Deciphering the glycocode: the complexity and analytical challenge of glycomics

CH-π Interactions Are Required for Human Galectin-3 Function

Glycan-binding proteins, or lectins, recognize distinct structural elements of polysaccharides, to mediate myriad biological functions. Targeting glycan-binding proteins involved in human disease has been challenging due to an incomplete understanding of the molecular mechanisms that govern protein-glycan interactions. Bioinformatics and structural studies of glycan-binding proteins indicate that aromatic residues with the potential for CH-π interactions are prevalent in glycan-binding sites. However, the contributions of these CH-π interactions to glycan binding and their relevance in downstream function remain unclear. An emblematic lectin, human galectin-3, recognizes lactose and N-acetyllactosamine-containing glycans by positioning the electropositive face of a galactose residue over the tryptophan 181 (W181) indole forming a CH-π interaction. We generated a suite of galectin-3 W181 variants to assess the importance of these CH-π interactions to glycan binding and function. As determined experimentally and further validated with computational modeling, variants with smaller or less electron-rich aromatic side chains (W181Y, W181F, W181H) or sterically similar but nonaromatic residues (W181M, W181R) showed poor or undetectable binding to lactose and attenuated ability to bind mucins or agglutinate red blood cells. The latter functions depend on multivalent binding, highlighting that weakened CH-π interactions cannot be overcome by avidity. Two galectin-3 variants with disrupted hydrogen bonding interactions (H158A and E184A) showed similarly impaired lactose binding. Molecular simulations demonstrate that all variants have decreased binding orientation stability relative to native galectin-3. Thus, W181 collaborates with the endogenous hydrogen bonding network to enhance binding affinity for lactose, and abrogation of these CH-π interactions is as deleterious as eliminating key hydrogen bonding interactions. These findings underscore the critical roles of CH-π interactions in carbohydrate binding and lectin function and will aid the development of novel lectin inhibitors.

Functional structural domain synthesis of anti-pancreatic carcinoma pectin-like polysaccharide RN1

The great structural and functional diversity supports polysaccharides as favorable candidates for new drug development. Previously we reported that a drug candidate pectin-like natural polysaccharide, RN1 might target galectin-3 (Gal-3) to impede pancreatic cancer cell growth in vivo. However, the quality control of polysaccharide-based drug research faces great challenges due to the heterogeneity. A potential solution is to synthesize structurally identified subfragments of this polysaccharide as alternatives. In this work, we took RN1 as an example, and synthesized five subfragments derived from the putative repeating units of RN1. Among them, pentasaccharide 4 showed an approximative binding affinity to Gal-3 in vitro, as well as an antiproliferative activity against pancreatic BxPC-3 cells comparable to that of RN1. Further, we scaled up pentasaccharide 4 to gram-scale in an efficient synthetic route with a 6.9 % yield from D-galactose. Importantly, pentasaccharide 4 significantly suppressed the growth of pancreatic tumor in vivo. Based on the mechanism complementarity of galactin-3 inhibitor and docetaxel, the combination administration of pentasaccharide 4 and docetaxel afforded better result. The result suggested pentasaccharide 4 was one of the functional structural domains of polysaccharide RN1 and might be a leading compound for anti-pancreatic cancer new drug development.

Competitive electrochemical sensing for cancer cell evaluation based on thionine-interlinked signal probes

The development of effective methods for tracking cancer cells is of significant importance in the early diagnosis and treatment of tumor diseases. Compared with the developed techniques, the electrochemical assay has shown considerable potential for monitoring glycan expression on the cell surface using nondestructive means. However, the application expansion of the electrochemical strategy is strongly impeded owing to its dependence on electroactive species. In this study, a competitive electrochemical strategy was reported for monitoring cancer cells based on mannose (a typical glycan) as a clinical biomarker. Herein, functionalized carbon nanotubes were used to load the thiomannosyl dimer, and thionine-interlinking signal probes were designed for competitive recognition. After effective competition between cancer cells and the anchored mannose, a decreased current was obtained as the cell concentration increased. Under optimal conditions, the proposed biosensor exhibited attractive performance for cancer cell analysis with a detection limit as low as 20 cells per mL for QGY-7701 and 35 cells per mL for QGY-7703, facilitating great promise for the sensitive detection of cancer cells and thus showing potential applications in cancer diagnosis.

Biocatalytic Approaches to Building Blocks for Enzymatic and Chemical Glycan Synthesis

While the field of biocatalysis has bloomed over the past 20-30 years, advances in the understanding and improvement of carbohydrate-active enzymes, in particular, the sugar nucleotides involved in glycan building block biosynthesis, have progressed relatively more slowly. This perspective highlights the need for further insight into substrate promiscuity and the use of biocatalysis fundamentals (rational design, directed evolution, immobilization) to expand substrate scopes toward such carbohydrate building block syntheses and/or to improve enzyme stability, kinetics, or turnover. Further, it explores the growing premise of using biocatalysis to provide simple, cost-effective access to stereochemically defined carbohydrate materials, which can undergo late-stage chemical functionalization or automated glycan synthesis/polymerization.

Sulfation at Glycopolymer Side Chains Switches Activity at the Macrophage Mannose Receptor (CD206) In Vitro and In Vivo

The mannose receptor (CD206) is an endocytic receptor expressed by selected innate immune cells and nonvascular endothelium, which plays a critical role in both homeostasis and pathogen recognition. Although its involvement in the development of several diseases and viral infections is well established, molecular tools able to both provide insight on the chemistry of CD206-ligand interactions and, importantly, effectively modulate its activity are currently lacking. Using novel SO4-3-Gal-glycopolymers targeting its cysteine-rich lectin ectodomain, this study uncovers and elucidates a previously unknown mechanism of CD206 blockade involving the formation of stable intracellular SO4-3-Gal-glycopolymer-CD206 complexes that prevents receptor recycling to the cell membrane. Further, we show that SO4-3-Gal glycopolymers inhibit CD206 both in vitro and in vivo, revealing hitherto unknown receptor function and demonstrating their potential as CD206 modulators within future immunotherapies.

High sensitivity glycomics in biomedicine

Many analytical challenges in biomedicine arise from the generally high heterogeneity and complexity of glycan- and glycoconjugate-containing samples, which are often only available in minute amounts. Therefore, highly sensitive workflows and detection methods are required. In this review mass spectrometric workflows and detection methods are evaluated for glycans and glycoproteins. Furthermore, glycomic methodologies and innovations that are tailored for enzymatic treatments, chemical derivatization, purification, separation, and detection at high sensitivity are highlighted. The discussion is focused on the analysis of mammalian N-linked and GalNAc-type O-linked glycans.

Measuring the multifaceted roles of mucin-domain glycoproteins in cancer

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.

Polymer-tethered glycosylated gold nanoparticles recruit sialylated glycoproteins into their protein corona, leading to off-target lectin binding

Upon exposure to biological fluids, the fouling of nanomaterial surfaces results in non-specific capture of proteins, which is particularly important when in contact with blood for in vivo and ex vivo applications. It is crucial to evaluate not just the protein components but also the glycans attached to those proteins. Polymer-tethered glycosylated gold nanoparticles have shown promise for use in biosensing/diagnostics, but the impact of the glycoprotein corona has not been established. Here we investigate how polymer-tethered glycosylated gold nanoparticles interact with serum proteins and demonstrate that the protein corona introduces new glycans and hence off-specific targeting capability. Using a panel of RAFT-derived polymers grafted to the gold surface, we show that the extent of corona formation is not dependent on the type of polymer. In lectin-binding assays, a glycan (galactose) installed on the chain-end of the polymer was available for binding even after protein corona formation. However, using sialic-acid binding lectins, it was found that there was significant off-target binding due to the large density of sialic acids introduced in the corona, confirmed by western blotting. To demonstrate the importance, we show that the nanoparticles can bind Siglec-2, an immune-relevant lectin post-corona formation. Pre-coating with (non-glycosylated) bovine serum albumin led to a significant reduction in the total glycoprotein corona. However, sufficient sialic acids were still present in the residual corona to lead to off-target binding. These results demonstrate the importance of the glycans when considering the protein corona and how 'retention of the desired function' does not rule out 'installation of undesired function' when considering the performance of glyco-nanomaterials.

Convergent Synthesis and Anti-Pancreatic Cancer Cell Growth Activity of a Highly Branched Heptadecasaccharide from Carthamus tinctorius

Bioactive polysaccharides from natural resources target various biological processes and are increasingly used as potential target molecules for drug development. However, the accessibility of branched and long complex polysaccharide active domains with well-defined structures remains a major challenge. Herein we describe an efficient first total synthesis of a highly branched heptadecasaccharide moiety of the native bioactive galectin-3-targeting polysaccharide from Carthamus tinctorius L. as well as shorter fragments of the heptadecasaccharide. The key feature of the approach is that a photo-assisted convergent [6+4+7] one-pot coupling strategy enables rapid assembly of the heptadecasaccharide, whereby a photoremovable o-nitrobenzyl protecting group is used to generate the corresponding acceptor for glycosylation in situ upon ultraviolet radiation. Biological activity tests suggest that the heptadecasaccharide can target galectin-3 and inhibit pancreatic cancer cell growth.

On the Origin of Sugar Handedness: Facts, Hypotheses and Missing Links-A Review

By paraphrasing one of Kipling's most amazing short stories (How the Leopard Got His Spots), this article could be entitled "How Sugars Became Homochiral". Obviously, we have no answer to this still unsolved mystery, and this perspective simply brings recent models, experiments and hypotheses into the homochiral homogeneity of sugars on earth. We shall revisit the past and current understanding of sugar chirality in the context of prebiotic chemistry, with attention to recent developments and insights. Different scenarios and pathways will be discussed, from the widely known formose-type processes to less familiar ones, often viewed as unorthodox chemical routes. In particular, problems associated with the spontaneous generation of enantiomeric imbalances and the transfer of chirality will be tackled. As carbohydrates are essential components of all cellular systems, astrochemical and terrestrial observations suggest that saccharides originated from environmentally available feedstocks. Such substances would have been capable of sustaining autotrophic and heterotrophic mechanisms integrating nutrients, metabolism and the genome after compartmentalization. Recent findings likewise indicate that sugars' enantiomeric bias may have emerged by a transfer of chirality mechanisms, rather than by deracemization of sugar backbones, yet providing an evolutionary advantage that fueled the cellular machinery.

Sweet impersonators: Molecular mimicry of host glycans by bacteria

All bacteria display surface-exposed glycans that can play an important role in their interaction with the host and in select cases mimic the glycans found on host cells, an event called molecular or glycan mimicry. In this review, we highlight the key bacteria that display human glycan mimicry and provide an overview of the involved glycan structures. We also discuss the general trends and outstanding questions associated with human glycan mimicry by bacteria. Finally, we provide an overview of several techniques that have emerged from the discipline of chemical glycobiology, which can aid in the study of the composition, variability, interaction and functional role of these mimicking glycans.

Toward Glycomaterials with Selectivity as Well as Affinity

Multivalent glycosylated materials (polymers, surfaces, and particles) often show high affinity toward carbohydrate binding proteins (e.g., lectins) due to the nonlinear enhancement from the cluster glycoside effect. This affinity gain has potential in applications from diagnostics, biosensors, and targeted delivery to anti-infectives and in an understanding of basic glycobiology. This perspective highlights the question of selectivity, which is less often addressed due to the reductionist nature of glycomaterials and the promiscuity of many lectins. The use of macromolecular features, including architecture, heterogeneous ligand display, and the installation of non-natural glycans, to address this challenge is discussed, and examples of selectivity gains are given.

Recent Progress in Chemo-Enzymatic Methods for the Synthesis of N-Glycans

Asparagine (N)-linked glycosylation is one of the most common co- and post-translational modifications of both intra- and extracellularly distributing proteins, which directly affects their biological functions, such as protein folding, stability and intercellular traffic. Production of the structural well-defined homogeneous N-glycans contributes to comprehensive investigation of their biological roles and molecular basis. Among the various methods, chemo-enzymatic approach serves as an alternative to chemical synthesis, providing high stereoselectivity and economic efficiency. This review summarizes some recent advances in the chemo-enzymatic methods for the production of N-glycans, including the preparation of substrates and sugar donors, and the progress in the glycosyltransferases characterization which leads to the diversity of N-glycan synthesis. We discuss the bottle-neck and new opportunities in exploiting the chemo-enzymatic synthesis of N-glycans based on our research experiences. In addition, downstream applications of the constructed N-glycans, such as automation devices and homogeneous glycoproteins synthesis are also described.

Self-Assembled Saccharide-Functionalized Amphiphilic Metallacycles as Biofilms Inhibitor via "Sweet Talking"

Bacterial biofilms are troublesome in the treatment of bacterial infectious diseases due to their inherent resistance to antibiotic therapy. Exploration of alternative antibiofilm reagents provides opportunities to achieve highly effective treatments. Herein, we propose a strategy to employ self-assembled saccharide-functionalized amphiphilic metallacycles ([2+2]-Gal, [3+3]-Gal, and [6+6]-Gal) with multiple positive charges as a different type of antibacterial reagent, marrying saccharide functionalization that interact with bacteria via "sweet talking". These self-assembled glyco-metallacycles gave various nanostructures (nanoparticles, vesicles or micron-sized vesicles) with different biofilms inhibition effect on Staphylococcus aureus (S. aureus). Especially, the peculiar self-assembly mechanism, superior antibacterial effect and biofilms inhibition distinguished the [6+6]-Gal from other metallacycles. Meanwhile, in vivo S. aureus pneumonia animal model experiments suggested that [6+6]-Gal could relieve mice pneumonia aroused by S. aureus effectively. In addition, the control study of metallacycle [3+3]-EG₅ confirmed the significant role of galactoside both in the self-assembly process and the antibacterial efficacy. In view of the superior effect against bacteria, the saccharide-functionalized metallacycle could be a promising candidate as biofilms inhibitor or treatment agent for pneumonia.

Keratan Sulphate in the Tumour Environment

Keratan sulphate (KS) is a bioactive glycosaminoglycan (GAG) of some complexity composed of the repeat disaccharide D-galactose β1→4 glycosidically linked to N-acetyl glucosamine. During the biosynthesis of KS, a family of glycosyltransferase and sulphotransferase enzymes act sequentially and in a coordinated fashion to add D-galactose (D-Gal) then N-acetyl glucosamine (GlcNAc) to a GlcNAc acceptor residue at the reducing terminus of a nascent KS chain to effect chain elongation. D-Gal and GlcNAc can both undergo sulphation at C6 but this occurs more frequently on GlcNAc than D-Gal. Sulphation along the developing KS chain is not uniform and contains regions of variable length where no sulphation occurs, regions which are monosulphated mainly on GlcNAc and further regions of high sulphation where both of the repeat disaccharides are sulphated. Each of these respective regions in the KS chain can be of variable length leading to KS complexity in terms of chain length and charge localization along the KS chain. Like other GAGs, it is these variably sulphated regions in KS which define its interactive properties with ligands such as growth factors, morphogens and cytokines and which determine the functional properties of tissues containing KS. Further adding to KS complexity is the identification of three different linkage structures in KS to asparagine (N-linked) or to threonine or serine residues (O-linked) in proteoglycan core proteins which has allowed the categorization of KS into three types, namely KS-I (corneal KS, N-linked), KS-II (skeletal KS, O-linked) or KS-III (brain KS, O-linked). KS-I to -III are also subject to variable addition of L-fucose and sialic acid groups. Furthermore, the GlcNAc residues of some members of the mucin-like glycoprotein family can also act as acceptor molecules for the addition of D-Gal and GlcNAc residues which can also be sulphated leading to small low sulphation glycoforms of KS. These differ from the more heavily sulphated KS chains found on proteoglycans. Like other GAGs, KS has evolved molecular recognition and information transfer properties over hundreds of millions of years of vertebrate and invertebrate evolution which equips them with cell mediatory properties in normal cellular processes and in aberrant pathological situations such as in tumourogenesis. Two KS-proteoglycans in particular, podocalyxin and lumican, are cell membrane, intracellular or stromal tissue-associated components with roles in the promotion or regulation of tumour development, mucin-like KS glycoproteins may also contribute to tumourogenesis. A greater understanding of the biology of KS may allow better methodology to be developed to more effectively combat tumourogenic processes.

Sugar-Based Organogelators for Various Applications

In this Feature Article, we discuss the design strategy, syntheses, and the self-assembly of various sugar-based gelators to form organogels. We illustrate the use of organogels formed by these sugar-based gelators for various applications such as (a) development of scratch-free, shatter-free, soft-optical devices using oil gels formed by mannitol-based gelators, (b) marine oil-spill recovery using sugar-based phase selective organogelators, (c) preparation of semiconducting cotton cloths using a diyne functionalized sugar gelator, (d) development of sugar arrays on glass slides using a polymerizable diyne functionalized sugar gelator for efficient lectin binding, (e) development of sintering resistant hybrid CaO-silica material for the absorption of CO₂, (f) preparation of porous polystyrene-crown ether matrix for the selective alkali metal ions sequestration, and (g) preparation of porous polystyrene, structured silica, and fluorescent gels using a library of sugar-based gelators, and also the mechanism of gelation of some of these gelators have been discussed. We have also given our perspective toward exploring sugar-based gelators for advanced applications.

A microscale double labelling of GAG oligosaccharides compatible with enzymatic treatment and mass spectrometry

A novel double labelling of glycosaminoglycans (GAG) oligosaccharides by thia-Michael addition and deuterium incorporation at the non-reducing and reducing ends, respectively, was introduced. This was demonstrated to be both compatible with the heparin microgram scale and amenable for mass spectrometry analysis, without impairing enzymatic activities such as heparinase I and sulfatase HSulf-2.

An automated platform for the enzyme-mediated assembly of complex oligosaccharides

An automated platform that can synthesize a wide range of complex carbohydrates will greatly increase their accessibility and should facilitate progress in glycoscience. Here we report a fully automated process for enzyme-mediated oligosaccharide synthesis that can give easy access to different classes of complex glycans including poly-N-acetyllactosamine derivatives, human milk oligosaccharides, gangliosides and N-glycans. Our automated platform uses a catch and release approach in which glycosyltransferase-catalysed reactions are performed in solution and product purification is accomplished by solid phase extraction. We developed a sulfonate tag that can easily be installed and enables highly efficient solid phase extraction and product release using a single set of washing conditions, regardless of the complexity of the glycan. Using this custom-built synthesizer, as many as 15 reaction cycles can be performed in an automated fashion without a need for lyophilization or buffer exchange steps.

Lectin engineering: the possible and the actual

Lectins are a widespread group of sugar-binding proteins occurring in all types of organisms including animals, plants, bacteria, fungi and even viruses. According to a recent report, there are more than 50 lectin scaffolds (∼Pfam), for which three-dimensional structures are known and sugar-binding functions have been confirmed in the literature, which far exceeds our view in the twentieth century (Fujimoto et al. 2014 Methods Mol. Biol. 1200, 579-606 (doi:10.1007/978-1-4939-1292-6_46)). This fact suggests that new lectins will be discovered either by a conventional screening approach or just by chance. It is also expected that new lectin domains including those found in enzymes as carbohydrate-binding modules will be generated in the future through evolution, although this has never been attempted on an experimental level. Based on the current state of the art, various methods of lectin engineering are available, by which lectin specificity and/or stability of a known lectin scaffold can be improved. However, the above observation implies that any protein scaffold, including those that have never been described as lectins, may be modified to acquire a sugar-binding function. In this review, possible approaches to confer sugar-binding properties on synthetic proteins and peptides are described.

Neuropeptide Y receptor interactions regulate its mitogenic activity

Neuropeptide Y (NPY) is a multifunctional neurotransmitter acting via G protein-coupled receptors - Y1R, Y2R and Y5R. NPY activities, such as its proliferative effects, are mediated by multiple receptors, which have the ability to dimerize. However, the role of this receptor interplay in NPY functions remains unclear. The goal of the current study was to identify NPY receptor interactions, focusing on the ligand-binding fraction, and determine their impact on the mitogenic activity of the peptide. Y1R, Y2R and Y5R expressed in CHO-K1 cells formed homodimers detectable on the cell surface by cross-linking. Moreover, Y1R and Y5R heterodimerized, while no Y2R/Y5R heterodimers were detected. Nevertheless, Y5R failed to block internalization of its cognate receptor in both Y1R/Y5R and Y2R/Y5R transfectants, indicating Y5R transactivation upon stimulation of the co-expressed receptor. These receptor interactions correlated with an augmented mitogenic response to NPY. In Y1R/Y5R and Y2R/Y5R transfectants, the proliferative response started at picomolar NPY concentrations, while nanomolar concentrations were needed to trigger proliferation in cells transfected with single receptors. Thus, our data identify direct and indirect heterotypic NPY receptor interactions as the mechanism amplifying its activity. Understanding these processes is crucial for the design of treatments targeting the NPY system.

Healthy human serum N-glycan profiling reveals the influence of ethnic variation on the identified cancer-relevant glycan biomarkers

Background

Most glycomics studies have focused on understanding disease mechanisms and proposing serum markers for various diseases, yet the influence of ethnic variation on the identified glyco-biomarker remains poorly addressed. This study aimed to investigate the inter-ethnic serum N-glycan variation among US origin control, Japanese, Indian, and Ethiopian healthy volunteers.

Methods

Human serum from 54 healthy subjects of various ethnicity and 11 Japanese hepatocellular carcinoma (HCC) patients were included in the study. We employed a comprehensive glycoblotting-assisted MALDI-TOF/MS-based quantitative analysis of serum N-glycome and fluorescence HPLC-based quantification of sialic acid species. Data representing serum N-glycan or sialic acid levels were compared among the ethnic groups using SPSS software.

Results

Total of 51 N-glycans released from whole serum glycoproteins could be reproducibly quantified within which 33 glycoforms were detected in all ethnicities. The remaining N-glycans were detected weakly but exclusively either in the Ethiopians (13 glycans) or in all the other ethnic groups (5 glycans). Highest abundance (p < 0.001) of high mannose, core-fucosylated, hyperbranched/hypersialylated N-glycans was demonstrated in Ethiopians. In contrast, only one glycan (m/z 2118) significantly differed among all ethnicities being highest in Indians and lowest in Ethiopians. Glycan abundance trend in Ethiopians was generally close to that of Japanese HCC patients. Glycotyping analysis further revealed ethnic-based disparities mainly in the branched and sialylated structures. Surprisingly, some of the glycoforms greatly elevated in the Ethiopian subjects have been identified as serum biomarkers of various cancers. Sialic acid level was significantly increased primarily in Ethiopians, compared to the other ethnicities.

Conclusion

The study revealed ethnic-specific differences in healthy human serum N-glycome with highest abundance of most glycoforms in the Ethiopian ethnicity. The results strongly emphasized the need to consider ethnicity matching for accurate glyco-biomarker identification. Further large-scale study employing various ethnic compositions is needed to verify the current result.

Streamlining the chemoenzymatic synthesis of complex N-glycans by a stop and go strategy

Contemporary chemoenzymatic approaches can provide highly complex multi-antennary N-linked glycans. These procedures are, however, very demanding and typically involve as many as 100 chemical steps to prepare advanced intermediates that can be diversified by glycosyltransferases in a branch selective manner to give asymmetrical structures commonly found in Nature. Only highly specialized laboratories can perform such syntheses, which greatly hampers progress in glycoscience. Here we describe a biomimetic approach in which a readily available bi-antennary glycopeptide can be converted in 10 or fewer chemical and enzymatic steps into multi-antennary N-glycans that at each arm can be uniquely extended by glycosyltransferases to give access to highly complex asymmetrically branched N-glycans. A key feature of our approach is the installation of additional branching points using recombinant MGAT4 and MGAT5 in combination with unnatural sugar donors. At an appropriate point in the enzymatic synthesis, the unnatural monosaccharides can be converted into their natural counterpart allowing each arm to be elaborated into a unique appendage.

Nonenzymatic Amperometric Aptamer Cytosensor for Ultrasensitive Detection of Circulating Tumor Cells and Dynamic Evaluation of Cell Surface N-Glycan Expression

Dynamic assessment of glycan expression on the cell surface and accurate determination of circulating tumor cells are increasingly imperative for cancer diagnosis and therapeutics. Herein, a unique and versatile nonenzymatic sandwich-structured electrochemical cytosensor was developed. The cytosensor was constructed based on a cell-specific aptamer, the lectin-functionalized porous core-shell palladium gold nanoparticles (Pd@Au NPs). To establish the cytosensor, amine-modified-SYL3C aptamer was first attached to the surface of aminated Fe₃O₄@SiO₂ nanoparticles (Fe₃O₄@SiO₂-NH₂ NPs) through cross-linked reaction via glutaraldehyde. Besides, in terms of noncovalent assembly of concanavalin A on Pd@Au NPs, a lectin-functionalized nanoprobe was established. This nanoprobe had the capabilities of both the specific carbohydrate recognition and the current signal amplification in view of the Pd@Au NPs as the electrocatalyst for the reduction of hydrogen peroxide (H₂O₂). Herein, we used MCF-7 cells as a model target, and the constructed cytosensor showed a low detection limit (down to three cells), a wide linear detection ranging from 100 to 1 × 10⁶ cells mL^-1. The established method sensitively realized the detection of the amount of cell and exact evaluation of glycan expression on cell surface, demonstrating great application prospects.

In Situ Cellular Glycan Analysis

Glycan decorates all mammalian cell surfaces through glycosylation, which is one of the most important post-modifications of proteins. Glycans mediate a wide variety of biological processes, including cell growth and differentiation, cell-cell communication, immune response, pathogen interaction, and intracellular signaling events. Besides, tumor cells aberrantly express distinct sets of glycans, which can indicate different tumor onsets and progression processes. Thus, analysis of cellular glycans may contribute to understanding of glycan-related biological processes and correlation of glycan patterns with disease states for clinical diagnosis and treatment. Although proteomics and glycomics have included great efforts for in vitro study of glycan structures and functions using lysis samples of cells or tissues, they cannot offer real-time qualitative or quantitative information, especially spatial distribution, of glycans on/in intact cells, which is important to the revelation of glycan-related biological events. Moreover, the complex lysis and separation procedures may bring unpredictable loss of glycan information. Focusing on the great urgency for in situ analysis of cellular glycans, our group developed a series of methods for in situ analysis of cellular glycans in the past 10 years. By construction of electrochemical glycan-recognizable probes, glycans on the cell surface can be quantified by direct or competitive electrochemical detection. Using multichannel electrodes or encoded lectin probes, multiple glycans on the cell surface can be dynamically monitored simultaneously. Through design of functional nanoprobes, the cell surface protein-specific glycans and intracellular glycan-related enzymes can be visualized by fluorescence or Raman imaging. Besides, some biological enzymes-based methods have been developed for remodeling or imaging of protein-specific glycans and other types of glycoconjugates, such as gangliosides. Through tracing the changes of glycan expression induced by drugs or gene interference, some glycan-related biological processes have been deduced or proved, demonstrating the reliability and practicability of the developed methods. This Account surveys the key technologies developed in this area, along with the discussion on the shortages of current methodology as well as the possible strategies to overcome those shortages. The future trend in this topic is also discussed. It is expected that this Account can provide a versatile arsenal for chemical and biological researchers to unravel the complex mechanisms involved in glycan-related biological processes and light new beacons in tumor diagnosis and treatment.

Organogel-assisted topochemical synthesis of multivalent glyco-polymer for high-affinity lectin binding

An organogelator, 2,4-undeca-diynyl-4',6'-O-benzylidene-β-d-galactopyranoside, which aligns its diacetylene upon gelation, has been synthesized. UV irradiation of its gel resulted in topochemical polymerization of the gelator forming polydiacetylene (PDA). We have used this gel-state reaction for the synthesis of surface-immobilized multi-valent glycoclusters, which showed 1000-fold enhanced binding, compared to monomers, with various galactose-binding lectins.

Sequencing the Dermatan Sulfate Chain of Decorin

Glycomics represents one of the last frontiers and most challenging in omic analysis. Glycosylation occurs in the endoplasmic reticulum and the Golgi organelle and its control is neither well-understood nor predictable based on proteomic or genomic analysis. One of the most structurally complex classes of glycoconjugates is the proteoglycans (PGs) and their glycosaminoglycan (GAG) side chains. Previously, our laboratory solved the structure of the chondroitin sulfate chain of the bikunin PG. The current study examines the much more complex structure of the dermatan sulfate GAG chain of decorin PG. By utilizing sophisticated separation methods followed by compositional analysis, domain mapping, and tandem mass spectrometry coupled with analysis by a modified genetic algorithm approach, the structural motif for the decorin dermatan sulfate chain was determined. This represents the second example of a GAG with a prominent structural motif, suggesting that the structural variability of this class of glycoconjugates is somewhat simpler than had been expected.

A Secondary Structural Element in a Wide Range of Fucosylated Glycoepitopes

The increasing understanding of the essential role of carbohydrates in development, and in a wide range of diseases fuels a rapidly growing interest in the basic principles governing carbohydrate-protein interactions. A still heavily debated issue regarding the recognition process is the degree of flexibility or rigidity of oligosaccharides. Combining NMR structure determination based on extensive experimental data with DFT and database searches, we have identified a set of trisaccharide motifs with a similar conformation that is characterized by a non-conventional C-H⋅⋅⋅O hydrogen bond. These motifs are present in numerous classes of oligosaccharides, found in everything from bacteria to mammals, including Lewis blood group antigens but also unusual motifs from amphibians and marine invertebrates. The set of trisaccharide motifs can be summarized with the consensus motifs X-β1,4-[Fucα1,3]-Y and X-β1,3-[Fucα1,4]-Y-a secondary structure we name [3,4]F-branch. The wide spectrum of possible modifications of this scaffold points toward a large variety of glycoepitopes, which nature generated using the same underlying architecture.

Influence of Feed Composition on the Monomeric Structure of Free Bacterial Extracellular Polysaccharides in Anaerobic Digestion

Six 5.0-L fill-and-draw batch reactors were used with different feed compositions containing a range of carbohydrates (glucose, sucrose, fructose) and nitrogen sources (urea, NH₄Cl) at various concentrations to investigate free extracellular polysaccharide (EPS) production during anaerobic digestion (AD). This work analyzed not only their monosaccharide components, but also their specific linkage patterns and the change associated with different chemical nature in carbon substrates or nitrogen sources; all of these parameters can have profound biological consequences, and were correlated to macronutrients present in the feed. It is believed that feed composition is a major factor which determines the physicochemical characteristics of the free EPS. Our findings also suggest that the differences associated with the digestion of various carbon substrates and/or nitrogen sources could alter monomeric saccharide composition and concentrations of the free EPS. Such insights demonstrate that previous studies on feed C/N ratios tended to overestimate EPS production, while variations in the chemical nature of the nitrogen source were overlooked. Our results also link the physiochemical properties of free EPS with underlying biofouling mechanisms, and demonstrate that membrane fouling is to some extent dependent upon the prevailing nutritional environment and feed composition.

The Expanding World of Small Molecule Microarrays

Speed and throughput are vital ingredients for discovery driven, "-omics" research. The small molecule microarray (SMM) succeeds at delivering phenomenal screening throughput and versatility. The concept at the heart of the technology is elegant, yet simple: by presenting large collections of molecules in high density on a flat surface, one is able to interrogate all possible interactions with desired targets, in just a single step. SMMs have become established as the choice platform for screening, lead discovery, and molecular characterization. This introduction describes the principles governing microarray construction and use, focusing on practical challenges faced when conducting SMM experiments. It will explain the key design considerations and lay the foundation for the chapters that follow. (An earlier version of this chapter appeared in Small Molecule Microarrays: Methods and Protocols, published in 2010.).

Paper analytical devices for dynamic evaluation of cell surface N-glycan expression via a bimodal biosensor based on multibranched hybridization chain reaction amplification

A novel colorimetric/fluorescence bimodal lab-on-paper cyto-device was fabricated based on concanavalin A (Con A)-integrating multibranched hybridization chain reaction (mHCR). The product of mHCR was modified PtCu nanochains (colorimetric signal label) and graphene quantum dot (fluorescence signal label) for in situ and dynamically evaluating cell surface N-glycan expression. In this strategy, preliminary detection was carried out through colorimetric method, if needed, then the fluorescence method was applied for a precise determination. Au-Ag-paper devices increased the surface areas and active sites for immobilizing larger amount of aptamers, and then specifically and efficiently captured more cancer cells. Moreover, it could effectively reduce the paper background fluorescence. Due to the specific recognition of Con A with mannose and the effective signal amplification of mHCR, the proposed strategy exhibited excellent high sensitivity for the cytosensing of MCF-7 cells ranging from 100 to 1.0×10(7) and 80-5.0×10(7) cellsmL(-1) with the detection limit of 33 and 26 cellsmL(-1) for colorimetric and fluorescence, respectively. More importantly, this strategy was successfully applied to dynamically monitor cell-surface multi-glycans expression on living cells under external stimuli of inhibitors as well as for N-glycan expression inhibitor screening. These results implied that this biosensor has potential in studying complex native glycan-related biological processes and elucidating the N-glycan-related diseases in biological and physiological processes.

Glycan heterogeneity on gold nanoparticles increases lectin discrimination capacity in label-free multiplexed bioassays

The development of new analytical tools as point-of-care biosensors is crucial to combat the spread of infectious diseases, especially in the context of drug-resistant organisms, or to detect biological warfare agents. Glycan/lectin interactions drive a wide range of recognition and signal transduction processes within nature and are often the first site of adhesion/recognition during infection making them appealing targets for biosensors. Glycosylated gold nanoparticles have been developed that change colour from red to blue upon interaction with carbohydrate-binding proteins and may find use as biosensors, but are limited by the inherent promiscuity of some of these interactions. Here we mimic the natural heterogeneity of cell-surface glycans by displaying mixed monolayers of glycans on the surface of gold nanoparticles. These are then used in a multiplexed, label-free bioassay to create 'barcodes' which describe the lectin based on its binding profile. The increased information content encoded by using complex mixtures of a few sugars, rather than increased numbers of different sugars makes this approach both scalable and accessible. These nanoparticles show increased lectin identification power at a range of lectin concentrations, relative to single-channel sensors. It was also found that some information about the concentration of the lectins can be extracted, all from just a simple colour change, taking this technology closer to being a realistic biosensor.

Glycosylated gold nanoparticle libraries for label-free multiplexed lectin biosensing

Glycan/lectin interactions drive a wide range of recognition and signal transduction processes within nature. However, their measurement is complicated or limited by the analytical tools available. Most technologies require fluorescently labelled proteins (e.g. microarrays) or expensive infrastructure (such as surface plasmon resonance). This also limits their application in biosensing, especially for low-resource settings, where detection of pathogens based on glycan binding could speed up diagnosis. Here we employ a library-oriented approach to immobilise a range of monosaccharides onto polymer-stabilised gold nanoparticles to enable rapid and high-throughput evaluation of their binding specificities with a panel of lectins. The red to blue colour shift upon gold nanoparticle aggregation is used as the output, removing the need for labelled protein, enabling compatibility with 96-well microplates. Furthermore, we demonstrate the use of a flatbed scanner (or digital camera) to extract biophysical data, ensuring that only minimal resources are required. Finally, linear discriminant analysis is employed to demonstrate how the glyconanoparticles can be applied as a multiplexed biosensor capable of identifying pathogenic lectins without the need for any infrastructure and overcoming some of the issues of lectin promiscuity.

An electrochemical glycan biosensor based on a thionine-bridged multiwalled carbon nanotube/gold nanoparticle composite-modified electrode

A MWCNT/Th/AuNP composite, used to construct an electrochemical biosensor for the mannose assay of living cancer cells, contained thionine as an electron mediator and simplified detection based on enzymatic catalysis for signal amplification.

Targeted superparamagnetic iron oxide nanoparticles for early detection of cancer: Possibilities and challenges

Nanomedicine, the integration of nanotechnological tools in medicine demonstrated promising potential to revolutionize the diagnosis and treatment of various human health conditions. Nanoparticles (NPs) have shown much promise in diagnostics of cancer, especially since they can accommodate targeting molecules on their surface, which search for specific tumor cell receptors upon injection into the blood stream. This concentrates the NPs in the desired tumor location. Furthermore, such receptor-specific targeting may be exploited for detection of potential metastases in an early stage. Some NPs, such as superparamagnetic iron oxide NPs (SPIONs), are also compatible with magnetic resonance imaging (MRI), which makes their clinical translation and application rather easy and accessible for tumor imaging purposes. Furthermore, multifunctional and/or theranostic NPs can be used for simultaneous imaging of cancer and drug delivery. In this review article, we will specifically focus on the application of SPIONs in early detection and imaging of major cancer types.

FROM THE CLINICAL EDITOR

Super-paramagnetic iron oxide nanoparticles (SPIONs) have been reported by many to be useful as an MRI contrast agent in the detection of tumors. To further enhance the tumor imaging, SPIONs can be coupled with tumor targeting motifs. In this article, the authors performed a comprehensive review on the current status of using targeted SPIONS in tumor detection and also the potential hurdles to overcome.

Reusable and dual-potential responses electrogenerated chemiluminescence biosensor for synchronously cytosensing and dynamic cell surface N-glycan evaluation

A novel reusable and dual-potential responsive electrogenerated chemiluminescence (ECL) biosensor was fabricated for synchronous detection of cancer cells and their surface N-glycan. In this strategy, a cancer cell recognized aptamer hybridized with a capture DNA was immobilized on electrochemically reduced MoS2 nanosheets, and Ru(phen)3(2+) as ECL probes was intercalated into the grooves of the double-strand DNA. In the presence of target cells, the capture DNA and Ru(phen)3(2+) were released from the electrode interface owing to the specific interaction between cancer cells and the aptamer. Meanwhile, concanavalin A (Con A), a mannose binding protein, and a conjugated gold nanoparticle modified graphite-C3N4 (Con A@Au-C3N4) was used as a negative ECL nanoprobe and applied for the cell surface N-glycan evaluation owing to the excellent ECL properties of g-C3N4 at negative potential. The cytosensing and cell surface N-glycan evaluation could be simultaneously realized with high sensitivity and excellent selectivity based on the ratio of ECL intensity between the negative potential and positive potential (ΔECLn/ΔECLp), avoiding the traditional routing cell counting procedures. Moreover, the aptamer modified electrode can be regenerated in the presence of capture DNA solutions for cyclic utilization. As a proof-of-concept, the ECL cytosensor showed excellent performances for the analysis of the MCF-7 cancer cell and its surface N-glycan evaluation in human serum samples. The reusable and dual potential response ECL biosensor endows a feasibility tool for clinical diagnosis and drug screening especially in complex biological systems.

Micro-competition system for Raman quantification of multiple glycans on intact cell surface

A micro-competition system integrated functionalized silica bubbles and Raman encoded nanoprobes to simultaneously assay multiple glycans on intact cell surfaces.

A micro-competition system is designed for simultaneous quantification of multiple glycans on intact cell surfaces, by integrating two-surface–one-molecule competition with surface enhanced Raman scattering (SERS). The micro-competition is achieved among multiple-polysaccharide-coated gold nanostars functionalized silica bubbles, target cells and gold nanoprobes at a micron scale. The gold nanoprobes are prepared by coating distinct Raman molecules and lectins on gold nanoparticles for signal resolution and glycan recognition, respectively. The silica bubble surface serves as an artificial glycan surface and a SERS substrate. Upon the competitive recognition of lectin to the corresponding glycan, the gold nanoprobes can be specifically captured by the bubbles and cells in a homogeneous system, and the amounts of different gold nanoprobes on bubbles are simultaneously detected by SERS to reflect the corresponding glycan amounts on the cell surface. This micro-competition system with multiple quantification capability provides a powerful tool for investigation of the complex glycan-related biological processes.

Advances in lectin microarray technology: optimized protocols for piezoelectric print conditions

Lectin microarray technology has been used to profile the glycosylation of a multitude of biological and clinical samples, leading to new clinical biomarkers and advances in glycobiology. Lectin microarrays, which include >90 plant lectins, recombinant lectins, and selected antibodies, are used to profile N-linked, O-linked, and glycolipid glycans. The specificity and depth of glycan profiling depends upon the carbohydrate-binding proteins arrayed. The current set targets mammalian carbohydrates including fucose, high mannose, branched and complex N-linked, α- and β-galactose and GalNAc, α-2,3- and α-2,6-sialic acid, LacNAc, and Lewis X epitopes. Previous protocols have described the use of a contact microarray printer for lectin microarray production. Here, an updated protocol that uses a non-contact, piezoelectric printer, which leads to increased lectin activity on the array, is presented. Optimization of print and sample hybridization conditions and methods of analysis are discussed.

Revealing the carbohydrate pattern on a cell surface by super-resolution imaging

Carbohydrates are involved in various physiological and pathological activities including cell adhesion, signal transduction and tumor invasion. The distribution of carbohydrates is the molecular basis of their multiple functions, but remains poorly understood. Here, we employed direct stochastic optical reconstruction microscopy (dSTORM) to visualize the pattern of N-acetylglucosamine (N-GlcNAc) on Vero cell membranes at the nanometer level of resolution. We found that N-GlcNAcs exist in irregular clusters on the apical membrane with an average cluster area of about 0.37 μm(2). Most of these N-GlcNAc clusters are co-localized with lipid rafts by dual-color dSTORM imaging, suggesting that carbohydrates are closely associated with lipid rafts as the functional domains. Our results demonstrate that super-resolution imaging is capable of characterizing the distribution of carbohydrates on the cellular surface at the molecular level.

Sensitive electrochemical aptamer biosensor for dynamic cell surface N-glycan evaluation featuring multivalent recognition and signal amplification on a dendrimer-graphene electrode interface

We demonstrate a multivalent recognition and highly selective aptamer signal amplification strategy for electrochemical cytosensing and dynamic cell surface N-glycan expression evaluation by the combination of concanavalin A (Con A), a mannose binding protein, as a model, conjugated poly(amidoamine) dendrimer on a chemically reduced graphene oxide (rGO-DEN) interface, and aptamer- and horseradish peroxidase-modified gold nanoparticles (HRP-aptamer-AuNPs) as nanoprobes. In this strategy, the rGO-DEN can not only enhance the electron transfer ability but also provide a multivalent recognition interface for the conjugation of Con A that avoids the weak carbohydrate-protein interaction and dramatically improves the cell capture efficiency and the sensitivity of the biosensor for cell surface glycan. The high-affinity aptamer- and HRP-modified gold nanoparticles provide an ultrasensitive electrochemical probe with excellent specificity. As proof-of-concept, the detection of CCRF-CEM cell (human acute lymphoblastic leukemia) and its surface N-glycan was developed. It has demonstrated that the as-designed biosensor can be used for highly sensitive and selective cell detection and dynamic evaluation of cell surface N-glycan expression. A detection limit as low as 10 cells mL(-1) was obtained with excellent selectivity. Moreover, this strategy was also successfully applied for N-glycan expression inhibitor screening. These results imply that this biosensor has potential in clinical diagnostic and drug screening applications and endows a feasibility tool for insight into the N-glycan function in biological processes and related diseases.

Adaptive immune activation: glycosylation does matter

Major histocompatibility complex (MHC) class I and II are glycoproteins that can present antigenic peptides at the cell surface for recognition and activation of circulating T lymphocytes. Here, the importance of the modification of protein antigens by glycans on cellular uptake, proteolytic processing, presentation by MHC and subsequent T-cell priming is reviewed. Antigen glycosylation is important for a number of diseases and vaccine design. All of the key proteins involved in antigen recognition and the orchestration of downstream effector functions are glycosylated. The influence of protein glycosylation on immune function and disease is covered.

Investigating biomolecular recognition at the cell surface using atomic force microscopy

Probing the interaction forces that drive biomolecular recognition on cell surfaces is essential for understanding diverse biological processes. Force spectroscopy has been a widely used dynamic analytical technique, allowing measurement of such interactions at the molecular and cellular level. The capabilities of working under near physiological environments, combined with excellent force and lateral resolution make atomic force microscopy (AFM)-based force spectroscopy a powerful approach to measure biomolecular interaction forces not only on non-biological substrates, but also on soft, dynamic cell surfaces. Over the last few years, AFM-based force spectroscopy has provided biophysical insight into how biomolecules on cell surfaces interact with each other and induce relevant biological processes. In this review, we focus on describing the technique of force spectroscopy using the AFM, specifically in the context of probing cell surfaces. We summarize recent progress in understanding the recognition and interactions between macromolecules that may be found at cell surfaces from a force spectroscopy perspective. We further discuss the challenges and future prospects of the application of this versatile technique.