Glycosylation in health and disease

Interleukin-2 receptor α (IL-2Rα/CD25) shedding is differentially regulated by N- and O-glycosylation

The cytokine interleukin-2 (IL-2) is a critical regulator of immune responses, with an especially well-characterized role in regulating T-cell homeostasis. IL-2 signaling involves three distinct receptor subunits: the IL-2Rα (CD25), IL-2Rβ, and IL-2Rγ. The intracellular transduction of IL-2-induced signals is strictly dependent on IL-2Rβ and IL-2Rγ, while the IL-2Rα is not directly involved in signaling. Instead, it has the highest affinity towards IL-2 and is thus responsible for regulating the affinity of a cell for IL-2. In addition to the membrane-bound IL-2Rα, a soluble form of the receptor (sIL-2Rα) has been described, which is present in the blood of healthy individuals, increased under various pathological conditions, and able to bind IL-2 and thus modulate its function. The sIL-2Rα is generated by proteolytic cleavage of the membrane-bound receptor. Here, we analyze whether glycosylation of the IL-2Rα regulates its proteolysis. We find that constitutive IL-2Rα shedding is affected by glycosylation and discover distinct roles for N- and O-glycosylation. Furthermore, we show that induced shedding by the metalloproteases ADAM10 and ADAM17 is also differentially regulated by distinct types of glycans. Finally, we identify a specific role for an N-glycan at an exosite in ADAM17-mediated proteolysis that does not affect ADAM10, indicating distinct substrate recognition mechanisms. These results further the understanding of the mechanisms leading to sIL-2Rα generation, and thus offer the opportunity to specifically modulate the generation of the soluble receptor.

High-abundance serum glycoproteins as valuable resources for glycopeptide standards

High-abundance serum proteins, mostly modified by N-glycans, are usually depleted from human sera to achieve in-depth analyses of serum proteome and sub-proteomes. In this study, we show that these high-abundance glycoproteins (HAGPs) can be used as valuable standard glycopeptide resources, as long as the structural features of their glycans have been well defined at the glycosite-specific level. By directly analyzing intact glycopeptides enriched from serum, we identified 1322 unique glycopeptides at 48 N-glycosites from the top 12 HAGPs (19 subclasses). These HAGPs could be further classified into four major groups based on the structural features of their attached N-glycans. Immunoglobins including IGHG1/2/3/4, IGHA1/2 and IGHM were mostly modified by core fucosylated and bisected N-glycans with rarely sialic acids. Alpha-1-acid glycoproteins (ORM1/2) and haptoglobins (HP) were mainly modified by tri-and tetra-antennary (40 %) N-glycans with antenna-fucoses and sialic acids. Complement components C3 and C4A/B were highly modified by oligo-mannose glycans. The other HAGPs including SERPINA1, A2M, TF, FGB/G and APOB mainly contain bi-antennary complex glycans with the common core structure and (sialyl-) LacNAc branch structures. These HAGPs are easily detected by LC-MS analysis and therefore could be used as standard glycopeptides for glycoproteomic methodology studies as well as possible clinical utilities.

Further exploration of the physicochemical nature of μ2-bridge-relevant deprotonations via the elucidation of four kinds of alditol complexes

Single-crystal structures of four alditol complexes are presented. In LuCl3/galactitol and ScCl3/myo-inositol complexes, μ2-bridge-relevant deprotonations were observed. The polarization from two rare earth ions in the μ2-bridge activates the chemically inert OH and promotes deprotonation. Additionally, mass spectrometry, pH experiments, and quantum chemistry calculations were conducted to enhance our understanding of the μ2-bridge-relevant deprotonations. A common structural feature of the complexes where μ2-bridge-relevant deprotonation takes place is that two metal ions and two oxygen atoms in two μ2-bridges form an M2O2 cluster. The four atoms in the M2O2 cluster make up a parallelogram. Such a structure is useful to balance the strong coulombic repulsions between two M3+ and between two O-. In the ScCl3/myo-inositol complex, the deprotonation exhibits a characteristic of regional/chiral selectivity. Galactitol is a third alditol ligand where μ2-bridge-relevant deprotonation is observed. The flexible backbone of the galactitol allows the formation of more five-membered chelating rings and six-membered chelating rings, which are used to stabilize the rare earth ions of the μ2-bridge. The coordination makes the backbone of galactitol deviate from the zigzag conformation. The above results are helpful in the rational design of high-performance catalysts.

Development of a FUT8 Inhibitor with Cellular Inhibitory Properties

Core fucosylation is catalyzed by α-1,6-fucosyltransferase (FUT8), which fucosylates the innermost GlcNAc of N-glycans. Given the association of FUT8 with various diseases, including cancer, selective FUT8 inhibitors applicable to in vivo or cell-based systems are highly sought-after. Herein, we report the discovery of a compound that selectively inhibits FUT8 in cell-based assays. High-throughput screening revealed a FUT8-inhibiting pharmacophore, and further structural optimization yielded an inhibitor with a KD value of 49 nM. Notably, this binding occurs only in the presence of GDP (a product of the enzymatic reaction catalyzed by FUT8). Mechanistic studies suggested that this inhibitor generates a highly reactive naphthoquinone methide derivative at the binding site in FUT8, which subsequently reacts with FUT8. Furthermore, prodrug derivatization of this inhibitor improved its stability, enabling suppression of core fucose expression and subsequent EGFR and T-cell signaling in cell-based assays, paving the way for the development of drugs targeting core fucosylation.

Tools and techniques for quantitative glycoproteomic analysis

Recent advances in mass spectrometry (MS)-based methods have significantly expanded the capabilities for quantitative glycoproteomics, enabling highly sensitive and accurate quantitation of glycosylation at intact glycopeptide level. These developments have provided valuable insights into the roles of glycoproteins in various biological processes and diseases. In this short review, we summarize pertinent studies on quantitative techniques and tools for site-specific glycoproteomic analysis published over the past decade. We also highlight state-of-the-art MS-based software that facilitate multi-dimension quantification of the glycoproteome, targeted quantification of specific glycopeptides, and the analysis of glycopeptide isomers. Additionally, we discuss the potential applications of these technologies in clinical biomarker discovery and the functional characterization of glycoproteins in health and disease. The review concludes with a discussion of current challenges and future perspectives in the field, emphasizing the need for more precise, high-throughput and efficient methods to further advance quantitative glycoproteomics and its applications.

Site-Specific Immobilization Boosts the Performance of a Galectin-1 Biosensor

The analysis of protein-bound glycans has gained significant attention due to their pivotal roles in physiological and pathological processes like cell-cell recognition, immune response, and disease progression. Routine methods for glycan analysis are challenged by the very similar physicochemical properties of their carbohydrate components. As an alternative, lectins, which are proteins that specifically bind to glycans, have been integrated into biosensors for glycan detection. However, the effectiveness of protein-based biosensors depends heavily on the immobilization of proteins on the sensor surface. To enhance the sensitivity and/or selectivity of lectin biosensors, it is crucial to immobilize the lectin in an optimal orientation for ligand binding without compromising its function. Random immobilization methods often result in arbitrary orientation and reduced sensitivity. To address this, we explored a directed immobilization strategy relying on a reactive noncanonical amino acid (ncAA) and bioorthogonal chemistry. In this study, we site-specifically incorporated the reactive noncanonical lysine derivative, Nε-((2-azidoethoxy)carbonyl)-l-lysine, into a cysteine-less single-chain variant of human galectin-1 (scCSGal-1). The reactive bioorthogonal azide group allowed the directed immobilization of the lectin on a biosensor surface using strain-promoted azide-alkyne cycloaddition. Biolayer interferometry data demonstrated that the controlled, directed attachment of scCSGal-1 to the biosensor surface enhanced the binding sensitivity to glycosylated von Willebrand factor by about 12-fold compared to random immobilization. These findings emphasize the importance of controlled protein orientation in biosensor design. They also highlight the power of single site-specific genetic encoding of reactive ncAAs and bioorthogonal chemistry to improve the performance of lectin-based diagnostic tools.

Updates implemented in version 4 of the GlyCosmos Glycoscience Portal

Glycosylation, characterized by its complexity and diversity, is a common system across all domains of life. The glycosylation of proteins or lipids imparts them with structural and functional roles, ranging from development to infectious or Mendelian disease. The high-throughput-based omics data has revealed that glycans are involved in important cellular processes. Comprehensive knowledge of glycosylation has contributed not only to the fundamental concepts in glycoscience but also to its applications, including the development of molecular markers for diagnosis and therapeutic tools for treating diseases. The GlyCosmos Glycoscience Portal (GlyCosmos) has undergone significant updates to better support the scientific community in studying glycosylation-related phenomena. Key enhancements include the integration of expanded datasets linking glycans to other omics fields, improved tools for glycan structure prediction and analysis, and upgraded visualization capabilities to streamline data interpretation. A strengthened focus on data standardization has also been introduced, fostering interoperability between glycoscience resources and external databases. Since its release in 2019, the portal has seen a fivefold increase in user engagement, reflecting its growing relevance. These recent advancements aim to provide researchers with a more comprehensive and user-friendly platform, enabling deeper insights into glycan roles in cellular processes and disease mechanisms. GlyCosmos will continue to evolve, prioritizing community needs and advancing the integration of glycoscience with broader biological and biomedical research.

Tumor-Associated Carbohydrate Antigen 19-9 (CA 19-9), a Promising Target for Antibody-Based Detection, Diagnosis, and Immunotherapy of Cancer

Carbohydrate antigen 19-9 (CA 19-9) also known as sialyl Lewis A is a tetrasaccharide overexpressed on a wide range of cancerous cells. CA 19-9 has been detected at elevated levels in sera of patients with various types of malignancies, most prominently pancreatic ductal adenocarcinoma. After its identification in 1979, multiple studies have highlighted the significant roles of CA 19-9 in cancer progression, including facilitating extravasation and eventually metastases, proliferation of cancer cells, and suppression of the immune system. Therefore, CA 19-9 has been considered an attractive target for cancer diagnosis, prognosis, and therapy. This review discusses the synthesis of CA 19-9 antigen, elicitation of antibodies through vaccination, development of anti-CA 19-9 monoclonal antibodies, and their applications as imaging tracers and therapeutics for a variety of CA 19-9-positive cancer.

ALG13-Related Epilepsy: Current Insights and Future Research Directions

The ALG13 gene encodes a subunit of the uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) transferase enzyme, which plays a key role in the N-linked glycosylation pathway. This pathway involves the attachment of carbohydrate structures to asparagine (Asn) residues in proteins within the endoplasmic reticulum, by which N-glycosylated proteins produced participate a wide range of processes such as electrical gradients formation and neurotransmission. Mutations in the ALG13 gene have been identified as a causative factor for congenital disorders of glycosylation (CDG) and have been frequently associated with epilepsy in affected individuals. Several studies have demonstrated a strong correlation between abnormal N-glycosylation due to ALG13 deficiency and the onset of epilepsy. Despite these findings, the precise role of ALG13 in the pathogenesis of epilepsy remains unclear. This review provides a comprehensive overview of the current literature on ALG13-related disorders, with a focus on recent evidence regarding its role in epilepsy development and progression. Future research directions are also proposed to further elucidate the molecular mechanisms underlying this association.

Spatial organization of the sperm cell glycoproteome

Sperm cells are terminally differentiated cells that are essential for reproduction in sexually reproducing species. Consistent with their highly specialized function, sperm cells harbor a unique proteome containing many proteins not expressed in somatic cells. In contrast, the post-translational landscape of the sperm proteome remains largely unexplored, limiting our understanding of how modifications such as glycosylation impact sperm function and sperm-egg interactions. Here, we used glycopeptide-centric glycoproteomics to comprehensively characterize protein N-glycosylation in sperm from three mammalian species, revealing clear conservation of glycosylation profiles. We find that glycosylation patterns in sperm proteins are distinct from those in plasma, with as clear distinctive features less sialyation and more paucimannosylation in sperm. Moreover, based on their subcellular location, sperm protein glycosylation varies, with paucimannose species enriched in the acrosomal vesicle, oligomannose species in the sperm head membrane, and complex glycan species in the acrosomal membrane.

Non-natural sialic acid derivatives with o-nitrobenzyl alcohol substituents for light-mediated protein conjugation and cell imaging

We have synthesized two sialic acid derivatives substituted with an ortho-nitrobenzyl alcohol (o-NBA) group that can undergo light-mediated conjugation with primary amines at their 5- or 9-carbon position. The o-NBA derivatives were shown to react with multiple lysine residues of human serum albumin (HSA) when exposed to 365 nm light irradiation within 10 min. The resulting sugar conjugates were characterized by mass spectroscopy and used for fluorescence-based cell imaging.

Expression of ALG8 in hepatocellular carcinoma and its diagnostic and prognostic significance

BACKGROUND

Alpha-1,3-glucosyltransferase (ALG8), a key enzyme in protein glycosylation, is implicated in the oncogenesis and progression of several human malignancies. This study aimed to define the role of ALG8 in hepatocellular carcinoma (HCC) and uncover its mechanisms of action.

METHODS

ALG8 expression in HCC and normal tissues was analyzed using the TCGA and GEO databases, validated by RT-qPCR and western blot. Survival outcomes were evaluated via Cox analyses, and ALG8's impact on HCC behavior was examined through functional assays. GO, KEGG, and GSEA identified ALG8-related pathways, validated by biochemical assays.

RESULTS

In bioinformatics analyses, ALG8 was overexpressed in HCC tissues (p < 0.05 for all comparisons) and correlated with poorer survival (p = 0.006 and p = 0.025, respectively), establishing its role as an independent prognostic factor. In vitro experiments showed that knockdown of ALG8 reduced HCC cell proliferation, migration, and invasion. Using the STRING platform and TCGA-LIHC dataset, we identified ALG8-interacting genes and their associated differentially expressed genes (DEGs). GO and KEGG analyses further linked ALG8 to genes involved in glycosylation, signal release, and other processes, as well as pathways including neuroactive ligand-receptor interaction and N-Glycan biosynthesis. GSEA, corroborated by western blot and immunofluorescence, points to the Wnt/β-catenin signaling cascade as a probable mechanistic pathway through which ALG8 may modulate HCC progression.

CONCLUSION

Elevated ALG8 expression in HCC is linked to worse outcomes and increased tumor aggressiveness, with silencing ALG8 reducing Wnt/β-catenin signaling, highlighting ALG8 as a potential therapeutic target.

Leucine zipper-based SAIM imaging identifies therapeutic agents to disrupt the cancer cell glycocalyx for enhanced immunotherapy

The abnormally thick glycocalyx of cancer cells can provide a physical barrier to immune cell recognition and effective immunotherapy. Here, we demonstrate an optical method based on Scanning Angle Interference Microscopy (SAIM) for the screening of therapeutic agents that can disrupt the glycocalyx layer as a strategy to improve anti-cancer immune responses. We developed a new membrane labeling strategy utilizing leucine zipper pairs to fluorescently mark the glycocalyx layer boundary for precise and robust measurement of glycocalyx thickness with SAIM. Using this platform, we evaluated the effects of glycosylation inhibitors and targeted enzymatic degraders of the glycocalyx, with particular focus on strategies for cholangiocarcinoma (CCA), a highly lethal malignancy with limited therapeutic options. We found that CCA had the highest mean expression of the cancer-associated mucin, MUC1, across all cancers represented in the cancer cell line encyclopedia. Pharmacological inhibitors of mucin-type O-glycosylation and mucin-specific proteases, such as StcE, could dramatically reduce the glycocalyx layer in the YSCCC model of intrahepatic CCA. Motivated by these findings, we engineered Natural Killer (NK) cells tethered with StcE to enhance NK cell-mediated cytotoxicity against CCA. In a CCA xenograft model, these engineered NK cells demonstrated superior anti-tumor efficacy compared to wild-type NK cells, with no observable adverse effects. Our findings not only provide a reliable imaging-based screening platform for evaluating glycocalyx-targeting pharmacological interventions but also offer mechanistic insights into how CCA may avoid immune elimination through fortification of the glycocalyx layer with mucins. Additionally, this work presents a novel therapeutic strategy for mucin-overexpressing cancers, potentially improving immunotherapy efficacy across various cancer types.

The Circulating Proteome─Technological Developments, Current Challenges, and Future Trends

Recent improvements in proteomics technologies have fundamentally altered our capacities to characterize human biology. There is an ever-growing interest in using these novel methods for studying the circulating proteome, as blood offers an accessible window into human health. However, every methodological innovation and analytical progress calls for reassessing our existing approaches and routines to ensure that the new data will add value to the greater biomedical research community and avoid previous errors. As representatives of HUPO's Human Plasma Proteome Project (HPPP), we present our 2024 survey of the current progress in our community, including the latest build of the Human Plasma Proteome PeptideAtlas that now comprises 4608 proteins detected in 113 data sets. We then discuss the updates of established proteomics methods, emerging technologies, and investigations of proteoforms, protein networks, extracellualr vesicles, circulating antibodies and microsamples. Finally, we provide a prospective view of using the current and emerging proteomics tools in studies of circulating proteins.

Nutrient control of growth and metabolism through mTORC1 regulation of mRNA splicing

Cellular growth and organismal development are remarkably complex processes that require the nutrient-responsive kinase mechanistic target of rapamycin complex 1 (mTORC1). Anticipating that important mTORC1 functions remained to be identified, we employed genetic and bioinformatic screening in C. elegans to uncover mechanisms of mTORC1 action. Here, we show that during larval growth, nutrients induce an extensive reprogramming of gene expression and alternative mRNA splicing by acting through mTORC1. mTORC1 regulates mRNA splicing and the production of protein-coding mRNA isoforms largely independently of its target p70 S6 kinase (S6K) by increasing the activity of the serine/arginine-rich (SR) protein RSP-6 (SRSF3/7) and other splicing factors. mTORC1-mediated mRNA splicing regulation is critical for growth; mediates nutrient control of mechanisms that include energy, nucleotide, amino acid, and other metabolic pathways; and may be conserved in humans. Although mTORC1 inhibition delays aging, mTORC1-induced mRNA splicing promotes longevity, suggesting that when mTORC1 is inhibited, enhancement of this splicing might provide additional anti-aging benefits.

The Dectin-1 and Dectin-2 clusters: C-type lectin receptors with fundamental roles in immunity

The ability of myeloid cells to recognize and differentiate endogenous or exogenous ligands rely on the presence of different transmembrane protein receptors. C-type lectin receptors (CLRs), defined by the presence of a conserved structural motif called C-type lectin-like domain (CTLD), are a crucial family of receptors involved in this process, being able to recognize a diverse range of ligands from glycans to proteins or lipids and capable of initiating an immune response. The Dectin-1 and Dectin-2 clusters involve two groups of CLRs, with genes genomically linked within the natural killer cluster of genes in both humans and mice, and all characterized by the presence of a single extracellular CTLD. Fundamental immune cell functions such as antimicrobial effector mechanisms as well as internalization and presentation of antigens are induced and/or regulated through activatory, or inhibitory signalling pathways triggered by these receptors after ligand binding. In this review, we will discuss the most recent concepts regarding expression, ligands, signaling pathways and functions of each member of the Dectin clusters of CLRs, highlighting the importance and diversity of their functions.

The forecasting power of the mucin-microbiome interplay in livestock respiratory diseases

Complex respiratory diseases are a significant challenge for the livestock industry worldwide. These diseases considerably impact animal health and welfare and cause severe economic losses. One of the first lines of pathogen defense combines the respiratory tract mucus, a highly viscous material primarily composed of mucins, and a thriving multi-kingdom microbial ecosystem. The microbiome-mucin interplay protects from unwanted substances and organisms, but its dysfunction may enable pathogenic infections and the onset of respiratory disease. Emerging evidence also shows that noncoding regulatory RNAs might modulate the structure and function of the microbiome-mucin relationship. This opinion paper unearths the current understanding of the triangular relationship between mucins, the microbiome, and noncoding RNAs in the context of respiratory infections in animals of veterinary interest. There is a need to look at these molecular underpinnings that dictate distinct health and disease outcomes to implement effective prevention, surveillance, and timely intervention strategies tailored to the different epidemiological contexts.

N-glycan as new potential biomarker for predicting treatment response in patients with type 2 diabetes mellitus

AIMS

To investigate the N-glycans related to the metformin efficacy in patients with type 2 diabetes mellitus (T2DM).

MATERIALS AND METHODS

We enrolled 141 healthy controls and 195 newly diagnosed T2DM patients treated with metformin for 3 months. Serum N-glycan profile was determined by DNA sequencer - assisted fluorophore-assisted carbohydrate electrophoresis (DSA-FACE). The N-glycan model was established by logistic regression analysis. Receiver operating characteristic curve (ROC) analysis was used to analyze the predictive power of the N-glycan model for metformin efficacy.

RESULTS

The abundances of several N-glycans in serum of T2DM patients at baseline were significantly different from those of healthy controls and tended to recover the N-glycan of controls after 3 months treatment. Serum N-glycans changes were more significant in the good response group (FPG <7 mmol/L) after metformin treatment. In addition, the abundance of peak9 at baseline had an opposite tendency between HbA1c increased and decreased groups post-treatment, which could be a biomarker for predicting metformin efficacy. Peak9 combined with other 11 N-glycans at baseline was used to establish the predictive model to distinguish non-response from response patients (AUROC = 0.780, sensitivity = 70.6% and specificity = 77.5%).

CONCLUSIONS

Serum N-glycans may have potential value as biomarkers for indicating the efficacy of metformin.

Rational development of functional hydrophilic polymer to characterize site-specific glycan differences between bovine milk and colostrum

As vastly modified on secreted proteins, N-glycosylation is found on milk proteins and undergo dynamic changes during lactation, characterizing milk protein glycosylation would benefit the elucidation of glycosylation pattern differences between samples. However, their low abundance required specific enrichment. Herein, through rational design and controllable synthesis, we developed a novel multi-functional polymer for the isolation of protein glycosylation. It efficiently separated glycopeptides from complex background inferences with mutual efforts of hydrophilic interaction chromatography (HILIC), metal ion affinity and ion exchange. By fine-tuning Ca2+ as regulators of aldehyde hyaluronic acid (HA) conformation, the grafting density of HA was remarkably improved. Moreover, grafting Ti4+ further enhanced the enrichment performance. Application of this material to characterize bovine milk and colostrum proteins yields 479 and 611 intact glycopeptides, respectively. Comparative analysis unraveled the distinct glycosylation pattern as well the different distribution of glycoprotein abundances between the two samples, offering insights for functional food development.

Dang-Gui-Bu-Xue decoction against diabetic nephropathy via modulating the carbonyl compounds metabolic profile and AGEs/RAGE pathway

BACKGROUND

Dang-Gui-Bu-Xue decoction (DBD) is a traditional Chinese medicine prescription clinically employed for diabetic nephropathy (DN). However, the components and pharmacological mechanisms of DBD against DN remain incompletely understood.

PURPOSE

To clarify the beneficial effect of DBD on DN and to explore its nephroprotective effect's probable mechanism and the main components.

METHODS

A diabetic mice model was established by feeding a high-fat diet (HFD) and intraperitoneal injections of streptozotocin (STZ, 40 mg‧kg-1). Subsequently, the mice were maintained on a HFD and administered with DBD. The benefits of DBD against DN were comprehensively assessed by monitoring energy and water intake, blood glucose and lipids, renal functions and pathological status. The UPLC-MS/MS was measured to detect chemical constituents in DBD and absorbed components in DBD-treated plasma under physiological and pathological states. Network pharmacology was employed to forecast the probable pathways of DBD intervention in DN, with subsequent validation of these predictions through testing biochemical parameters, anti-glycation and ELISA assays, immunofluorescence, immunohistochemistry, and western blotting. Then, a chemical derivatization method paired with UPLC-MS/MS analysis was performed to detect the carbonyl compounds in renal tissue. Finally, the main components of DBD against DN were screened by anti-glycation and MTT assays.

RESULTS

DBD regulated energy and water intakes, glucose and lipid metabolism disorders, renal dysfunction, glomerular filtration rate, renal interstitial glycogen accumulation and fibrosis in HFD/STZ-induced DN mice. A total of 129 distinct chemical constituents in DBD were characterized, of which 28 were detected in the DBD-treated plasma under a pathological state. The network pharmacological results suggested AGEs/RAGE and its downstream pathway may be a potential pathway for DBD intervention in DN. Further experiments confirmed that DBD reduced renal oxidative stress by modulating the AGEs/RAGE pathway. Moreover, 21 differential carbonyl compounds were detected between normal and DN mice, and DBD significantly modulated 16. Ultimately, seven components were screened out in DBD, which may be the main components of DBD regulating carbonyl compounds metabolic profile and AGEs/RAGE pathway.

CONCLUSION

Our findings suggested for the first time that DBD could regulate the carbonyl compounds metabolic profile and AGEs/RAGE signaling pathway to ameliorate DN.

Role of N-Glycosylation in Gastrointestinal Cancers

Gastrointestinal cancers pose a significant global health challenge. N-glycosylation modulates various cellular processes, including key cancer-related mechanisms. Elucidating its involvement in the onset and advancement of these cancers can offer critical insights for enhancing diagnostic and therapeutic approaches. This review outlines the core process of protein N-glycosylation and highlights its contribution to the progression of gastrointestinal cancers, encompassing cell proliferation, survival, invasion, metastasis, and immune evasion, mainly through its impact on critical signaling pathways. Notably, aberrant N-glycosylation patterns have emerged as crucial biomarkers for the diagnosis and prognosis of various gastrointestinal cancers, providing the foundation for more personalized therapeutic approaches. Therapeutic strategies targeting N-glycosylation, such as glycosyltransferase inhibitors and glycoengineering, show significant promise in mitigating tumor aggressiveness and enhancing immune recognition. However, the clinical implementation of N-glycosylation biomarkers requires the standardization of glycosylation analysis techniques and solutions to challenges in sample processing and data interpretation. Future research efforts should concentrate on overcoming these obstacles to unlock the full potential of N-glycosylation in enhancing cancer management and advancing patient outcomes.

Cell- and tissue-specific glycosylation pathways informed by single-cell transcriptomics

While single-cell studies have made significant impacts in various subfields of biology, they lag in the Glycosciences. To address this gap, we analyzed single-cell glycogene expressions in the Tabula Sapiens dataset of human tissues and cell types using a recent glycosylation-specific gene ontology (GlycoEnzOnto). At the median sequencing (count) depth, ∼40-50 out of 400 glycogenes were detected in individual cells. Upon increasing the sequencing depth, the number of detectable glycogenes saturates at ∼200 glycogenes, suggesting that the average human cell expresses about half of the glycogene repertoire. Hierarchies in glycogene and glycopathway expressions emerged from our analysis: nucleotide-sugar synthesis and transport exhibited the highest gene expressions, followed by genes for core enzymes, glycan modification and extensions, and finally terminal modifications. Interestingly, the same cell types showed variable glycopathway expressions based on their organ or tissue origin, suggesting nuanced cell- and tissue-specific glycosylation patterns. Probing deeper into the transcription factors (TFs) of glycogenes, we identified distinct groupings of TFs controlling different aspects of glycosylation: core biosynthesis, terminal modifications, etc. We present webtools to explore the interconnections across glycogenes, glycopathways and TFs regulating glycosylation in human cell/tissue types. Overall, the study presents an overview of glycosylation across multiple human organ systems.

Eph receptor signaling complexes in the plasma membrane

Eph receptor tyrosine kinases, together with their cell surface-anchored ephrin ligands, constitute an important cell-cell communication system that regulates physiological and pathological processes in most cell types. This review focuses on the multiple mechanisms by which Eph receptors initiate signaling via the formation of protein complexes in the plasma membrane. Upon ephrin binding, Eph receptors assemble into oligomers that can further aggregate into large complexes. Eph receptors also mediate ephrin-independent signaling through interplay with intracellular kinases or other cell-surface receptors. The distinct characteristics of Eph receptor family members, as well as their conserved domain structure, provide a framework for understanding their functional differences and redundancies. Possible areas of interest for future investigations of Eph receptor signaling complexes are also highlighted.

GLS2 links glutamine metabolism and atherosclerosis by remodeling artery walls

Metabolic dysregulation, including perturbed glutamine-glutamate homeostasis, is common among patients with cardiovascular diseases, but the underlying mechanisms remain largely unknown. Using the human MESA cohort, here we show that plasma glutamine-glutamate ratio is an independent risk factor for carotid plaque progression. Mice deficient in glutaminase-2 (Gls2), the enzyme that mediates hepatic glutaminolysis, developed accelerated atherosclerosis and susceptibility to catastrophic cardiac events, while Gls2 overexpression partially protected from disease progression. High-throughput transcriptional profiling and high-resolution structural biology imaging of aortas showed that Gls2 deficiency perturbed extracellular matrix composition and increased vessel stiffness. This results from an imbalance of glutamine- and glutamate-dependent cross-linked proteins within atherosclerotic lesions and cellular remodeling of plaques. Thus, hepatic glutaminolysis functions as a potent regulator of glutamine homeostasis, which affects the aortic wall structure during atherosclerotic plaque progression.

Comprehensive Analysis of Sialylation-Related Gene Profiles and Their Impact on the Immune Microenvironment in Periodontitis

Periodontitis is a chronic inflammatory disease strongly influenced by host's immune response. Aberrant sialylation on cell surface plays a key role in inflammation and immunity. This study aims to identify sialylation-related genes associated with periodontitis and explore their impact on periodontal immune microenvironment. Differential expression analysis and machine learning were employed to determine core sialylation-related genes after datasets were retrieved and integrated. A diagnostic model incorporating these genes was constructed, following the immune cell infiltration analysis. Consensus clustering and weighted gene co-expression network analysis stratified periodontitis patients into subgroups and identified associated module genes. Single-cell sequencing data was further utilized to investigate the impact of sialylation on the periodontal immune microenvironment with pseudo-time series analysis and cell communication analysis. Periodontitis had a higher sialylation score with six key sialylation genes (CHST2, SELP, ST6GAL1, ST3GAL1, NEU1, FCN1) identified. The multi-gene diagnostic model demonstrated high accuracy and efficacy. Significant associations were observed between the key genes and immune cell populations, such as monocytes and B cells, in the periodontal immune microenvironment. Clustering analysis revealed two distinct sialylation-related subgroups with differential immune profiles. Single-cell data showed a significantly higher expression of sialylation-related genes in monocytes, which was found to significantly impact their developmental processes as well as their intercellular communication with B cells. The six identified sialylation-related genes hold potential as periodontitis biomarkers. High sialylation expression can impact the differentiation and cell-cell communication of monocytes. Sialylation-related genes are closely associated with alterations in the periodontal immune microenvironment.

Ni-Catalyzed Stereodivergent Synthesis of N-Glycosides

Herein, we describe a stereoselective Ni-catalyzed N-glycosylation of glycals. The reaction is enabled by addition of an in situ generated nickel hydride across an olefin prior to C-N bond-formation. Stereodivergence can be accomplished on kinetic or thermodynamic grounds, thus giving access to either α- or β-N-glycosides with equal ease. The protocol is distinguished by its operational simplicity, generality and exquisite selectivity, thus offering a new gateway to expedite the synthesis of N-glycosides.

Molecular Spies in Action: Genetically Encoded Fluorescent Biosensors Light up Cellular Signals

Cellular function is controlled through intricate networks of signals, which lead to the myriad pathways governing cell fate. Fluorescent biosensors have enabled the study of these signaling pathways in living systems across temporal and spatial scales. Over the years there has been an explosion in the number of fluorescent biosensors, as they have become available for numerous targets, utilized across spectral space, and suited for various imaging techniques. To guide users through this extensive biosensor landscape, we discuss critical aspects of fluorescent proteins for consideration in biosensor development, smart tagging strategies, and the historical and recent biosensors of various types, grouped by target, and with a focus on the design and recent applications of these sensors in living systems.

Metabolomics and 13C labelled glucose tracing to identify carbon incorporation into aberrant cell membrane glycans in cancer

Cell membrane glycans contribute to immune recognition, signaling, and cellular adhesion and migration, and altered membrane glycosylation is a feature of cancer cells that contributes to cancer progression. The uptake and metabolism of glucose and other nutrients essential for glycan synthesis could underlie altered membrane glycosylation, but the relationship between shifts in nutrient metabolism and the effects on glycans have not been directly examined. We developed a method that combines stable isotope tracing with metabolomics to enable direct observations of glucose allocation to nucleotide sugars and cell-membrane glycans. We compared the glucose allocation to membrane glycans of two pancreatic cancer cell lines that are genetically identical but have differing energy requirements. The 8988-S cells had higher glucose allocation to membrane glycans and intracellular pathways relating to glycan synthesis, but the 8988-T cells had higher glucose uptake and commitment of glucose to non-glycosylation pathways. The cell lines differed in the requirements of glucose for energy production, resulting in differences in glucose bioavailability for glycan synthesis. The workflow demonstrated here enables studies on the effects of metabolic shifts on the commitment of nutrients to cell-membrane glycans. The results suggest that cell-membrane glycans are remodeled through shifts in glucose commitment to non-glycosylation pathways.

Cell-based glycoengineering of extracellular vesicles through precise genome editing

Engineering of extracellular vesicles (EVs) towards more efficient targeting and uptake to specific cells has large potentials for their application as therapeutics. Carbohydrates play key roles in various biological interactions and are essential for EV biology. The extent to which glycan modification of EVs can be achieved through genetic glycoengineering of their parental cells has not been explored yet. Here we introduce targeted glycan modification of EVs through cell-based glycoengineering via modification of various enzymes in the glycosylation machinery. In a "simple cell" strategy, we modified major glycosylation pathways by knocking-out (KO) essential genes for N-glycosylation (MGAT1), O-GalNAc glycosylation (C1GALT1C1), glycosphingolipids (B4GALT5/6), glycosaminoglycans (B4GALT7) and sialylation (GNE) involved in the elongation or biosynthesis of the glycans in HEK293F cells. The gene editing led to corresponding glycan changes on the cells as demonstrated by differential lectin staining. Small EVs (sEVs) isolated from the cells showed overall corresponding glycan changes, but also some unexpected differences to their parental cell including enrichment preference for certain glycan structures and absence of other glycan types. The genetic glycoengineering did not significantly impact sEVs production, size distribution, or syntenin-1 biomarker expression, while a clonal influence on sEVs production yields was observed. Our findings demonstrate the successful implementation of sEVs glycoengineering via genetic modification of the parental cell and a stable source for generation of glycoengineered sEVs. The utilization of glycoengineered sEVs offers a promising opportunity to study the role of glycosylation in EV biology, as well as to facilitate the optimization of sEVs for therapeutic purposes.

Recent Advances in Labeling-Based Quantitative Glycomics: From High-Throughput Quantification to Structural Elucidation

Glycosylation, a crucial posttranslational modification (PTM), plays important roles in numerous biological processes and is linked to various diseases. Despite its significance, the structural complexity and diversity of glycans present significant challenges for mass spectrometry (MS)-based quantitative analysis. This review aims to provide an in-depth overview of recent advancements in labeling strategies for N-glycomics and O-glycomics, with a specific focus on enhancing the sensitivity, specificity, and throughput of MS analyses. We categorize these advancements into three major areas: (1) the development of isotopic/isobaric labeling techniques that significantly improve multiplexing capacity and throughput for glycan quantification; (2) novel methods that aid in the structural elucidation of complex glycans, particularly sialylated and fucosylated glycans; and (3) labeling techniques that enhance detection ionization efficiency, separation, and sensitivity for matrix-assisted laser desorption/ionization (MALDI)-MS and capillary electrophoresis (CE)-based glycan analysis. In addition, we highlight emerging trends in single-cell glycomics and bioinformatics tools that have the potential to revolutionize glycan quantification. These developments not only expand our understanding of glycan structures and functions but also open new avenues for biomarker discovery and therapeutic applications. Through detailed discussions of methodological advancements, this review underscores the critical role of derivatization methods in advancing glycan identification and quantification.

Oriental covalent immobilization of N-glycan binding protein via N-terminal selective modification

Lectin affinity chromatography is one of powerful tools for the study of protein glycosylation. Different lectin proteins can recognize different structures of monosaccharides or oligosaccharide units, allowing for the selective separation of glycopeptides or glycoproteins containing different polysaccharide structures. However, the N-glycans were only partially captured by most of common lectins, reducing the coverage rate of identifying N-glycoconjugates. Recently, it has been reported that the engineering variant of glycan binding protein Fbs1 has a high affinity for innermost Man3GlcNAc2 structure and is able to bind diverse types of N-glycans, which can be suitable for the analysis of protein N-glycosylation. However, efficient immobilization of protein to separation matrix is particularly challenging as it requires the functionality and integrity of the protein to be preserved. Herein, we describe a simple and robust strategy for oriental covalent immobilization of proteins on magnetic nanoparticles by N-terminal selective labeling techniques. We inserted the enterokinase cleavage site to produce the specific N- terminal glycine of protein. Under physiological conditions, the protein was immobilized on the surface of the MNPs by this glycine tag, and the enrichment process could be completed within 30 min. A whole enrichment and purification of glycan and glycopeptides were completed and analyzed by MALDI TOF-MS. The functional materials achieved stable enrichment of glycan structure in different enzyme digestion systems or complex samples, showing excellent anti-interference and applicability.

Chemical glycoproteomic profiling in rice seedlings reveals N-glycosylation in the ERAD-L machinery

As a ubiquitous and essential posttranslational modification occurring in both plants and animals, protein N-linked glycosylation regulates various important biological processes. Unlike the well-studied animal N-glycoproteomes, the landscape of rice N-glycoproteome remains largely unexplored. Here, by developing a chemical glycoproteomic strategy based on metabolic glycan labeling (MGL), we report a comprehensive profiling of the N-glycoproteome in rice seedlings. The rice seedlings are incubated with N-azidoacetylgalactosamine (GalNAz) - a monosaccharide analog containing a bioorthogonal functional group - to metabolically label N-glycans, followed by conjugation with an affinity probe via click chemistry for enrichment of the N-glycoproteins. Subsequent mass spectrometry analyses identify a total of 403 N-glycosylation sites and 673 N-glycosylated proteins, which are involved in various important biological processes. In particular, the core components of the endoplasmic reticulum (ER)-associated protein degradation (ERAD) machinery are N-glycosylated, and the N-glycosylation is important for the ERAD-L function. This work not only provides an invaluable resource for studying rice N-glycosylation, but also demonstrates the applicability of MGL in glycoproteomic profiling for crop species.

Nanoparticles as Delivery Systems for Antigenic Saccharides: From Conjugation Chemistry to Vaccine Design

Glycoconjugate vaccines have been effective in preventing numerous bacterial infectious diseases and have shown recent potential to treat cancers through active immunotherapy. Soluble polysaccharides elicit short-lasting immune responses and are usually covalently linked to immunogenic carrier proteins to enhance the antigen-specific immune response by stimulating T-cell-dependent mechanisms. Nonetheless, the conjugation of purified polysaccharides to carrier proteins complexifies vaccine production, and immunization with protein glycoconjugates can lead to the undesirable immunogenic interference of the carrier. Recently, the use of nanoparticles and nanoassemblies for the delivery of antigenic saccharides has gathered attention from the scientific community. Nanoparticles can be easily functionalized with a diversity of functionalities, including T-cell epitope, immunomodulator and synthetic saccharides, allowing for the modulation and polarization of the glycoantigen-specific immune response. Notably, the conjugation of glycan to nanoparticles protects the antigens from degradation and enhances their uptake by immune cells. Different types of nanoparticles, such as liposomes assembled from lipids, inorganic nanoparticles, virus-like particles and dendrimers, have been explored for glycovaccine design. The versatility of nanoparticles and their ability to induce robust immune responses make them attractive delivery platforms for antigenic saccharides. The present review aims at summarizing recent advancements in the use of nano-scaled systems for the delivery of synthetic glycoantigens. After briefly presenting the immunological mechanisms required to promote a robust immune response against antigenic saccharides, this review will offer an overview of the current trends in the nanoparticle-based delivery of glycoantigens.

Rabbit and Human Angiotensin-Converting Enzyme-2: Structure and Electric Properties

The angiotensin-converting enzyme-2 (ACE2) is a transmembrane glycoprotein, consisting of two segments: a large carboxypeptidase catalytic domain and a small transmembrane collectrin-like segment. This protein plays an essential role in blood pressure regulation, transforming the peptides angiotensin-I and angiotensin-II (vasoconstrictors) into angiotensin-1-9 and angiotensin-1-7 (vasodilators). During the COVID-19 pandemic, ACE2 became best known as the receptor of the S-protein of SARS-CoV-2 coronavirus. The purpose of the following research is to reconstruct the 3D structure of the catalytic domain of the rabbit enzyme rACE2 using its primary amino acid sequence, and then to compare it with the human analog hACE2. For this purpose, we have calculated the electric properties and thermodynamic stability of the two protein globules employing computer programs for protein electrostatics. The analysis of the amino acid content and sequence demonstrates an 85% identity between the two polypeptide chains. The 3D alignment of the catalytic domains of the two enzymes shows coincidence of the α-helix segments, and a small difference in two unstructured segments of the chain. The electric charge of the catalytic domain of rACE2, determined by 70 positively chargeable amino acid residues, 114 negatively chargeable ones, and two positive charges of the Zn2+ atom in the active center exceeds that of hACE2 by one positively and four negatively chargeable groups; however, in 3D conformation, their isoelectric points pI 5.21 coincide. The surface electrostatic potential is similarly distributed on the surface of the two catalytic globules, but it strongly depends on the pH of the extracellular medium: it is almost positive at pH 5.0 but strongly negative at pH 7.4. The pH dependence of the electrostatic component of the free energy discloses that the 3D structure of the two enzymes is maximally stable at pH 6.5. The high similarity in the 3D structure, as well as in the electrostatic and thermodynamic properties, suggests that rabbit can be successfully used as an animal model to study blood pressure regulation and coronavirus infection, and the results can be extrapolated to humans.

Profiling of insulin-resistant kidney models and human biopsies reveals common and cell-type-specific mechanisms underpinning Diabetic Kidney Disease

Diabetic kidney disease (DKD) is the leading cause of end stage kidney failure worldwide, of which cellular insulin resistance is a major driver. Here, we study key human kidney cell types implicated in DKD (podocytes, glomerular endothelial, mesangial and proximal tubular cells) in insulin sensitive and resistant conditions, and perform simultaneous transcriptomics and proteomics for integrated analysis. Our data is further compared with bulk- and single-cell transcriptomic kidney biopsy data from early- and advanced-stage DKD patient cohorts. We identify several consistent changes (individual genes, proteins, and molecular pathways) occurring across all insulin-resistant kidney cell types, together with cell-line-specific changes occurring in response to insulin resistance, which are replicated in DKD biopsies. This study provides a rich data resource to direct future studies in elucidating underlying kidney signalling pathways and potential therapeutic targets in DKD.

CRISPR screens and lectin microarrays identify high mannose N-glycan regulators

Glycans play critical roles in cellular signaling and function. Unlike proteins, glycan structures are not templated from genetic sequences but synthesized by the concerted activity of many genes, making them historically challenging to study. Here, we present a strategy that utilizes CRISPR screens and lectin microarrays to uncover and characterize regulators of glycosylation. We applied this approach to study the regulation of high mannose glycans - the starting structure of all asparagine(N)-linked-glycans. We used CRISPR screens to uncover the expanded network of genes controlling high mannose levels, followed by lectin microarrays to fully measure the complex effect of select regulators on glycosylation globally. Through this, we elucidated how two high mannose regulators - TM9SF3 and the CCC complex - control complex N-glycosylation via regulating Golgi morphology and function. Notably, this allows us to interrogate Golgi function in-depth and reveals that similar disruption to Golgi morphology can lead to drastically different glycosylation outcomes. Collectively, this work demonstrates a generalizable approach for systematically dissecting the regulatory network underlying glycosylation.

Characterization of Cell Surface Glycoproteins Using Enzymatic Treatment and Mass Spectrometry

Almost all proteins on the cell surface are modified by glycosylation. Cell surface glycoproteins participate in various cellular pathways, such as cell adhesion, cell-cell communication, and immune response. Due to their functional importance, glycoproteins on the cell surface often serve as potential therapeutic targets. Recent advancements in mass spectrometry (MS) have facilitated the characterization of glycoproteins that are generally localized on the cell surface, secreted to the extracellular environment, or found in intracellular organelles such as the endoplasmic reticulum, Golgi apparatus, and peroxisome. However, the selective characterization of glycoproteins on the cell surface remains challenging. In this study, we applied enzymatic treatment to live cells, followed by MS-based glycoproteomics analysis, to assess changes in protein glycosylation at different treatment time points as a method to identify cell surface glycoproteins. To demonstrate this approach, a renal cell carcinoma cell line, A498, was treated with glycosidases, sialidase and PNGase F, over two treatment time intervals, 2 and 24 h. Glycoproteins were identified as cell surface glycoproteins from A498 cells when enzyme treatment altered the glycosylation of the glycoproteins. The results revealed the effectiveness of integrating enzymatic treatment with MS-based glycoproteomics for analyzing cell surface glycoproteins. Our established method has demonstrated the potential applications for assessing accessibility of therapeutic targets on the cell surface over time and supporting the development of new targeted therapies.

Nanopore approaches for single-molecule temporal omics: promises and challenges

The great molecular heterogeneity within single cells demands omics analysis from a single-molecule perspective. Moreover, considering the perpetual metabolism and communication within cells, it is essential to determine the time-series changes of the molecular library, rather than obtaining data at only one time point. Thus, there is an urgent need to develop a single-molecule strategy for this omics analysis to elucidate the biosystem heterogeneity and temporal dynamics. In this Perspective, we explore the potential application of nanopores for single-molecule temporal omics to characterize individual molecules beyond mass, in both a single-molecule and high-throughput manner. Accordingly, recent advances in nanopores available for single-molecule temporal omics are reviewed from the view of single-molecule mass identification, revealing single-molecule heterogeneity and illustrating temporal evolution. Furthermore, we discuss the primary challenges associated with using nanopores for single-molecule temporal omics in complex biological samples, and present the potential strategies and notes to respond to these challenges.

O-glycosylation is essential for cell surface expression of the transcobalamin receptor CD320

CD320 is a cell surface receptor that mediates vitamin B12 uptake in most tissues. To date, the mechanisms that regulate CD320 expression on the cell surface are not fully understood. In this work, we studied CD320 expression in transfected human embryonic kidney (HEK) 293 and hepatoma HepG2 cells. By glycosidase and trypsin digestion, monensin and brefeldin treatment, western blotting, flow cytometry, and lectin binding, we found that CD320 underwent N- and O-glycosylation and sialylation, resulting in a ∼70-kDa band that formed a high-molecular-weight complex on the cell surface. Site-directed mutagenesis altering Asn126, Asn195, and Asn213 residues, individually or together, abolished N-glycosylation in CD320 but did not block its intracellular trafficking and expression on the cell surface in HEK293 and HepG2 cells. In contrast, treatment of the cells with Ben-gal, a structural analog of GalNAc-α-1-O-Ser/Thr, inhibited O-glycosylation and cell surface expression of CD320 and decreased vitamin B12 uptake. Analysis of CD320 deletion mutants indicated that O-glycosylation sites in a Ser/Thr-rich region near the transmembrane domain were important for CD320 expression on the cell surface. These results reveal an important role of O-glycans, but not N-glycans, in the intracellular trafficking and cell surface expression of CD320, providing new insights into the cellular mechanisms in regulating CD320 function and vitamin B12 metabolism.

Deciphering the Cell Surface Sugar-Coating via Biochemical Pathways

Cell surface components, specifically glycans, play a significant role in several biological functions like cell structure, crosstalk between cells, and eventual target recognition of the cells for therapeutics. The dense layer of glycans, i. e., glycocalyx, could differ in taxon, species, and cell type. Glycans are coupled with lipids and proteins to form glycolipids, glycoproteins, proteoglycans, and glycosylphosphatidylinositol-anchored proteins, making their study challenging. However, understanding glycosylation at the cellular level is vital for fundamental research and advancing glycan-targeted therapy. Among different pathways, metabolic glycan labelling uses the natural metabolic processes of the cell to introduce abiotic functionality into glycan residues. The Bertozzi group pioneered metabolic oligosaccharide engineering using glycan salvage pathways to convert monosaccharides with unnatural modifications. This eventually results in the probe becoming part of the complex cellular glycan structures via click chemistry using copper. On the other hand, the boronic acid-based probe can recognise carbohydrates in a single step without any chemical modification of the surface. This review discusses the significance of glycans as biomarkers for different diseases and the necessity to evaluate them in situ within the physiological environment. The review also discusses the prospect of this field and its potential applications.

Bidirectional signals generated by Siglec-7 and its crucial ligand tri-sialylated T to escape of cancer cells from immune surveillance

Siglec-7, an inhibitory receptor expressed on natural killer (NK) cells, recognizes sialic acid-containing glycans. However, the ligand glycan structures of Siglec-7 and its carrier proteins have not been comprehensively investigated. Here, we identified four sialyltransferases that are used for the synthesis of ligand glycans of Siglec-7 and two ligand O-glycan-carrier proteins, PODXL and MUC13, using a colon cancer line. Upon binding of these ligand glycans, Siglec-7-expressing immune cells showed reduced cytotoxic activity, whereas cancer cells expressing ligand glycans underwent signal activation, leading to enhanced invasion activity. To clarify the structure of the ligand glycan, podoplanin (PDPN) identified as a Siglec-7 ligand-carrier protein, was transfected into HEK293T cells using sialyltransferase cDNAs. Mass spectrometry of the products revealed a ligand glycan, tri-sialylated T antigen. These results indicate that Siglec-7 interaction with its ligand generates bidirectional signals in NK and cancer cells, leading to the efficient escape of cancers from host immune surveillance.

Molecular Modeling of Glycosylated Catalytic Domain of Human Carbonic Anhydrase IX

Glycans exhibit significant structural diversity due to the flexibility of glycosidic bonds linking their constituent monosaccharides and the formation of numerous hydrogen bonds. The present work searches a simulated ensemble of glycan chain conformations attached to the catalytic domain of N-glycosylated human carbonic anhydrase IX (HCA IX-c) to identify conformations pointed away or back-folded toward the protein surface guided by different amino acid residues. A series of classical molecular dynamics (MD) simulation studies for a total of 30 μs followed by accelerated MD simulations for a total of 2 μs have been performed using two different force fields to capture varying degrees of fluctuations of both glycan chain and HCA IX. From the underlying free energy profile and kinetics derived using hidden Markov state model, several stable glycan orientations are identified that extend away from the protein surface and convert among each other with rate constants of the order 107-1010 S-1. Most importantly, we have identified a rare glycan conformation which reaches close to a catalytically important amino acid residue, Glu-106. We further enlist the protein residues that couple such less frequent event of the glycan chain back-folding toward the surface of the protein.

Screening and Characterization of Sialic Acid-Binding Variable Lymphocyte Receptors from Hagfish

Sialic acid is a diverse group of monosaccharides often found on the termini of N- and O-linked glycans as well as being components of glycoconjugates. Hypersialylation has been associated with the progression of chronic inflammation-mediated diseases such as cardiovascular disease and cancer. Given its role in infection and disease-related processes, sialic acid is a promising target for therapeutic approaches that utilize carbohydrate-binding molecules. In this study, we screened for sialic acid-recognizing variable lymphocyte receptors (VLRBs) or ccombodies from inshore hagfish (Eptatretus burgeri) using a synthetic Neu5Ac-glycoconjugate as an antigen in immunoassay. Resulting ccombodies, 2D8, 5G11, 4A1, and 5F8 were further characterized in terms of their binding activity and specificity. A competitive ELISA using free haptens showed strong inhibition using either N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc). The half-maximal inhibitory concentrations (IC50) for Neu5Ac ranged from 7.02 to 17.06 mM, with candidates 4A1 and 5G11 requiring the least and highest amounts, respectively. IC50 values for Neu5Gc ranged from 8.12 to 13.91 mM, for 4A1 and 5G11, respectively. Candidate ccombodies also detected naturally occurring sialic acid from known sialoglycoproteins using a dot blot assay. Neu5Gc-5G11 and Neu5Ac-2D8 yielded the strongest and weakest docking interactions with affinity values of -5.9 kcal/mol and -4.9 kcal/mol, respectively. Hydrogen bonding and hydrophobic interactions were predicted to be the predominant noncovalent forces observed between the ccombodies and sialic acid. This study demonstrates that glycan-binding VLRBs from hagfish hold promise in augmenting the glycobiologists' toolkit in investigating the roles of glycans in human and animal health and disease.

Processing of N-glycans in the ER and Golgi influences the production of surface sialylated glycoRNA

Glycoconjugates, including glycans on proteins and lipids, have obtained significant attention due to their critical roles in both intracellular and intercellular biological functions and processes. Notably, recent discoveries have revealed the presence of glycosylated RNAs (glycoRNAs) on cell surfaces. Despite the well-characterized roles of RNA modifications, RNA glycosylation remains relatively unexplored. In this study, we investigate the relationship between N-glycosylation and RNA glycosylation. Using a recombinant Siglec11-Fc as a probe, we detected surface sialylated glycoRNAs in human cell lines and identified their dependency on the catalytic isoforms of the oligosaccharyltransferase (OST) complex, implicating STT3A-dependent protein glycosylation as a predominant contributor for affecting indirect generation of glycoRNAs. Additionally, perturbations in N-glycan biosynthesis pathways or changes in N-glycan structure impact surface sialylated glycoRNA levels, indicating a regulatory role of glycan metabolic pathways in RNA glycosylation. Together, our results underscore the intricate relationship between protein N-glycosylation and processing and RNA biology.

N-Acetylated Monosaccharides and Derived Glycan Structures Occurring in N- and O-Glycans During Prostate Cancer Development

Post-translational modifications of proteins play an important role in their stability, solubility and in vivo function. Also, for several reasons, such as the Golgi fragmentation during cancerogenesis, glycosylation as the most common modification is especially promising in offering high cancer specificity which, in combination with tissue-specific biomarkers available in the case of prostate diseases (PSA, PSMA, PAP), may lead to the development of novel oncodiagnostic approaches. In this review, we present the importance of subterminal glycan structures based on the N-acetylated monosaccharides GlcNAc and GalNAc in N- and also O-glycans, structures of which they are a component (LacNAc, LacdiNAc, branched structures). We also discuss the importance and clinical performance of these structures in cases of prostate cancer diagnostics using lectin-based affinity methods, which could be implemented in clinical laboratory practice in the future.

Regulated N-glycosylation controls chaperone function and receptor trafficking

One-fifth of human proteins are N-glycosylated in the endoplasmic reticulum (ER) by two oligosaccharyltransferases, OST-A and OST-B. Contrary to the prevailing view of N-glycosylation as a housekeeping function, we identified an ER pathway that modulates the activity of OST-A. Genetic analyses linked OST-A to HSP90B1, an ER chaperone for membrane receptors, and CCDC134, an ER luminal protein. During its translocation into the ER, an N-terminal peptide in HSP90B1 templates the assembly of a translocon complex containing CCDC134 and OST-A that protects HSP90B1 during folding, preventing its hyperglycosylation and degradation. Disruption of this pathway impairs WNT and IGF1R signaling and causes the bone developmental disorder osteogenesis imperfecta. Thus, N-glycosylation can be regulated by specificity factors in the ER to control cell surface receptor signaling and tissue development.

A B cell screen against endogenous retroviruses identifies glycan-reactive IgM that recognizes a broad array of enveloped viruses

Endogenous retroviruses (ERVs), comprising a substantial portion of the vertebrate genome, are remnants of ancient genetic invaders. ERVs with near-intact coding potential reactivate in B cell-deficient mice. To study how B cells contribute to host anti-ERV immunity, we used an antigen-baiting strategy to enrich B cells reactive to ERV surface antigens. We identified ERV-reactive B-1 cells expressing germline-encoded natural IgM antibodies in naïve mice, the level of which further increases upon innate immune sensor stimulation. B cell receptor repertoire profiling of ERV-reactive B-1 cells revealed increased usage of the Igh VH gene that gives rise to glycan-specific antibodies targeting terminal N-acetylglucosamine moieties on ERV glycoproteins, which further engage the complement pathway to mediate anti-ERV responses. These same antibodies also recognize glycoproteins of other enveloped viruses but not self-proteins. These results reveal an innate antiviral mechanism of germline-encoded antibodies with broad reactivity to enveloped viruses, which constitutes a natural antibody repertoire capable of preventing the emergence of infectious ERVs.

A dual-capture-system polymer based on imprinted cavities and post-imprinting modification sites with significantly improved affinity and specificity for sialic acid and sialylated glycoprotein

The abnormal expression of N-acetylneuraminic acid (SA) and sialylated glycoproteins in biological fluids are closely associated with various diseases including cancer. However, the low content of SA and the strong interference of complex matrix greatly influence the effective capture of SA in biosamples prior to analysis. Herein, a dual-capture-system strategy based on molecular imprinting and post-imprinting modification (PIM) was proposed to precisely capture SA with improved binding affinity and specificity. After imprinting with SA as template, dynamic imine bonds are introduced by post-imprinting modification, enabling sufficiently high specificity to capture SA through imprinting cavities and the dynamic imine bonds hydrolysis reaction simultaneously. The prepared magnetic PIM polymers (Mag-MIPs-PIM) exhibited significantly high specificity both for SA (IF = 4.24) and sialylated glycoprotein (IFTRF = 3.50). In addition, the feasibility of Mag-MIPs-PIM for practical application was demonstrated by association with HPLC for the determination of SA in human serum, and an LOD of 0.01 × 10-2 g L-1 was obtained. The proposed strategy based on molecular imprinting and PIM provides a new inspiration for the improvement of selectivity of the molecularly imprinted polymers.

Remediation of the NMR data of natural glycans

Primary structure elucidation in glycobiology is strongly affected by published structure-reporting NMR signals, especially on the 13C nucleus. The glycan NMR simulation accuracy and machine learning outcome depend on the quality of the NMR signal assignment in glycan databases. Within our work on improving the data quality in the Carbohydrate Structure Database (CSDB), we have applied a systematic search for inconsistencies in the published NMR data. The search was based on a bulk comparison between the experimental and simulated 13C NMR chemical shifts and manual analysis of the mismatches. On the basis of this analysis, CSDB was remediated by marking and correcting the NMR errors found in 272 structure elucidation reports published over the past 40 years.

Mechanistic and Therapeutic Implications of Protein and Lipid Sialylation in Human Diseases

Glycan structures of glycoproteins and glycolipids on the surface glycocalyx and luminal sugar layers of intracellular membrane compartments in human cells constitute a key interface between intracellular biological processes and external environments. Sialic acids, a class of alpha-keto acid sugars with a nine-carbon backbone, are frequently found as the terminal residues of these glycoconjugates, forming the critical components of these sugar layers. Changes in the status and content of cellular sialic acids are closely linked to many human diseases such as cancer, cardiovascular, neurological, inflammatory, infectious, and lysosomal storage diseases. The molecular machineries responsible for the biosynthesis of the sialylated glycans, along with their biological interacting partners, are important therapeutic strategies and targets for drug development. The purpose of this article is to comprehensively review the recent literature and provide new scientific insights into the mechanisms and therapeutic implications of sialylation in glycoproteins and glycolipids across various human diseases. Recent advances in the clinical developments of sialic acid-related therapies are also summarized and discussed.