligosaccharides membranes. Differential subcellular distribution 7- involved regulation.J. 10197-10206Abstract 49Lrhorfi L.A. Srinivasan G.V. Properties partial sialate-O-acetyltransferase bovine submandibular glands.Biol. 2007; 388: 297-306Crossref 50Ogura Nara Watanabe Kohno Tai Sanai Cloning GD3 ganglioside.Biochem. Biophys. 225: 932-938Crossref 51Kanamori Nakayama Fukuda M.N. Stallcup W.B. Sasaki Hirabayashi Expression required ganglioside: putative acetyl-CoA transporter.Proc. 1997; 94: 2897-2902Crossref 52Shi W.X. Chammas Induction 9-O-acetylation products: Implications O-acetyltransferases.Glycobiology. 8: 199-205Crossref Eventually, SIAE cloned 1996 whereas 2011 data mining genome acetyltransferase genes unknown 2015 (42Baumann Scholar).Table 1Occurrence microorganismsSpeciesO-Ac-Sia formSOATSIAEO-Ac-Sia GBPReferencesHomo sapiensDiverse 1C)CASD1SIAEnd(41Arming 43Guimaraes Scholar)Campylobacter jejuniNeu5,9Ac2 (α2-8-linked)aCapsular O-Ac-Sia.Orf11ndnd(190Houliston R.S. Endtz H.P. Yuki Jarrell H.C. Koga Belkum Karwaski M.F. Wakarchuk W.W. sialate O-acetyltransferase Campylobacter jejuni: Demonstration direct transfer terminalalpha-2, 8-linked acid.J. 281: 11480-11486Abstract Scholar)Escherichia coli K1Neu5,7/9Ac2 (α2-3/8-linked)aCapsular O-Ac-Sia.NeuO NeuDNeuAnd(194Higa Acetyl-coenzyme A:polysialic K1-positive Escherichia coli. responsible plus phenotype variation.J. 1988; 263: 8872-8878Abstract 195Deszo E.L. Steenbergen S.M. Vimr E.R. K1 polysialic gene, neuO, variation involving mobile contingency locus.Proc. 2005; 5564-5569Crossref 196Schulz E.C. Bergfeld Ficner Crystal structure specific NeuO.PLoS One. 6e17403Crossref (11) 197Bergfeld Claus Vogel Mühlenhoff Biochemical thepolysialic NeuO K1.J. 282: 22217-22227Abstract 198Steenbergen Lee Y.C. Vann W.F. Vionnet L.F. Separate O acetylation polymeric monomeric Bacteriol. 188: 6195-6206Crossref (51) Scholar)Enterohemorrhagic (EHEC)Neu5,9Ac2NANanS NanS-pnd(167Feuerbaum Saile Pohlentz Muthing Schmidt De-O-Acetylation mucin-derived recombinant NanS-p O157:H7 strain EDL933.Int. Med. 308: 1113-1120Crossref (5) 168Saile Schwarz Eissenberger Klumpp Fricke F.W. Growth advantage O104:H4 strains 5-N-acetyl-9-O-acetyl neuraminic carbon source dependent heterogeneous phage-Borne nanS-p esterases.Int. 459-468Crossref (6) 169Rangara

Language: Английский

---

Siglec Signaling in the Tumor Microenvironment

Frontiers in Immunology, Journal Year: 2021, Volume and Issue: 12

Published: Dec. 13, 2021

Sialic acid-binding immunoglobulin-like lectins (Siglecs) are a family of receptors that recognize sialoglycans – sialic acid containing glycans abundantly present on cell membranes. Siglecs expressed most immune cells and can modulate their activity function. The majority contains inhibitory motifs comparable to the checkpoint receptor PD-1. In tumor microenvironment (TME), signaling through Siglec-sialoglycan axis appears be enhanced multiple mechanisms favoring evasion similar PD-1/PD-L1 pathway. Siglec expression tumor-infiltrating increased in suppressive microenvironment. At same time, ligand has been reported for several types as result aberrant glycosylation, glycan modifications, proteins lipids. identified important regulator anti-tumor immunity TME, but key factors contributing activation by tumor-associated diverse poorly defined. Among others, co-determined levels, surface distribution, binding preferences cis- trans -ligands TME. preference nature proteins/lipids which attached multivalency interaction. Here, we review current understanding emerging conditions involved TME identify knowledge gaps exist field.

Language: Английский

---

Tools for mammalian glycoscience research

Cell, Journal Year: 2022, Volume and Issue: 185(15), P. 2657 - 2677

Published: July 1, 2022

Language: Английский

---

Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Oct. 4, 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 mucin-domain containing family proteins (TIM-1, -3, -4) decorate immune cells act as key regulators cellular immunity. However, their dense O-glycosylation remains enigmatic, primarily due to challenges associated with studying mucin domains. Here, we demonstrate that mucinase SmE has unique ability cleave at residues bearing very complex glycans. enables improved mass spectrometric analysis several mucins, including entire TIM family. With this information in-hand, perform molecular dynamics (MD) simulations TIM-3 -4 understand how glycosylation affects structural features these proteins. Finally, use models investigate functional relevance for function ligand binding. Overall, present powerful workflow better detailed structures functions mucinome.

Language: Английский

---