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Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications 2021

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (28 February 2022) | Viewed by 32400

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Special Issue Editor

Dr. Alexander O. Chizhov

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Guest Editor

N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky pr. 47, 119991 Moscow, Russia
Interests: carbohydrate analysis; carbohydrate structure; glycoconjugates; mass spectrometry; electrospray ionization; MALDI; fragmentation of ions; activation of ions; sample preparation
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Special Issue Information

Dear Colleagues,

The study of carbohydrates has a long history, spanning across two centuries, during which research paved the way from “sweet matter” to glycomics. The complexity of cabohydrates under such studies grew enormously: The term “complex carbohydrates” includes large oligosaccharides (dozens of carbohydrate units) and polysaccharides, both regular and irregular. Carbohydrate studies were inevitably expanded to adjacent areas, which is reflected by the general term “glycoconjugate” (a compound, in which molecule carbohydrate part(s) is/are covalently bonded with noncarbohydrate part(s)).

At present, carbohydrate science is an integral part of molecular biology along with genomics and proteomics. It includes structural studies of glycans, glycoproteins, proteoglycans, glycolipids, and low-molecular and complex glycosides of plant, animal, fungal, and bacterial origin. Supramolecular structural studies such as cell wall reconstruction are developed. The functional studies of carbohydrates concern molecular recognition such as carbohydrate–lectin or glycoside–enzyme interactions, cell recognition (normal and in pathologies), viral adhesion/penetration, oligo- and polysaccharide biosynthesis, and many other phenomena. In such studies, artificial carbohydrate-containing molecular probes (synthetic glycoconjugates) are widely used now.

Structural and functional studies are extremely stimulated by the progress of instrumental methods, especially in chromatography, electrophoresis, multidimensional NMR spectrometry, high-resolution mass spectrometry, and surface plasmon resonance (SPR). There is no modern carbohydrate analysis without hyphenated techniques, such as HPLC-MS.

This Special Issue welcomes the submission of original research papers or comprehensive reviews that demonstrate or summarize significant advances in the field of carbohydrate chemistry and biochemistry. The papers may be devoted to targeted synthesis of complex carbohydrates and glycoconjugates, isolation and structure determination of complex carbohydrates and glycoconjugates, and elucidation of their biological activities. Papers concerning development of applications of instrumental methods in carbohydrate chemistry and biology are also welcome in this Special Issue. Critical reviews and discussion papers revealing problems and drawing future perspectives of the carbohydrate science are especially invited (though we are not looking for papers with a far too general focus). Nontargeted syntheses and manuscripts without chemical structures will not be considered. All molecular structures must be firmly established. Clinical trials and animal and cell testings are not suitable for this Special Issue if they are not strongly needed to support hypotheses or theories concerning structure–function correlations.

Dr. Alexander O. Chizhov
Guest Editor

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

Complex carbohydrates
Glycoconjugates
Structure
Oligosaccharides
Polysaccharides
Glycomics
Carbohydrate analysis
Carbohydrate synthesis
Glycoside bond
Glycoproteins
Proteoglycans
Molecular recognition
Lectin
Cell wall
Cell surface
Molecular probe
Biosynthesis of complex carbohydrates
High-resolution mass spectrometry
Nuclear magnetic resonance
Chromatography
Capillary electrophoresis

Published Papers (13 papers)

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Research

Jump to: Review

10 pages, 1651 KiB

Open AccessArticle

Analysis of ¹⁶O/¹⁸O and H/D Exchange Reactions between Carbohydrates and Heavy Water Using High-Resolution Mass Spectrometry

by Lidiia Rumiantseva, Sergey Osipenko, Artem Zharikov, Albert Kireev, Evgeny N. Nikolaev and Yury Kostyukevich

Int. J. Mol. Sci. 2022, 23(7), 3585; https://doi.org/10.3390/ijms23073585 - 25 Mar 2022

Cited by 4 | Viewed by 2267

Abstract

Mono- and polysaccharides are an essential part of every biological system. Identifying underivatized carbohydrates using mass spectrometry is still a challenge because carbohydrates have a low capacity for ionization. Normally, the intensities of protonated carbohydrates are relatively low, and in order to increase the corresponding peak height, researchers add Na⁺, K⁺, or NH₄⁺to the solution. However, the fragmentation spectra of the corresponding ions are very poor. Based on this, reliably identifying carbohydrates in complex natural and biological objects can benefit frommeasuring additional molecular descriptors, especially those directly connected to the molecular structure. Previously, we reported that the application of the isotope exchange approach (H/D and ¹⁶O/¹⁸O) to high-resolution mass spectrometry can increase the reliability of identifying drug-like compounds. Carbohydrates possess many –OH and –COOH groups, making it reasonable to expect that the isotope exchange approach would have considerable potential for detecting carbohydrates. Here, we used a collection of standard carbohydrates to investigate the isotope exchange reaction (H/D and ¹⁶O/¹⁸O) in carbohydrates and estimate its analytical applications. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications 2021)

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17 pages, 2827 KiB

Open AccessArticle

New Insights into the Structure of Kappa/Beta-Carrageenan: A Novel Potential Inhibitor of HIV-1

by Irina Yermak, Stanislav Anastyuk, Anna Kravchenko, William Helbert, Valery Glazunov, Andrey Shulgin, Pavel Spirin and Vladimir Prassolov

Int. J. Mol. Sci. 2021, 22(23), 12905; https://doi.org/10.3390/ijms222312905 - 29 Nov 2021

Cited by 9 | Viewed by 2668

Abstract

New insights into the structure of the hybrid κ/β-carrageenan (κ/β-CRG) of the red alga Tichocarpus crinitus have been obtained. Carrageenan oligosaccharides were prepared through the chemical and enzymatic depolymerization of κ/β-CRG with κ-carrageenase and its the enzyme-resistant fraction. The composition and distribution of the repetition units of κ/β- CRG were investigated by using the negative ion tandem MALDI-TOFMS and ESIMS method, which made it possible to prove and characterize the hybrid structure of this polysaccharide. An analysis revealed the blockwise distribution of the long β-blocks along the polysaccharide chain, with the inclusion of κ/β, μ/ν-blocks and some ι-blocks. Furthermore, the desulfated κ/β-CRG was shown to contain of –G–D– repeating units up to 3.5 kDa. Previous studies have demonstrated that CRGs suppress the replication of several viruses. Here, we established that κ/β-CRG and its oligosaccharides significantly inhibit the transduction efficiency of replication-defective lentiviral particles pseudotyped with the envelope proteins of three different viruses. We found that the polysaccharide and its oligosaccharides strongly reduced the transduction efficiency of lentiviral particles pseudotyped with GP160—the envelope protein of the human immunodeficiency virus HIV-1—when added to T-lymphocyte Jurkat cells. The CRG oligosaccharides displayed significantly higher antiviral activity. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications 2021)

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12 pages, 2344 KiB

Open AccessArticle

Structural Determination and Genetic Identification of the O-Antigen from an Escherichia coli Strain, LL004, Representing a Novel Serogroup

by Jing Wang, Yujuan Xu, Chunjun Qin, Jing Hu, Jian Yin and Xi Guo

Int. J. Mol. Sci. 2021, 22(23), 12746; https://doi.org/10.3390/ijms222312746 - 25 Nov 2021

Cited by 2 | Viewed by 1763

Abstract

The O-antigen is the outermost component of the lipopolysaccharide layer in Gram-negative bacteria, and the variation of O-antigen structure provides the basis for bacterial serological diversity. Here, we determined the O-antigen structure of an Escherichia coli strain, LL004, which is totally different from all of the E. coli serogroups. The tetrasaccharide repeating unit was determined as →4)-β-d-Galp-(1→3)-β-d-GlcpNAc6OAc(~70%)-(1→3)-β-d-GalpA-(1→3)-β-d-GalpNAc-(1→ with monosaccharide analysis and NMR spectra. We also characterized the O-antigen gene cluster of LL004, and sequence analysis showed that it correlated well with the O-antigen structure. Deletion and complementation testing further confirmed its role in O-antigen biosynthesis, and indicated that the O-antigen of LL004 is assembled via the Wzx/Wzy dependent pathway. Our findings, in combination, suggest that LL004 should represent a novel serogroup of E. coli. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications 2021)

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15 pages, 1945 KiB

Open AccessArticle

Midecamycin Is Inactivated by Several Different Sugar Moieties at Its Inactivation Site

by Ru Lin, Li-Li Hong, Zhong-Ke Jiang, Ke-Meng Li, Wei-Qing He and Jian-Qiang Kong

Int. J. Mol. Sci. 2021, 22(23), 12636; https://doi.org/10.3390/ijms222312636 - 23 Nov 2021

Cited by 2 | Viewed by 1791

Abstract

Glycosylation inactivation is one of the important macrolide resistance mechanisms. The accumulated evidences attributed glycosylation inactivation to a glucosylation modification at the inactivation sites of macrolides. Whether other glycosylation modifications lead to macrolides inactivation is unclear. Herein, we demonstrated that varied glycosylation modifications could cause inactivation of midecamycin, a 16-membered macrolide antibiotic used clinically and agriculturally. Specifically, an actinomycetic glycosyltransferase (GT) OleD was selected for its glycodiversification capacity towards midecamycin. OleD was demonstrated to recognize UDP-D-glucose, UDP-D-xylose, UDP-galactose, UDP-rhamnose and UDP-N-acetylglucosamine to yield corresponding midecamycin 2′-O-glycosides, most of which displayed low yields. Protein engineering of OleD was thus performed to improve its conversions towards sugar donors. Q327F was the most favorable variant with seven times the conversion enhancement towards UDP-N-acetylglucosamine. Likewise, Q327A exhibited 30% conversion enhancement towards UDP-D-xylose. Potent biocatalysts for midecamycin glycosylation were thus obtained through protein engineering. Wild OleD, Q327F and Q327A were used as biocatalysts for scale-up preparation of midecamycin 2′-O-glucopyranoside, midecamycin 2′-O-GlcNAc and midecamycin 2′-O-xylopyranoside. In contrast to midecamycin, these midecamycin 2′-O-glycosides displayed no antimicrobial activities. These evidences suggested that besides glucosylation, other glycosylation patterns also could inactivate midecamycin, providing a new inactivation mechanism for midecamycin resistance. Cumulatively, glycosylation inactivation of midecamycin was independent of the type of attached sugar moieties at its inactivation site. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications 2021)

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13 pages, 4008 KiB

Open AccessArticle

Chemoenzymatic Synthesis and Antibody Binding of HIV-1 V1/V2 Glycopeptide-Bacteriophage Qβ Conjugates as a Vaccine Candidate

by Guanghui Zong, Christian Toonstra, Qiang Yang, Roushu Zhang and Lai-Xi Wang

Int. J. Mol. Sci. 2021, 22(22), 12538; https://doi.org/10.3390/ijms222212538 - 21 Nov 2021

Cited by 3 | Viewed by 1660

Abstract

The broadly neutralizing antibody PG9 recognizes a unique glycopeptide epitope in the V1V2 domain of HIV-1 gp120 envelope glycoprotein. The present study describes the design, synthesis, and antibody-binding analysis of HIV-1 V1V2 glycopeptide-Qβ conjugates as a mimic of the proposed neutralizing epitope of PG9. The glycopeptides were synthesized using a highly efficient chemoenzymatic method. The alkyne-tagged glycopeptides were then conjugated to the recombinant bacteriophage (Qβ), a virus-like nanoparticle, through a click reaction. Antibody-binding analysis indicated that the synthetic glycoconjugates showed significantly enhanced affinity for antibody PG9 compared with the monomeric glycopeptides. It was also shown that the affinity of the Qβ-conjugates for antibody PG9 was dependent on the density of the glycopeptide antigen display. The glycopeptide-Qβ conjugates synthesized represent a promising candidate of HIV-1 vaccine. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications 2021)

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28 pages, 10119 KiB

Open AccessArticle

Comparison and Optimization of Quantification Methods for Shigella flexneri Serotype 6 O-antigen Containing Galacturonic Acid and Methyl-Pentose

by Maria Michelina Raso, Oscar Vassallo, Francesca Micoli and Carlo Giannelli

Int. J. Mol. Sci. 2021, 22(22), 12160; https://doi.org/10.3390/ijms222212160 - 10 Nov 2021

Cited by 2 | Viewed by 2128

Abstract

Shigella is a leading diarrheal cause of morbidity and mortality worldwide, especially in low- and middle-income countries and in children under five years of age. Increasing levels of antimicrobial resistance make vaccine development an even higher global health priority. S. flexneri serotype 6 is one of the targets of many multicomponent vaccines in development to ensure broad protection against Shigella. The O-antigen (OAg) is a key active ingredient and its content is a critical quality attribute for vaccine release in order to monitor their stability and to ensure appropriate immune response. Here, the optimization of two methods to quantify S. flexneri 6 OAg is reported together with the characterization of their performances. The optimized Dische colorimetric method allows a tenfold increment of the sensitivity with respect to the original method and is useful for fast analysis detecting selectively methyl-pentoses, as rhamnose in S. flexneri 6 OAg. Also, a more specific HPAEC-PAD method was developed, detecting the dimer galacturonic acid-galactosamine (GalA-GalN) coming from S. flexneri 6 OAg acid hydrolysis. These methods will facilitate characterization of S. flexneri 6 OAg based vaccines. The colorimetric method can be used for quantification of other polysaccharide containing methyl-pentoses, and the HPAEC-PAD could be extended to other polysaccharides containing uronic acids. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications 2021)

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20 pages, 6314 KiB

Open AccessArticle

Characterization of Human Medullary Thyroid Carcinoma Glycosphingolipids Identifies Potential Cancer Markers

by Karin Säljö, Anders Thornell, Chunsheng Jin, Olov Norlén and Susann Teneberg

Int. J. Mol. Sci. 2021, 22(19), 10463; https://doi.org/10.3390/ijms221910463 - 28 Sep 2021

Viewed by 1681

Abstract

Medullary thyroid carcinoma (MTC) accounts for only 1–2% of thyroid cancers; however, metastatic MTC is a mortal disease with no cure. In this study, glycosphingolipids were isolated from human MTCs and characterized by mass spectrometry and binding of carbohydrate recognizing ligands. The tissue distribution of selected compounds was investigated by immunohistochemistry. The amount of acid glycosphingolipids in the MTCs was higher than in the normal thyroid glands. The major acid glycosphingolipid was the GD3 ganglioside. Sulfatide and the gangliosides GM3 and GD1a were also present. The majority of the complex non-acid glycosphingolipids had type 2 (Galβ4GlcNAc) core chains, i.e., the neolactotetraosylceramide, the Le^x, H type 2 and x₂ pentaosylceramides, the Le^y and A type 2 hexaosylceramides, and the A type 2 heptaosylceramide. There were also compounds with globo (GalαGalβ4Glc) core, i.e., globotriaosylceramide, globotetraosylceramide, the Forssman pentaosylceramide, and the Globo H hexaosylceramide. Immunohistochemistry demonstrated an extensive expression av Le^y in the MTC cells and also a variable intensity and prevalence of Globo H and Le^x. One individual with multiple endocrine neoplasia type 2B expressed the Forssman determinant, which is rarely found in humans. This study of human MTC glycosphingolipids identifies glycans that could serve as potential tumor-specific markers. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications 2021)

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15 pages, 1759 KiB

Open AccessArticle

Mass Spectrometric Evaluation of β-Cyclodextrins as Potential Hosts for Titanocene Dichloride

by Pia S. Bruni and Stefan Schürch

Int. J. Mol. Sci. 2021, 22(18), 9789; https://doi.org/10.3390/ijms22189789 - 10 Sep 2021

Cited by 1 | Viewed by 2058

Abstract

Bent metallocene dichlorides (Cp₂MCl₂, M = Ti, Mo, Nb, …) have found interest as anti-cancer drugs in order to overcome the drawbacks associated with platinum-based therapeutics. However, they suffer from poor hydrolytic stability at physiological pH. A promising approach to improve their hydrolytic stability is the formation of host-guest complexes with macrocyclic structures, such as cyclodextrins. In this work, we utilized nanoelectrospray ionization tandem mass spectrometry to probe the interaction of titanocene dichloride with β-cyclodextrin. Unlike the non-covalent binding of phenylalanine and oxaliplatin to β-cyclodextrin, the mixture of titanocene and β-cyclodextrin led to signals assigned as [βCD + Cp₂Ti–H]⁺, indicating a covalent character of the interaction. This finding is supported by titanated cyclodextrin fragment ions occurring from collisional activation. Employing di- and trimethylated β-cyclodextrins as hosts enabled the elucidation of the influence of the cyclodextrin hydroxy groups on the interaction with guest structures. Masking of the hydroxy groups was found to impair the covalent interaction and enabling the encapsulation of the guest structure within the hydrophobic cavity of the cyclodextrin. Findings are further supported by breakdown curves obtained by gas-phase dissociation of the various complexes. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications 2021)

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15 pages, 3963 KiB

Open AccessArticle

Two Paralogous Gb3/CD77 Synthases in Birds Show Different Preferences for Their Glycoprotein and Glycosphingolipid Substrates

by Anna Bereznicka, Krzysztof Mikolajczyk, Katarzyna Szymczak-Kulus, Katarzyna Kapczynska, Edyta Majorczyk, Anna Modlinska, Tomasz Piasecki, Radoslaw Kaczmarek and Marcin Czerwinski

Int. J. Mol. Sci. 2021, 22(18), 9761; https://doi.org/10.3390/ijms22189761 - 9 Sep 2021

Viewed by 1898

Abstract

Most glycosyltransferases show remarkable gross and fine substrate specificity, which is reflected in the old one enzyme-one linkage paradigm. While human Gb3/CD77 synthase is a glycosyltransferase that synthesizes the Galα1→4Gal moiety mainly on glycosphingolipids, its pigeon homolog prefers glycoproteins as acceptors. In this study, we characterized two Gb3/CD77 synthase paralogs found in pigeons (Columba livia). We evaluated their specificities in transfected human teratocarcinoma 2102Ep cells by flow cytofluorometry, Western blotting, high-performance thin-layer chromatography, mass spectrometry and metabolic labelling with ¹⁴C-galactose. We found that the previously described pigeon Gb3/CD77 synthase (called P) can use predominately glycoproteins as acceptors, while its paralog (called M), which we serendipitously discovered while conducting this study, efficiently synthesizes Galα1→4Gal caps on both glycoproteins and glycosphingolipids. These two paralogs may underlie the difference in expression profiles of Galα1→4Gal-terminated glycoconjugates between neoavians and mammals. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications 2021)

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16 pages, 3608 KiB

Open AccessArticle

OGT Protein Interaction Network (OGT-PIN): A Curated Database of Experimentally Identified Interaction Proteins of OGT

by Junfeng Ma, Chunyan Hou, Yaoxiang Li, Shufu Chen and Ci Wu

Int. J. Mol. Sci. 2021, 22(17), 9620; https://doi.org/10.3390/ijms22179620 - 6 Sep 2021

Cited by 13 | Viewed by 3968

Abstract

Interactions between proteins are essential to any cellular process and constitute the basis for molecular networks that determine the functional state of a cell. With the technical advances in recent years, an astonishingly high number of protein–protein interactions has been revealed. However, the interactome of O-linked N-acetylglucosamine transferase (OGT), the sole enzyme adding the O-linked β-N-acetylglucosamine (O-GlcNAc) onto its target proteins, has been largely undefined. To that end, we collated OGT interaction proteins experimentally identified in the past several decades. Rigorous curation of datasets from public repositories and O-GlcNAc-focused publications led to the identification of up to 929 high-stringency OGT interactors from multiple species studied (including Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Arabidopsis thaliana, and others). Among them, 784 human proteins were found to be interactors of human OGT. Moreover, these proteins spanned a very diverse range of functional classes (e.g., DNA repair, RNA metabolism, translational regulation, and cell cycle), with significant enrichment in regulating transcription and (co)translation. Our dataset demonstrates that OGT is likely a hub protein in cells. A webserver OGT-Protein Interaction Network (OGT-PIN) has also been created, which is freely accessible. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications 2021)

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13 pages, 1818 KiB

Open AccessArticle

Acinetobacter baumannii K106 and K112: Two Structurally and Genetically Related 6-Deoxy-l-talose-Containing Capsular Polysaccharides

by Anastasiya A. Kasimova, Nikolay P. Arbatsky, Jacob Tickner, Johanna J. Kenyon, Ruth M. Hall, Michael M. Shneider, Alina A. Dzhaparova, Alexander S. Shashkov, Alexander O. Chizhov, Anastasiya V. Popova and Yuriy A. Knirel

Int. J. Mol. Sci. 2021, 22(11), 5641; https://doi.org/10.3390/ijms22115641 - 26 May 2021

Cited by 8 | Viewed by 2693

Abstract

Whole genome sequences of two Acinetobacter baumannii clinical isolates, 48-1789 and MAR24, revealed that they carry the KL106 and KL112 capsular polysaccharide (CPS) biosynthesis gene clusters, respectively, at the chromosomal K locus. The KL106 and KL112 gene clusters are related to the previously described KL11 and KL83 gene clusters, sharing genes for the synthesis of l-rhamnose (l-Rhap) and 6-deoxy-l-talose (l-6dTalp). CPS material isolated from 48-1789 and MAR24 was studied by sugar analysis and Smith degradation along with one- and two-dimensional 1H and 13C NMR spectroscopy. The structures of K106 and K112 oligosaccharide repeats (K units) l-6dTalp-(1→3)-D-GlcpNAc tetrasaccharide fragment share the responsible genes in the respective gene clusters. The K106 and K83 CPSs also have the same linkage between K units. The KL112 cluster includes an additional glycosyltransferase gene, Gtr183, and the K112 unit includes α l-Rhap side chain that is not found in the K106 structure. K112 further differs in the linkage between K units formed by the Wzy polymerase, and a different wzy gene is found in KL112. However, though both KL106 and KL112 share the atr8 acetyltransferase gene with KL83, only K83 is acetylated. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications 2021)

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Review

Jump to: Research

23 pages, 1126 KiB

Open AccessReview

Immunoglobulin G N-glycan Biomarkers for Autoimmune Diseases: Current State and a Glycoinformatics Perspective

by Konstantinos Flevaris and Cleo Kontoravdi

Int. J. Mol. Sci. 2022, 23(9), 5180; https://doi.org/10.3390/ijms23095180 - 6 May 2022

Cited by 12 | Viewed by 4289

Abstract

The effective treatment of autoimmune disorders can greatly benefit from disease-specific biomarkers that are functionally involved in immune system regulation and can be collected through minimally invasive procedures. In this regard, human serum IgG N-glycans are promising for uncovering disease predisposition and monitoring progression, and for the identification of specific molecular targets for advanced therapies. In particular, the IgG N-glycome in diseased tissues is considered to be disease-dependent; thus, specific glycan structures may be involved in the pathophysiology of autoimmune diseases. This study provides a critical overview of the literature on human IgG N-glycomics, with a focus on the identification of disease-specific glycan alterations. In order to expedite the establishment of clinically-relevant N-glycan biomarkers, the employment of advanced computational tools for the interpretation of clinical data and their relationship with the underlying molecular mechanisms may be critical. Glycoinformatics tools, including artificial intelligence and systems glycobiology approaches, are reviewed for their potential to provide insight into patient stratification and disease etiology. Challenges in the integration of such glycoinformatics approaches in N-glycan biomarker research are critically discussed. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications 2021)

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17 pages, 755 KiB

Open AccessReview

Prospects and Challenges of the Study of Anti-Glycan Antibodies and Microbiota for the Monitoring of Gastrointestinal Cancer

by Eugeniy P. Smorodin

Int. J. Mol. Sci. 2021, 22(21), 11608; https://doi.org/10.3390/ijms222111608 - 27 Oct 2021

Cited by 2 | Viewed by 1880

Abstract

Over the past decades, a large amount of data has been accumulated in various subfields of glycobiology. However, much clinically relevant data and many tools are still not widely used in medicine. Synthetic glycoconjugates with the known structure of glycans are an accurate tool for the study of glycan-binding proteins. We used polyacrylamide glycoconjugates (PGs) including PGs with tumour-associated glycans (TAGs) in immunoassays to assess the prognostic potential of the serum level of anti-glycan antibodies (AG Abs) in gastrointestinal cancer patients and found an association of AG Abs with survival. The specificity of affinity-isolated AG Abs was investigated using synthetic and natural glycoconjugates. AG Abs showed mainly a low specificity to tumour-associated and tumour-derived mucins; therefore, the protective role of the examined circulating AG Abs against cancer remains a challenge. In this review, our findings are analysed and discussed in the context of the contribution of bacteria to the AG Abs stimulus and cancer progression. Examples of the influence of pathogenic bacteria colonising tumours on cancer progression and patient survival through mechanisms of interaction with tumours and dysregulated immune response are considered. The possibilities and problems of the integrative study of AG Abs and the microbiome using high-performance technologies are discussed. Full article

(This article belongs to the Special Issue Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications 2021)

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