Glycosylation in health and disease

Natural, modified and conjugated carbohydrates in nucleic acids

Storage of genetic information in DNA occurs through a unique ordering of canonical base pairs. However, this would not be possible in the absence of the sugar-phosphate backbone which is essential for duplex formation. While over a hundred nucleobase modifications have been identified (mainly in RNA), Nature is rather conservative when it comes to alterations at the level of the (deoxy)ribose sugar moiety. This trend is not reflected in synthetic analogues of nucleic acids where modifications of the sugar entity is commonplace to improve the properties of DNA and RNA. In this review article, we describe the main incentives behind sugar modifications in nucleic acids and we highlight recent progress in this field with a particular emphasis on therapeutic applications, the development of xeno-nucleic acids (XNAs), and on interrogating nucleic acid etiology. We also describe recent strategies to conjugate carbohydrates and oligosaccharides to oligonucleotides since this represents a particularly powerful strategy to improve the therapeutic index of oligonucleotide drugs. The advent of glycoRNAs combined with progress in nucleic acid and carbohydrate chemistry, protein engineering, and delivery methods will undoubtedly yield more potent sugar-modified nucleic acids for therapeutic, biotechnological, and synthetic biology applications.

DOGpred: A Novel Deep Learning Framework for Accurate Identification of Human O-linked Threonine Glycosylation Sites

O-linked glycosylation is a crucial post-translational modification that regulates protein function and biological processes. Dysregulation of this process is associated with various diseases, underscoring the need to accurately identify O-linked glycosylation sites on proteins. Current experimental methods for identifying O-linked threonine glycosylation (OTG) sites are often complex and costly. Consequently, developing computational tools that predict these sites based on protein features is crucial. Such tools can complement experimental approaches, enhancing our understanding of the role of OTG dysregulation in diseases and uncovering potential therapeutic targets. In this study, we developed DOGpred, a deep learning-based predictor for precisely identifying human OTGs using high-latent feature representations. Initially, we extracted nine different conventional feature descriptors (CFDs) and nine pre-trained protein language model (PLM)-based embeddings. Notably, each feature was encoded as a 2D tensor, capturing both the sequential and inherent feature characteristics. Subsequently, we designed a stacked convolutional neural network (CNN) module to learn spatial feature representations from CFDs and a stacked recurrent neural network (RNN) module to learn temporal feature representations from PLM-based embeddings. These features were integrated using attention-based fusion mechanisms to generate high-level feature representations for final classification. Ablation analysis and independent tests demonstrated that the optimal model (DOGpred), employing a stacked 1D CNN and a stacked attention-based RNN modules with cross-attention feature fusion, achieved the best performance on the training dataset and significantly outperformed machine learning-based single-feature models and state-of-the-art methods on independent datasets. Furthermore, DOGpred is publicly available at https://github.com/JeonRPM/DOGpred/ for free access and usage.

Two-Level Spatially Localized Proximity Labeling for Cross-Biological-Hierarchy Measurement and Manipulation

Proximity labeling (PL) has emerged as a powerful technique for the in situ elucidation of biomolecular interaction networks. However, PL methods generally rely on single-biological-hierarchy control of spatial localization at the labeling site, which limits their application in multi-tiered biological systems. Here, we introduced another enzymatic reaction upstream of an enzyme-based PL reaction and targeted the two enzymes to markers indicating different biological hierarchies, establishing a two-level spatially localized proximity labeling (P2L) platform for in situ molecular measurement and manipulation. Using the cellular- and glycan-level as the hierarchical models, we demonstrated the ability of P2L to efficiently execute a two-step logic operation and to discriminate target cells with different levels of glycosylation within mixed cell populations. By mounting clickable handles via P2L, we reprogrammed the robust covalent assembly of cells at designated sites. The combination of P2L with proteomics led to the profiling of the protein microenvironment of specific glycans on target cells, revealing changes in tumor-cell-surface interactions under immune pressure from a glycan perspective. P2L provides not only a solution for revealing the heterogeneity of biological systems, but also new insights in the fields of intelligent logic computation, enzyme engineering, tissue engineering, etc.

Recent Progress in Developing Extracellular Vesicles as Nanovehicles to Deliver Carbohydrate-Based Therapeutics and Vaccines

Cell-derived, nanoscale extracellular vesicles (EVs) have emerged as promising tools in diagnostic, therapeutic, and vaccine applications. Their unique properties including the capability to encapsulate diverse molecular cargo as well as the versatility in surface functionalization make them ideal candidates for safe and effective vehicles to deliver a range of biomolecules including gene editing cassettes, therapeutic proteins, glycans, and glycoconjugate vaccines. In this review, we discuss recent advances in the development of EVs derived from mammalian and bacterial cells for use in a delivery of carbohydrate-based protein therapeutics and vaccines. We highlight key innovations in EVs' molecular design, characterization, and deployment for treating diseases including Alzheimer's disease, infectious diseases, and cancers. We discuss challenges for their clinical translation and provide perspectives for future development of EVs within biopharmaceutical research and the clinical translation landscape.

Serum N-Glycomics with Nano-LC-QToF LC-MS/MS Reveals N-Glycan Biomarkers for Glioblastoma, Meningioma, and High-Grade Meningioma

Alteration of glycosylation in cancer cells leads to the expression of tumor-associated glycans, which can be used as biomarkers for diagnosis and prognostic prediction of diseases. In this study, we used nano-LC-QToF to identify serum N-glycan biomarkers for the detection of brain tumors. We observed an increase in sialylated N-glycans and a decrease in fucosylated N-glycans in the serum of patients with glioblastoma (GBM) and meningioma (MG) compared to healthy individuals. In GBM, a combination of increased serum sialylated N-glycan (6_4_0_2 compound) and decreased fucosylated N-glycan (4_4_1_0 compound) was identified as the most appropriate panel, with an area under the curve (AUC) of 0.8660, 78.95% sensitivity, 84.21% specificity, and 82.89% accuracy. For MG, a combination of decreased 6_6_2_0 and 5_5_2_0 compounds and increased 4_4_1_1 compound achieved an AUC of 0.9260, 82.35% sensitivity, 78.57% specificity, and 80.26% accuracy for diagnosis of MG. Additionally, an increase in 5_5_1_0 and 4_3_0_0 compounds combined with a decrease in 7_7_4_3 was associated with high-grade MG (WHO grades II-III). In conclusion, we identified serum N-glycan profiles associated with brain tumors, highlighting their potential as biomarkers for the diagnosis and prognosis of these diseases.

Parkinson-like wild-type superoxide dismutase 1 pathology induces nigral dopamine neuron degeneration in a novel murine model

Atypical wild-type superoxide dismutase 1 (SOD1) protein misfolding and deposition occurs specifically within the degenerating substantia nigra pars compacta (SNc) in Parkinson disease. Mechanisms driving the formation of this pathology and relationship with SNc dopamine neuron health are yet to be fully understood. We applied proteomic mass spectrometry and synchrotron-based biometal quantification to post-mortem brain tissues from the SNc of Parkinson disease patients and age-matched controls to uncover key factors underlying the formation of wild-type SOD1 pathology in this disorder. We also engineered two of these factors - brain copper deficiency and upregulated SOD1 protein levels - into a novel mouse strain, termed the SOCK mouse, to verify their involvement in the development of Parkinson-like wild-type SOD1 pathology and their impact on dopamine neuron health. Soluble SOD1 protein in the degenerating Parkinson disease SNc exhibited altered post-translational modifications, which may underlie changes to the enzymatic activity and aggregation of the protein in this region. These include decreased copper binding, dysregulation of physiological glycosylation, and atypical oxidation and glycation of key SOD1 amino acid residues. We demonstrated that the biochemical profile introduced in SOCK mice promotes the same post-translational modifications and the development of Parkinson-like wild-type SOD1 pathology in the midbrain and cortex. This pathology accumulates progressively with age and is accompanied by nigrostriatal degeneration and dysfunction, which occur in the absence of α-synuclein deposition. These mice do not exhibit weight loss nor spinal cord motor neuron degeneration, distinguishing them from transgenic mutant SOD1 mouse models. This study provides the first in vivo evidence that mismetallation and altered post-translational modifications precipitates wild-type SOD1 misfolding, dysfunction, and deposition in the Parkinson disease brain, which may contribute to SNc dopamine neuron degeneration. Our data position this pathology as a novel drug target for this disorder, with a particular focus on therapies capable of correcting alterations to SOD1 post-translational modifications.

Recent advances in the clinical spectrum and pathomechanisms associated with X-linked myopathy with excessive autophagy and other VMA21-related disorders

X-linked myopathy with excessive autophagy (XMEA) is a rare neuromuscular disorder caused by mutations in the VMA21 gene, encoding a chaperone protein present in the endoplasmic reticulum (ER). In yeast and human, VMA21 has been shown to chaperone the assembly of the vacuolar (v)-ATPase proton pump required for the acidification of lysosomes and other organelles. In line with this, VMA21 deficiency in XMEA impairs autophagic degradation steps, which would be key in XMEA pathogenesis. Recent years have witnessed a surge of interest in VMA21, with the identification of novel mutations causing a congenital disorder of glycosylation (CDG) with liver affection, and its potent implication in cancer predisposition. With this, VMA21 deficiency has been further linked to defective glycosylation, lipid metabolism dysregulation and ER stress. Moreover, the identification of two VMA21 isoforms, namely VMA21-101 and VMA21-120, has opened novel avenues regarding the pathomechanisms leading to XMEA and VMA21-CDG. In this review, we discuss recent advances on the clinical spectrum associated with VMA21 deficiency and on the pathophysiological roles of VMA21.

O-GalNAc glycans are enriched in neuronal tracts and regulate nodes of Ranvier

Protein O-glycosylation is a critical modification in the brain, as genetic variants in the pathway are associated with common and severe neuropsychiatric phenotypes. However, little is known about the most abundant O-glycans in the mammalian brain, which are N-acetylgalactosamine (O-GalNAc) linked. Here, we determined the spatial localization, protein carriers, and cellular function of O-GalNAc glycans in the mouse brain. We observed striking spatial enrichment of O-GalNAc glycans in neuronal tracts, and specifically at nodes of Ranvier, specialized structures involved in signal propagation in the brain. Glycoproteomic analysis revealed that more than half of the identified O-GalNAc glycans were present on chondroitin sulfate proteoglycans termed lecticans, and display both domain enrichment and regional heterogeneity. Inhibition of O-GalNAc synthesis in neurons reduced binding of Siglec-4, a known regulator of neurite growth, and shortened the length of nodes of Ranvier. This work establishes a function of O-GalNAc glycans in the brain and will inform future studies on their role in development and disease.

The main sources of molecular organization in the cell. Atlas of self-organized and self-regulated dynamic biostructures

One of the most important goals of contemporary biology is to understand the principles of the molecular order underlying the complex dynamic architecture of cells. Here, we present an overview of the main driving forces involved in the cellular molecular complexity and in the emergent functional dynamic structures, spanning from the most basic molecular organization levels to the complex emergent integrative systemic behaviors. First, we address the molecular information processing which is essential in many complex fundamental mechanisms such as the epigenetic memory, alternative splicing, regulation of transcriptional system, and the adequate self-regulatory adaptation to the extracellular environment. Next, we approach the biochemical self-organization, which is central to understand the emergency of metabolic rhythms, circadian oscillations, and spatial traveling waves. Such a complex behavior is also fundamental to understand the temporal compartmentalization of the cellular metabolism and the dynamic regulation of many physiological activities. Numerous examples of biochemical self-organization are considered here, which show that practically all the main physiological processes in the cell exhibit this type of dynamic molecular organization. Finally, we focus on the biochemical self-assembly which, at a primary level of organization, is a basic but important mechanism for the order in the cell allowing biomolecules in a disorganized state to form complex aggregates necessary for a plethora of essential structures and physiological functions. In total, more than 500 references have been compiled in this review. Due to these main sources of order, systemic functional structures emerge in the cell, driving the metabolic functionality towards the biological complexity.

Photocrosslinking and capture for the analysis of carbohydrate-dependent interactions

Carbohydrates play crucial roles in biological systems, including by mediating cell and protein interactions. The complexity and transient nature of carbohydrate-dependent interactions pose significant challenges for their characterization, as traditional techniques often fail to capture these low-affinity binding events. This review highlights the increasing utility of photocrosslinkers in studying carbohydrate-mediated interactions. Photocrosslinkers, such as aryl azides, benzophenones, and diazirines, allow for the capture of fleeting interactions by forming covalent bonds upon UV irradiation, enabling the downstream application of standard biochemical techniques. I discuss the three primary strategies for incorporating photocrosslinkers: synthetic small molecules, metabolic labeling, and exo-enzymatic labeling. I predict that the continued development and application of these methodologies will enhance our understanding of glycan-mediated interactions and their implications in health and disease.

Regulation of PD-L1 glycosylation and advances in cancer immunotherapy

Protein glycosylation plays a versatile role in regulating homeostasis, such as cell migration, protein sorting, and the immune response. Drugs aimed at targeting glycosylation have strong implications for immunity enhancement, diagnosis, and cancer regression. Programmed death-ligand 1 (PD-L1), expressed in cancer or antigen-presenting cells, binds to programmed cell death protein 1 (PD-1) and suppresses T cells. Glycosylation of PD-L1 at N35, N192, N200, and N219 stabilizes PD-L1 on the cancer cell surface, which contributes to immune evasion by inhibiting T cell activity. To date, at least six glycosyltransferases and four associate proteins are known to regulate PD-L1 glycosylation. Terminal modifications such as poly-N-acetyl-lactosamine (poly-LacNAC), sulfation, and sialylation are commonly found on PD-L1, acting as an immune recognition ligand and regulating certain immune responses. Studies have identified many mechanisms and potential therapeutic targets within the glycosylation pathways of PD-L1, revealing their involvement in cancer pathology, immune evasion, and resistance to immunotherapy. In this review, we covered the glycoforms, terminal moiety, binding lectin, glycosyltransferase, as well as sugar analogs focusing on glycosylated PD-L1. We present a mechanism that originates from the endoplasmic reticulum (ER)-Golgi apparatus (Golgi) and its subsequent translocation to the cell membrane. This pathway determines the immune suppression function of PD-L1 and therefore regulates the immune response such as T cells, monocytes, and macrophages. This collection of findings underscores the significance of glycosylation in the role of PD-L1 in cancer and highlights multiple potential targets and strategies for improving therapeutic intervention and diagnostic techniques.

Glycosylation on extracellular vesicles and its detection strategy: Paving the way for clinical use

Extracellular vesicles (EVs) contain various glycans during their life cycle, from biogenesis to cellular recognition and uptake by recipient cells. EV glycosylation has substantial diagnostic significance in multiple health conditions, highlighting the necessity of determining an accurate glycosylation pattern for EVs from diverse biological fluids. Reliable and accessible glycan detection techniques help to elaborate the glycosylation-related functional alterations of specific proteins or lipids. However, multiple obstacles exist, including the inconsistency in glycosylation patterns between an entire batch of EVs and a specific EV protein, and difficulty in distinguishing glycosylation types after tedious separation and purification procedures. This review outlines recent advances in EV glycan detection, either at the glycomic level for a collection of intact EVs or at the molecular level for a specific protein on EVs. Particular emphasis has been placed on the abundance of EVs in body fluids and their unique characteristics for drug delivery of EVs, indicating an opportunity for diagnostic and therapeutic purposes via EV glycans.

Sweet regulation - The emerging immunoregulatory roles of hexoses

BACKGROUND

It is widely acknowledged that dietary habits have profound impacts on human health and diseases. As the most important sweeteners and energy sources in human diets, hexoses take part in a broad range of physiopathological processes. In recent years, emerging evidence has uncovered the crucial roles of hexoses, such as glucose, fructose, mannose, and galactose, in controlling the differentiation or function of immune cells.

AIM OF REVIEW

Herein, we reviewed the latest research progresses in the hexose-mediated modulation of immune responses, provided in-depth analyses of the underlying mechanisms, and discussed the unresolved issues in this field.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Owing to their immunoregulatory effects, hexoses affect the onset and progression of various types of immune disorders, including inflammatory diseases, autoimmune diseases, and tumor immune evasion. Thus, targeting hexose metabolism is becoming a promising strategy for reversing immune abnormalities in diseases.

Insights on post-translational modifications in fatty liver and fibrosis progression

Metabolic dysfunction-associated steatotic liver disease [MASLD] is a pervasive multifactorial health burden. Post-translational modifications [PTMs] of amino acid residues in protein domains demonstrate pivotal roles for imparting dynamic alterations in the cellular micro milieu. The crux of identifying novel druggable targets relies on comprehensively studying the etiology of metabolic disorders. This review article presents how different chemical moieties of various PTMs like phosphorylation, methylation, ubiquitination, glutathionylation, neddylation, acetylation, SUMOylation, lactylation, crotonylation, hydroxylation, glycosylation, citrullination, S-sulfhydration and succinylation presents the cause-effect contribution towards the MASLD spectra. Additionally, the therapeutic prospects in the management of liver steatosis and hepatic fibrosis via targeting PTMs and regulatory enzymes are also encapsulated. This review seeks to understand the function of protein modifications in progression and promote the markers discovery of diagnostic, prognostic and drug targets towards MASLD management which could also halt the progression of a catalogue of related diseases.

Insight into distribution and composition of nonhuman N-Glycans in mammalian organs via MALDI-TOF and MALDI-MSI

The major hurdle of xenotransplantation is the immune response triggered by human natural antibodies interacting with carbohydrate antigens on the transplanted animal organ. Specifically, terminal glycoprotein motifs such as galactose-α1,3-galactose (α-Gal) and N-glycolylneuraminic acid (Neu5Gc) are significant obstacles. Little is known about the abundance and compositions of asparagine-linked complex carbohydrates (N-glycans) carrying these motifs in mammalian organs. By studying heart, kidney, and liver tissues from pig, cattle, and sheep, we aimed to gain insights into the abundance and spatial distribution of α-Gal- or Neu5Gc-containing N-glycans. N-glycomes were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), MALDI-mass spectrometry imaging (MSI), and capillary electrophoresis-electrospray ionization (CE-ESI)-MS. Both α-Gal- and Neu5Gc-containing N-glycans were present in all samples, with α-Gal-modified N-glycans being the most abundant nonhuman carbohydrate motif. The abundance of N-glycans terminating with α-Gal or Neu5Gc was higher in heart and kidney samples than livers. MSI revealed kidneys had the highest glycosylation levels, and α-Gal-containing N-glycans were abundant in the kidney cortex but scarce in the medulla. This study enhances our understanding of α-Gal- and Neu5Gc-modified N-glycans in animal organs and may guide research on carbohydrate antigen-induced immune rejection in xenotransplantation.

RCL glycosylation of serum corticosteroid-binding globulin: implications in cortisol delivery and septic shock

Corticosteroid-binding globulin (CBG) is a serum glycoprotein that binds and delivers anti-inflammatory cortisol to inflammatory sites through neutrophil elastase-mediated proteolysis of an exposed reactive centre loop (RCL) on CBG. Timely and tissue-specific delivery of cortisol is critical to alleviate inflammation including in life-threatening septic shock conditions. Herein, we firstly summarise our recently published report of functional RCL O- and N-glycosylation events of serum CBG (Chernykh, J Biol Chem, 2023). A key finding of that published work was the LC-MS/MS-based discovery of RCL O-glycans at Thr342 and Thr345 of serum CBG and their inhibitory roles in neutrophil elastase-mediated RCL proteolysis. While these observations are of significance as they implicate RCL O-glycosylation as a potential regulator of cortisol delivery, the link to septic shock remains unexplored. To this end, we used a similar LC-MS/MS approach to profile the RCL O-glycosylation of CBG purified from serum of twelve septic shock patients. Serum CBG from all patients exhibited RCL O-glycosylation comprising (di)sialyl T (NeuAc1-2Gal1GalNAc1) core 1-type O-glycan structures decorating exclusively the Thr342 site. Importantly, relative to less severe cases, individuals presenting with the most severe illness displayed elevated RCL O-glycosylation upon ICU admission, suggesting a previously unknown link to septic shock severity. Overall, we have elucidated the coordinated RCL N- and O-glycosylation events of serum CBG, which improve our understanding of molecular mechanisms governing the timely and tissue-specific delivery of cortisol to inflammatory sites. This work provides clues to molecular aberrations and disease mechanisms underpinning septic shock.

Bio-orthogonal Glycan Imaging of Cultured Cells and Whole Animal C. elegans with Expansion Microscopy

Complex carbohydrates called glycans play crucial roles in regulating cell and tissue physiology, but how they map to nanoscale anatomical features must still be resolved. Here, we present the first nanoscale map of mucin-type O-glycans throughout the entirety of the Caenorhabditis elegans model organism. We constructed a library of multifunctional linkers to probe and anchor metabolically labeled glycans in expansion microscopy (ExM). A flexible strategy was demonstrated for the chemical synthesis of linkers with a broad inventory of bio-orthogonal functional groups, fluorophores, anchorage chemistries, and linker arms. Employing C. elegans as a test bed, metabolically labeled O-glycans were resolved on the gut microvilli and other nanoscale anatomical features. Transmission electron microscopy images of C. elegans nanoanatomy validated the fidelity and isotropy of gel expansion. Whole organism maps of C. elegans O-glycosylation in the first larval stage revealed O-glycan "hotspots" in unexpected anatomical locations, including the body wall furrows. Beyond C. elegans, we validated ExM protocols for nanoscale imaging of metabolically labeled glycans on cultured mammalian cells. Together, our results suggest the broad applicability of the multifunctional reagents for imaging glycans and other metabolically labeled biomolecules at enhanced resolutions with ExM.

Malformations of Core M3 on α-Dystroglycan Are the Leading Cause of Dystroglycanopathies

Dystroglycanopathies (DGPs) are a group of autosomal recessive neuromuscular diseases with significant clinical and genetic heterogeneity. They originate due to defects in the O-mannosyl glycosylation of α-dystroglycan (α-DG), a prominent linker between the intracellular cytoskeleton and the extracellular matrix (ECM). Fundamentally, such interactions are crucial for the integrity of muscle fibers and neuromuscular synapses, where their defects are mainly associated with muscle and brain dysfunction. To date, biallelic variants in 18 genes have been associated with DGPs, where the underlying cause is still undefined in a significant proportion of patients. Glycosylation of α-DG generates three core motifs where the core M3 is responsible for interaction with the basement membrane. Consistently, all gene defects that corrupt core M3 maturation have been identified as causes of DGPs. POMGNT1 which stimulates the generation of core M1 is also associated with DGPs, as it plays a central role in core M3 processing. Other genes involved in the glycosylation of α-DG seem unrelated to DPGs. The current review illustrates the O-mannosylation pathway of α-DG highlighting the functional properties of related genes and their contribution to the progression of DPGs. Different classes of DPGs are also elaborated characterizing the clinical features of each distinct type and phenotypes associated with each single gene. Finally, current therapeutic approaches with favorable outcomes are addressed. Potential achievements of preclinical and clinical studies would introduce effective curative therapies for this group of disorders in the near future.

Cell-based glycoengineering for production of homogeneous and specific glycoform-enriched antibodies with improved effector functions

Glycosylation of humanized antibody at Fc-Asn297 significantly affects the Fc-mediated killing of target cells through effector functions, especially antibody-dependent cellular cytotoxicity (ADCC), antibody-dependent cell-mediated phagocytosis (ADCP), and antibody-dependent vaccinal effect (ADVE). Previous studies showed that therapeutic immunoglobulin G (IgG) antibodies with α2,6-sialyl complex type (SCT) glycan attached to Fc-Asn297 exhibited optimal binding to the Fc receptors on effector cells associated with ADCC, ADCP, and ADVE. However, the production of antibodies with homogeneous Fc-SCT glycan requires multiple in vitro enzymatic and purification steps. In this study, we report two cell-based methods to produce Fc-GlcNAc antibody and Fc-SCT-enriched antibodies with improved effector functions. First, we expressed endoglycosidase S2 in Expi293F GnT1- cells to trim all N-glycans to Fc-GlcNAc antibody for in vitro transglycosylation to generate homogeneous antibodies with well-defined Fc glycan. Second, we engineered the glycosylation pathway of HEK293T cells through knock-out of undesired glycosyltransferases and knock-in of desired glycosyltransferases to produce Fc-SCT-enriched antibodies and evaluated their binding to Fc receptors, and we found that the Fc-SCT-enriched antibody is like or better than the homogeneous Fc-SCT antibody in binding to the Fc receptors associated with ADCC, ADCP, and ADVE.

Identification of Oligosaccharide Isomers Using Electrostatically Asymmetric OmpF Nanopore

Glycans, unlike uniformly charged DNA and compositionally diverse peptides, are typically uncharged and possess rich stereoisomeric diversity in the glycosidic bonds between two monosaccharide units. These unique features, including charge heterogeneity and structural complexity, pose significant challenges for accurate analysis. Herein, we developed a novel single-molecule oligosaccharide sensor, OmpF nanopore. The natural electroosmotic flow within OmpF generates a robust driving force for unlabeled neutral oligosaccharides, enabling detection at a concentration as low as 6.4 μM. Furthermore, the asymmetric constriction zone of OmpF was employed to construct a stereoselective recognition site, enabling sensitive identification of glycosidic bond differences in cell lysate samples. With the assistance of machine learning algorithms, the OmpF nanopore achieved a recognition accuracy of 99.9 % for tetrasaccharides differing in only one glycosidic bond was achieved. This nanopore sensor provides a highly sensitive analytical tool with a broad dynamic range. It enables chiral recognition of oligosaccharides at low concentrations and is suitable for analysing both low-abundance and practical samples.

Decoding Protein Glycosylation by an Integrative Mass Spectrometry-Based De Novo Sequencing Strategy

Glycoproteins, representing more than 50% of human proteins and most biopharmaceuticals, are crucial for regulating various biological processes. The complexity of multiple glycosylation sites often leads to incomplete sequence coverage and ambiguous glycan modification profiles. Here, we developed an integrative mass spectrometry-based approach for decoding unknown glycoproteins, which is featured with the combination of deglycosylation-mediated de novo sequencing with glycosylation site characterization. We utilized the enzymatic deglycosylation of N-/ O-glycans to achieve comprehensive sequence coverage. Additionally, EThcD fragmentation enables the identification of high-quality long peptides, facilitating precise protein assembly. We subsequently applied this method to de novo sequencing of the highly glycosylated therapeutic fusion protein Etanercept (Enbrel). We also sequenced three new tumor necrosis factor receptor:Fc-fusion biologics with largely unknown sequences, unveiling subtle distinctions in the primary sequences. Furthermore, we characterized N- and O-glycosylation modifications of these proteins at subunit, glycopeptide, and glycan levels. This strategy bridges the gap between the de novo sequencing and glycosylation modification, providing comprehensive information on the primary structure and glycosylation modifications for glycoproteins. Notably, our method could be a robust solution for accurate sequencing of the glycoproteins and has practical value not only in basic research but also in the biopharmaceutical industry.

N-glycosylation signature and its relevance in cardiovascular immunometabolism

Glycosylation is a post-translational modification in which complex, branched carbohydrates (glycans) are covalently attached to proteins or lipids. Asparagine-link protein (N-) glycosylation is among the most common types of glycosylation. This process is essential for many biological and cellular functions, and impaired N-glycosylation has been widely implicated in inflammation and cardiovascular diseases. Different technical approaches have been used to increase the coverage of the N-glycome, revealing a high level of complexity of glycans, regarding their structure and attachment site on a protein. In this context, new insights from genomic studies have revealed a genetic regulation of glycosylation, linking genetic variants to total plasma N-glycosylation and N-glycosylation of immunoglobulin G (IgG). In addition, RNAseq approaches have revealed a degree of transcriptional regulation for the glycoenzymes involved in glycan structure. However, our understanding of the association between cardiovascular risk and glycosylation, determined by a complex overlay of genetic and environmental factors, remains limited. Mostly, plasma N-glycosylation profiling in different human cohorts or experimental investigations of specific enzyme functions in models of atherosclerosis have been reported. Most of the uncovered glycosylation associations with pathological mechanisms revolve around the recruitment of inflammatory cells to the vessel wall and lipoprotein metabolism. This review aims to summarise insights from omics studies into the immune and metabolic regulation of N-glycosylation and its association with cardiovascular and metabolic disease risk and to provide mechanistic insights from experimental models. The combination of emerging techniques for glycomics and glycoproteomics with already achieved omics approaches to map the transcriptomic, epigenomic, and metabolomic profile at single-cell resolution will deepen our understanding of the molecular regulation of glycosylation as well as identify novel biomarkers and targets for cardiovascular disease prevention and treatment.

Mechanistic computational modeling of sFLT1 secretion dynamics

Constitutively secreted by endothelial cells, soluble FLT1 (sFLT1 or sVEGFR1) binds and sequesters extracellular vascular endothelial growth factors (VEGF), thereby reducing VEGF binding to VEGF receptor tyrosine kinases and their downstream signaling. In doing so, sFLT1 plays an important role in vascular development and in the patterning of new blood vessels in angiogenesis. Here, we develop multiple mechanistic models of sFLT1 secretion and identify a minimal mechanistic model that recapitulates key qualitative and quantitative features of temporal experimental datasets of sFLT1 secretion from multiple studies. We show that the experimental data on sFLT1 secretion is best represented by a delay differential equation (DDE) system including a maturation term, reflecting the time required between synthesis and secretion. Using optimization to identify appropriate values for the key mechanistic parameters in the model, we show that two model parameters (extracellular degradation rate constant and maturation time) are very strongly constrained by the experimental data, and that the remaining parameters are related by two strongly constrained constants. Thus, only one degree of freedom remains, and measurements of the intracellular levels of sFLT1 would fix the remaining parameters. Comparison between simulation predictions and additional experimental data of the outcomes of chemical inhibitors and genetic perturbations suggest that intermediate values of the secretion rate constant best match the simulation with experiments, which would completely constrain the model. However, some of the inhibitors tested produce results that cannot be reproduced by the model simulations, suggesting that additional mechanisms not included here are required to explain those inhibitors. Overall, the model reproduces most available experimental data and suggests targets for further quantitative investigation of the sFLT1 system.

The effect of neighbouring group participation and possible long range remote group participation in O-glycosylation

Stereoselective glycosylations are one of the most challenging tasks of synthetic glycochemists. The protecting building blocks on the glycosides contribute significantly in attaining the required stereochemistry of the resulting glycosides. Strategic installation of suitable protecting groups in the C-2 position, vicinal to the anomeric carbon, renders neighbouring group participation, whereas protecting groups in the distal C-3, C-4, and C-6 positions are often claimed to exhibit remote group participation with the anomeric carbon. Neighbouring group participation and remote group participation are being widely studied to help the glycochemists design the synthetic protocols for multistep synthesis of complex oligosaccharides and in turn, standardise the process of the glycosylation towards a particular stereochemical output. While neighbouring group participation has been quite effective in achieving the required stereochemistry of the produced glycosides, remote participation exhibits comparatively less efficacy in achieving complete stereoselectivity in the glycosylation reactions. Remote participation is a still highly debated topic in the scientific community. However, implementing the participating role of the remote groups in glycosylation reactions is widely practised to achieve better stereocontrol and to facilitate the formation of synthetically challenging glycosidic linkages.

UGP2, a novel target gene of TP53, inhibits endothelial cells apoptosis and atherosclerosis

The dysfunction of the endothelial lining in lesion-prone areas of the arterial vasculature significantly contributes to the pathobiology of atherosclerotic cardiovascular disease. Recent studies suggested that UDP-glucose pyrophosphorylase 2 (UGP2) plays a role in cell proliferation and survival. This study investigates the anti-apoptotic and anti-atherogenic effects of UGP2 both in vitro and in vivo. We explored the effects and mechanisms of UGP2 on apoptosis in endothelial cells using flow cytometry and Western blot analysis. Additionally, we evaluate apoptosis levels in atherosclerotic lesions with ldlr-/- ugp2+/- mice. Microarray analysis revealed reduced UGP2 expression in human atherosclerotic plaques. In vitro experiments demonstrated that TP53 interacts with the promoter region of the UGP2 gene, upregulating UGP2 expression. Enhanced UGP2 expression led to decreased reactive oxygen species (ROS) levels, reduced Cleaved caspase-3 expression, and lower apoptosis levels in endothelial cells. The anti-apoptotic effects of UGP2 were significantly diminished by H2O2. In vivo, UGP2 deficiency in ldlr-/- mice fed a Western high-fat diet promoted atherosclerosis, increased ROS levels, and elevated Cleaved caspase-3 expression and apoptosis in atherosclerotic lesions. Our findings identify UGP2 as a novel TP53 target gene that contributes to anti-apoptotic effects by regulating ROS homeostasis via a non-canonical pathway. UGP2 represents a potential therapeutic target for ameliorating atherosclerosis-related diseases.

Unveiling the crucial role of glycosylation modification in lung adenocarcinoma metastasis through artificial neural network-based spatial multi-omics single-cell analysis and Mendelian randomization

BACKGROUND

Investigations into the intricacies of glycosylation modifications, a prevalent post-translational alteration observed in neoplasms, especially remain elusive in the context of lung adenocarcinoma. Through the integration of multiple omics approaches, the investigation aimed to delineate the significance of glycosylation in lung adenocarcinoma, with an objective to pinpoint viable biological targets.

METHODS

Initial steps involved the identification of genes differentially expressed in relation to glycosylation at the aggregate transcriptome level within lung adenocarcinoma tissues. This was followed by analyses of localization and function employing both single-cell and spatial transcriptomics to provide a more nuanced understanding. In pursuit of elucidating functional disparities in glycosylation patterns, a predictive framework employing artificial neural networks was constructed. To ascertain causal relationships between specific genes and lung adenocarcinoma, Mendelian randomization was applied, culminating in the experimental validation of these genes' roles.

RESULTS

Analysis at the single-cell level uncovered marked glycosylation modification expressions in metastatic tissues of lung adenocarcinoma. Moreover, tissues of lung adenocarcinoma with elevated expression of genes associated with glycosylation displayed enhanced differentiation and activation across signaling pathways including TGF-β, oxidative stress, and WNT. Through spatial transcriptomics, zones of intense glycosylation modification were pinpointed within tumor nests and proximate to tumor-associated blood vessels. An artificial neural network-derived prognostic model demonstrated outstanding predictive capability, with AUC scores achieving 0.84, 0.83, and 0.89 for 1, 3, and 5-year forecasts, respectively. The group identified as high-risk was characterized by pronounced immunosuppression and diminished responsiveness to immunotherapy. Mendelian randomization analysis pinpointed GLANT2 (OR = 1.3654, p < 0.05) and GYS1 (OR = 1.2668, p < 0.05) as genes contributing to the pathogenesis of lung adenocarcinoma. Cell assays have reaffirmed that the inhibition of GYS1 significantly reduces proliferation and invasion in lung adenocarcinoma cell lines, while also decreasing glycogen storage and the formation of glycosylation end products, indicating suppression of glycosylation processes. These findings identify GYS1 as a prospective glycosylation-linked biological target for lung adenocarcinoma therapy.

Unraveling Metabolic Dysfunction-Associated Steatotic Liver Disease Through the Use of Omics Technologies

Non-alcoholic fatty liver disease (NAFLD), now referred to as metabolic dysfunction-associated steatotic liver disease (MASLD), is the most prevalent liver disorder globally, linked to obesity, type 2 diabetes, and cardiovascular risk. Understanding its potential progression from simple steatosis to cirrhosis and hepatocellular carcinoma (HCC) is crucial for patient management and treatment strategies. The disease's complexity requires innovative approaches for early detection and personalized care. Omics technologies-such as genomics, transcriptomics, proteomics, metabolomics, and exposomics-are revolutionizing the study of MASLD. These high-throughput techniques allow for a deeper exploration of the molecular mechanisms driving disease progression. Genomics can identify genetic predispositions, whilst transcriptomics and proteomics reveal changes in gene expression and protein profiles during disease evolution. Metabolomics offers insights into the metabolic alterations associated with MASLD, while exposomics links environmental exposures to MASLD progression and pathology. By integrating data from various omics platforms, researchers can map out the intricate biochemical pathways involved in liver disease progression. This review discusses the roles of omics technologies in enhancing the understanding of disease progression and highlights potential diagnostic and therapeutic targets within the MASLD spectrum, emphasizing the need for non-invasive tools in disease staging and treatment development.

CD21low B cells reveal a unique glycosylation pattern with hypersialylation and hyperfucosylation

Background

The posttranslational modification of cellular macromolecules by glycosylation is considered to contribute to disease pathogenesis in autoimmune and inflammatory conditions. In a subgroup of patients with common variable immunodeficiency (CVID), the occurrence of such complications is associated with an expansion of naïve-like CD21low B cells during a chronic type 1 immune activation. The glycosylation pattern of B cells in CVID patients has not been addressed to date.

Objective

The objective of this study was to examine the surface glycome of B cells in patients with CVID and associated immune dysregulation.

Methods

We performed surface lectin staining on B cells from peripheral blood and tonsils, both ex vivo and after in vitro stimulation. Additionally, we examined the expression of glycosylation-related genes by RNAseq in naïve-like CD21low B cells ex vivo, as well as in naïve CD21pos B cells from healthy controls after in vitro stimulation.

Results

Unlike CD21pos B cells, naïve-like CD21low B cells from CVID patients and CD21low B cells from healthy controls exhibited a unique glycosylation pattern with high levels of α2,6 sialic acids and fucose. This hypersialylation and hyperfucosylation were particularly induced by activation with anti-IgM and interferon-γ (IFN-γ). Transcriptome analysis suggested that naïve-like CD21low B cells possess a comprehensively reorganised glycosylation machinery, with anti-IgM/IFN-γ having the potential to initiate these changes in vitro.

Conclusion

CD21low B cells are hypersialylated and hyperfucosylated. This may implicate altered lectin-ligand interactions on the cell surface potentially affecting the CD21low B-cell function. These glycome changes appear to be driven by the prominent type I immune response in complicated CVID patients. A better understanding of how altered glycosylation influences immune cell function could lead to new therapeutic strategies.

Metabolic glycan labelling with bio-orthogonal targeting and its potential in drug delivery

New modes of targeted drug delivery are emerging with promise of enhancing therapeutic efficacy while reducing side effects. This review examines the landscape of metabolic glycan labelling-a technique gaining traction for its potential in specific drug targeting. By exploiting the natural glycan synthetic pathway of monosaccharides, unnatural sugar analogues are incorporated into glycoproteins, allowing for the presentation of unique functional groups on cells. This enables specific targeting using 'clickable' probes with complementary click chemistry functional groups. The selection of sugar analogues and chemical tags are crucial components explored in this review, alongside considerations for cell lines, tissues, and cargo selection. The review discusses non-therapeutic and therapeutic applications of metabolic glycan labelling, as well as its potential beyond labelling of cell surfaces. The review also highlights underexplored areas of metabolic glycan labelling by assessing the limited literature addressing labelling efficiency, turnover rates, the impact of sugar supplements in cell culture, and the critical cell to functionalised sugar ratio. Furthermore, this review delves into the future landscape and goals of metabolic glycan labelling, envisioning its potential in targeted drug delivery.

Mutant glycosidases for labeling sialoglycans with high specificity and affinity

Affinity labeling of biomacromolecules is vital for bioimaging and functional studies. However, affinity probes recognizing glycans with high specificity remain scarce. Here we report the development of glycan recombinant affinity binders (GRABs) based on mutant bacterial sialidases, which are enzymatically inactive but preserve stringent specificity for sialoglycan substrates. By mutating a key catalytic residue of Streptococcus pneumoniae neuraminidase A (SpNanA) and Ruminococcus gnavus neuraminidase H (RgNanH), we develop GRAB-Sia and GRAB-Sia3 recognizing total sialoglycans and α2,3-sialosides, respectively. The GRABs exhibit strict substrate and linkage specificity, and tetramerization with streptavidin substantially increases their avidity. The GRABs and tetrameric GRABs (tetra-GRABs) are effective tools for probing sialoglycans in immunoblotting, flow cytometry, immunoprecipitation, and fluorescence imaging. Furthermore, multiplex analysis with tetra-GRABs uncovers spatially distinct sialoglycans in the various mouse organs. This work provides a versatile toolkit for labeling and analyzing sialoglycans with high specificity, sensitivity, and convenience.

Promoting ER stress in a plasmacytoid dendritic cell line drives fibroblast activation

BACKGROUND

Fibrosis remains a major complication in several chronic diseases, including systemic sclerosis (SSc). Plasmacytoid dendritic cells (pDCs) are innate immune cells that play a key role in the development of fibrosis in SSc patients, through still poorly defined mechanisms. Interestingly, endoplasmic reticulum (ER) stress signaling pathways are dysregulated in pDCs from patients with SSc, but their contribution to fibrosis remains unclear. Thus, this study aimed to unravel the mechanisms behind the involvement of pDCs and ER stress in fibrosis.

METHODS

To address this question, we established an in vitro model designed to study the interactions between pDCs and fibroblasts. More specifically, IMR-90 fibroblasts were co-cultured with CAL-1, a pDC cell line. ER stress was then induced by the bacterial toxin SubAB. Extracellular matrix (ECM) production was assessed using immunoblotting, qPCR and confocal microscopy. The importance of cell-to-cell contact was investigated using conditioned media (CM) and transwell assays.

RESULTS

Direct contact of CAL-1 and IMR-90 cells under ER stress conditions led to increased expression of fibronectin and alpha-smooth muscle actin (α-SMA). This effect required expression of the ER stress signaling sensor protein kinase R-like ER kinase (PERK) in pDCs and was observed only upon direct contact between both cell types.

CONCLUSIONS

Overall, our data suggest that ER stress induction in pDCs promotes fibroblast activation, which may contribute to the development of fibrosis in SSc.

Unraveling the Mechanism of Stereospecific Self-Promoted N-Glycosylations

In this study, the mechanism of self-promoted N-glycosylations is extensively investigated through kinetic experiments, computational studies, and nucleophilic competition experiments. Based on the findings, the mechanism is proposed to be initiated by proton transfer from the acidic sulfonyl carbamate to the trichloroacetimidate, upon formation of an associated contact ion pair. This ion pair then collapses in an SN1-like fashion, with formation of an oxocarbeniumion-like intermediate. According to the proposed mechanism, stereospecificity arises from the associated nature of all intermediates formed throughout the reaction. During the mechanistic study, it was also found that the sulfonyl carbamates have catalytic properties if a competing nucleophile is present.

Synergistic effects of mutation and glycosylation on disease progression

Glycosylation, a post-translational modification, plays a crucial role in proper localization and function of proteins. It is regulated by multiple glycosyltransferases and can be influenced by various factors. Inherited missense mutations in glycosylated proteins such as NOTCH3, Low-density lipoprotein receptor (LDLR), and Amyloid precursor protein (APP) could affect their glycosylation states, leading to cerebral small vessel disease, hypercholesterolemia, and Alzheimer's disease, respectively. Additionally, physiological states and aging-related conditions can affect the expression levels of glycosyltransferases. However, the interplay between mutations in glycosylated proteins and changes in their glycosylation levels remains poorly understood. This mini-review summarizes the effects of glycosylation on transmembrane proteins with pathogenic mutations, including NOTCH3, LDLR, and APP. We highlight the synergistic contributions of missense amino acids in the mutant proteins and alterations in their glycosylation states to their molecular pathogenesis.

The Synthesis of Glycosyl Amides from Unprotected Carbohydrates and Acylsilanes

We report on a new methodology for the stereoselective synthesis of β-anomeric N-glycosyl amides from unprotected carbohydrates via the reaction of in situ generated carbohydrate oximes with acylsilanes. By variation of the acylsilane, N-glycosyl amides with azide and chloride conjugation handles are prepared in excellent yield and β-selectivity from unprotected sugars.

A Rapid and Sensitive MicroPlate Assay (MPSA) Using an Alkyne-Modified CMP-Sialic Acid Donor to Evaluate Human Sialyltransferase Specificity

Human sialyltransferases primarily utilize CMP-Sias, especially transferring Neu5Ac from CMP-Neu5Ac to various acceptors. Advances in chemical biology have led to the synthesis of novel CMP-Sia donors suitable for bioorthogonal reactions in cell-based assays. However, the compatibility of these donors with all human enzymes remains uncertain. We synthesized a non-natural CMP-Sia donor with an alkyne modification on the N-acyl group of Neu5Ac, which was effectively used by human ST6Gal I and ST3Gal I. A sensitive MicroPlate Sialyltransferase Assay (MPSA) was developed and expanded to a panel of 13 human STs acting on glycoproteins. All assayed enzymes tolerated CMP-SiaNAl, allowing for the determination of kinetic parameters and turnover numbers. This study enhances the biochemical characterization of human sialyltransferases and opens new avenues for developing sialyltransferase inhibitors.

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.

Glycobiology of psoriasis: A review

Psoriasis is a chronic inflammatory skin disease with etiologies related to genetics, immunity, and the environment. It is characterized by excessive proliferation of keratinocytes and infiltration of inflammatory immune cells. Glycosylation is a post-translational modification of proteins that plays important roles in cell adhesion, signal transduction, and immune cell activation. Abnormal glycosylation is associated with inflammation, tumors, autoimmunity, and several diseases. Glycan profiles and glycosylation-related enzymes are altered in patients with psoriasis. Specific glycan structures, such as glycosaminoglycans and gangliosides, inhibit the development of psoriasis through various pathways. Lectins are glycan-binding proteins that are widely involved in the pathogenesis of psoriasis. The differential serum, epidermal, and dermal expression of galectins in patients with psoriasis distinguishes psoriasis from other nonspecific psoriasis-like dermatitis. This article summarizes relevant literature on psoriasis-related glycans to help clarify the potential molecular mechanisms of psoriasis and identify novel biomarkers and targets for the treatment of psoriasis.

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.

Improving the Depth and Reliability of Glycopeptide Identification Using Protein Prospector

Glycosylation is the most common and diverse modification of proteins. It can affect protein function and stability and is associated with many diseases. While proteomic methods to study most post-translational modifications are now quite mature, glycopeptide analysis is still a challenge, particularly from the aspect of data analysis. Several software packages have been developed in the last few years that aim to support omic-level N-linked glycopeptide analysis. This study presents developments of Protein Prospector for the analysis of N-glycopeptide data. Results are compared to other software, showing that Protein Prospector reports many more glycoforms of glycopeptides than competing software. The advantages and disadvantages of considering glycan adducts are also evaluated, showing how considering them can correct previously wrong assignments.

Roles of core fucosylation modification in immune system and diseases

Core fucosylation, catalyzed by α1,6-fucosyltransferase (FUT8), is an important N-glycosylation modification process that attaches a fucose residue via an α1,6-linkage to the core N-acetylglucosamine of N-glycans in mammals. Research over the past three decades has revealed the critical role of FUT8-mediated core fucosylation modification in various physiological and pathological processes, including cell growth, adhesion, receptor activation, antibody-dependent cellular cytotoxicity (ADCC), tumor metastasis and infections. This review discusses the immune system function involving FUT8 and the mechanisms by which core fucosylation regulates immunity and contributes to disease. A deeper understanding of these mechanisms can provide insights into cellular biology and suggest new therapeutic approaches and targets for related diseases.

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, we report a comprehensive profiling of the N-glycoproteome in rice seedlings. The rice seedlings are incubated with N-azidoacetylgalactosamine-a monosaccharide analog containing a bioorthogonal functional group-to metabolically label N-glycans, followed by conjugation with an affinity probe via click chemistry for the 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-associated protein degradation machinery are N-glycosylated, and the N-glycosylation is important for the endoplasmic reticulum-associated protein degradation-L function. This work not only provides an invaluable resource for studying rice N-glycosylation but also demonstrates the applicability of metabolic glycan labeling in glycoproteomic profiling for crop species.

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.

Divergent synthesis of amino acid-linked O-GalNAc glycan core structures

O-GalNAc glycans, also known as mucin-type O-glycans, are primary constituents of mucins on various mucosal sites of the body and also ubiquitously expressed on cell surface and secreted proteins. They have crucial roles in a wide range of physiological and pathological processes, including tumor growth and progression. In addition, altered expression of O-GalNAc glycans is frequently observed during different disease states. Research dedicated to unraveling the structure-function relationships of O-GalNAc glycans has led to the discovery of disease biomarkers and diagnostic tools and the development of O-glycopeptide-based cancer vaccines. Many of these efforts require amino acid-linked O-GalNAc core structures as building blocks to assemble complex O-glycans and glycopeptides. There are eight core structures (cores one to eight), from which all mucin-type O-glycans are derived. In this protocol, we describe the first divergent synthesis of all eight cores from a versatile precursor in practical scales. The protocol involves (i) chemical synthesis of the orthogonally protected precursor (3 days) from commercially available materials, (ii) chemical synthesis of five unique glycosyl donors (1-2 days for each donor) and (iii) selective deprotection of the precursor and assembly of the eight cores (2-4 days for each core). The procedure can be adopted to prepare O-GalNAc cores linked to serine, threonine and tyrosine, which can then be utilized directly for solid-phase glycopeptide synthesis or chemoenzymatic synthesis of complex O-glycans. The procedure empowers researchers with fundamental organic chemistry skills to prepare gram scales of any desired O-GalNAc core(s) or all eight cores concurrently.

TUDCA modulates drug bioavailability to regulate resistance to acute ER stress in Saccharomyces cerevisiae

Cells counter accumulation of misfolded secretory proteins in the endoplasmic reticulum (ER) through activation of the Unfolded Protein Response (UPR). Small molecules termed chemical chaperones can promote protein folding to alleviate ER stress. The bile acid tauroursodeoxycholic acid (TUDCA) has been described as a chemical chaperone. While promising in models of protein folding diseases, TUDCA's mechanism of action remains unclear. Here, we found TUDCA can rescue growth of yeast treated with the ER stressor tunicamycin (Tm), even in the absence of a functional UPR. In contrast, TUDCA failed to rescue growth on other ER stressors. Nor could TUDCA attenuate chronic UPR associated with specific gene deletions or overexpression of a misfolded mutant secretory protein. Neither pretreatment with nor delayed addition of TUDCA conferred protection against Tm. Importantly, attenuation of Tm-induced toxicity required TUDCA's critical micelle forming concentration, suggesting a mechanism where TUDCA directly sequesters drugs. Indeed, in several assays, TUDCA-treated cells closely resembled cells treated with lower doses of Tm. In addition, we found TUDCA can inhibit dyes from labeling intracellular compartments. Thus, our study challenges the model of TUDCA as a chemical chaperone and suggests that TUDCA decreases drug bioavailability, allowing cells to adapt to ER stress.

Novel anticancer drug discovery efforts targeting glycosylation: the emergence of fluorinated monosaccharides analogs

INTRODUCTION

Glycosylation is an essential enzymatic process of building glycan structures that occur mainly within the cell and gives rise to a diversity of cell surface and secreted glycoconjugates. These glycoconjugates play vital roles, for instance in cellcell adhesion, interaction and communication, activation of cell surface receptors, inflammatory response and immune recognition. This controlled and wellcoordinated enzymatic process is altered in cancer, leading to the biosynthesis of cancerassociated glycans, which impact glycandependent biological roles.

AREAS COVERED

In this review, the authors discuss the importance of targeting cancerassociated glycans through potent glycan biosynthesis inhibitors. It focuses on the use of analogs, providing an overview of findings involving these in cancer. The highly explored fluorinated monosaccharide analogs targeting aberrant glycosylation are described, aiming to inspire advances in the field.

EXPERT OPINION

Altered glycosylation, such as increased sialylation and fucosylation, is a feature in cancer and has been shown to play key roles in several malignant properties of cancer cells. Strategies aiming at remodeling cancer cells´ glycome are emerging and present a huge potential for cancer therapy. Fluorinated monosaccharides have been gathering promising preclinical results as novel cancer drugs. Nevertheless, cancer specific targeting strategies must be considered to avoid significant sideeffects.

Deep structure-level N-glycan identification using feature-induced structure diagnosis integrated with a deep learning model

Being a widely occurring protein post-translational modification, N-glycosylation features unique multi-dimensional structures including sequence and linkage isomers. There have been successful bioinformatics efforts in N-glycan structure identification using N-glycoproteomics data; however, symmetric "mirror" branch isomers and linkage isomers are largely unresolved. Here, we report deep structure-level N-glycan identification using feature-induced structure diagnosis (FISD) integrated with a deep learning model. A neural network model is integrated to conduct the identification of featured N-glycan motifs and boosts the process of structure diagnosis and distinction for linkage isomers. By adopting publicly available N-glycoproteomics datasets of five mouse tissues (17,136 intact N-glycopeptide spectrum matches) and a consideration of 23 motif features, a deep learning model integrated with a convolutional autoencoder and a multilayer perceptron was trained to be capable of predicting N-glycan featured motifs in the MS/MS spectra with previously identified compositions. In the test of the trained model, a prediction accuracy of 0.8 and AUC value of 0.95 were achieved; 5701 previously unresolved N-glycan structures were assigned by matched structure-diagnostic ions; and by using an explainable learning algorithm, two new fragmentation features of m/z = 674.25 and m/z = 835.28 were found to be significant to three N-glycan structure motifs with fucose, NeuAc, and NeuGc, proving the capability of FISD to discover new features in the MS/MS spectra.

Glycoscience in Advancing PD-1/PD-L1-Axis-Targeted Tumor Immunotherapy

Immune checkpoint blockade therapy, represented by anti-PD-1/PD-L1 monoclonal antibodies, has significantly changed the immunotherapy landscape. However, the treatment is still limited by unsatisfactory response rates, immune-related adverse effects, and drug resistance. Current studies have established that glycosylation, a common post-translational modification, is crucial in promoting cancer progression and immune invasion. Targeting aberrant glycosylation in cancers presents precision medicine regimens for monitoring cancer progression and developing personalized medicine. Notably, the immune checkpoints PD-1 and PD-L1 are highly glycosylated, which affects PD-1/PD-L1 interaction and the binding of anti-PD-1/PD-L1 monoclonal antibodies. Recent achievements in glycoscience to enhance patient outcomes, referred to as glycotherapy, have underscored their high potency in advancing PD-1/PD-L1 blockade therapies, i.e., glycoengineered antibodies with improved binding toward PD-1/PD-L1, pharmaceutic inhibitors for core fucosylation and sialylation, and synergistic treatment with the antibody-sialidase conjugate. This review briefly introduces the PD-1/PD-L1 axis and glycosylation and highlights the fundamental and applied advances in glycoscience that improve PD-1/PD-L1 immunoblockade therapies.

Protein sequence editing defines distinct and overlapping functions of SKN-1A/Nrf1 and SKN-1C/Nrf2

The Nrf/NFE2L family of transcription factors regulates redox balance, xenobiotic detoxification, metabolism, proteostasis, and aging. Nrf1/NFE2L1 is primarily responsible for stress-responsive upregulation of proteasome subunit genes and is essential for adaptation to proteotoxic stress. Nrf2/NFE2L2 is mainly involved in activating oxidative stress responses and promoting xenobiotic detoxification. Nrf1 and Nrf2 contain very similar DNA binding domains and can drive similar transcriptional responses. In C. elegans, a single gene, skn-1, encodes distinct protein isoforms, SKN-1A and SKN-1C, that function analogously to mammalian Nrf1 and Nrf2, respectively, and share an identical DNA binding domain. Thus, the extent to which SKN-1A/Nrf1 and SKN-1C/Nrf2 functions are distinct or overlapping has been unclear. Regulation of the proteasome by SKN-1A/Nrf1 requires post-translational conversion of N-glycosylated asparagine residues to aspartate by the PNG-1/NGLY1 peptide:N-glycanase, a process we term 'sequence editing'. Here, we reveal the consequences of sequence editing for the transcriptomic output of activated SKN-1A. We confirm that activation of proteasome subunit genes is strictly dependent on sequence editing. In addition, we find that sequence edited SKN-1A can also activate genes linked to redox homeostasis and xenobiotic detoxification that are also regulated by SKN-1C, but the extent of these genes' activation is antagonized by sequence editing. Using mutant alleles that selectively inactivate either SKN-1A or SKN-1C, we show that both isoforms promote optimal oxidative stress resistance, acting as effectors for distinct signaling pathways. These findings suggest that sequence editing governs SKN-1/Nrf functions by tuning the SKN-1A/Nrf1 regulated transcriptome.

Quantitative Glycan-Protein Cross-Linking Mass Spectrometry Using Enrichable Linkers Reveals Extensive Glycan-Mediated Protein Interaction Networks

Protein-protein interactions in the cell membrane are typically mediated by glycans, with terminal sialic acid often involved in these interactions. To probe the nature of the interactions, we developed quantitative cross-linking methods involving the glycans of the glycoproteins and the polypeptide moieties of proteins. We designed and synthesized biotinylated enrichable cross-linkers that were click-tagged to metabolically incorporate azido-sialic acid on cell surface glycans to allow cross-linking of the azido-glycans with lysine residues on proximal polypeptides. The glycopeptide-peptide cross-links (GPx) were enriched using biotin groups through affinity purification with streptavidin resin beads. Workflows using two linkers, one photocleavable and the other disulfide, were developed and applied to reveal the sialic acid-mediated cell-surface protein networks of PNT2 (prostate) cells. Glycopeptide-peptide pairs were identified, with 12000 GPx linked by sialylated glycoforms revealing interactions between source glycoproteins and nearly 700 target proteins. Protein-protein interactions were characterized by as many as 40 peptide pairs, and the extent of the interactions between proteins was prioritized by the number of GPx. Quantitation was performed by counting the number of GPx that identify the protein pairs. Abundant membrane proteins such as ITGB1 yielded an interactome consisting of around 400 other proteins, which were ranked from the most extensive interaction, having the largest number of GPx, to at least one. The interactome was further confirmed separately by published databases. This tool will enhance our understanding of glycosylation on protein-protein interactions and provide new potential targets for therapeutics.

Decoding the Molecular Basis of the Specificity of an Anti-sTn Antibody

The mucin O-glycan sialyl Tn antigen (sTn, Neu5Acα2-6GalNAcα1-O-Ser/Thr) is an antigen associated with different types of cancers, often linked with a higher risk of metastasis and poor prognosis. Despite efforts to develop anti-sTn antibodies with high specificity for diagnostics and immunotherapy, challenges in eliciting high-affinity antibodies for glycan structures have limited their effectiveness, leading to low titers and short protection durations. Experimental structural insights into anti-sTn antibody specificity are lacking, hindering their optimization for cancer cell recognition. In this study, we used a comprehensive structural approach, combining X-ray crystallography, NMR spectroscopy, computational methods, glycan/glycopeptide microarrays, and biophysical techniques, to thoroughly investigate the molecular basis of sTn recognition by L2A5, a novel preclinical anti-sTn monoclonal antibody (mAb). Our data unequivocally show that the L2A5 fragment antigen-binding (Fab) specifically binds to core sTn moieties. NMR and X-ray structural data suggest a similar binding mode for the complexes formed by the sTn moiety linked to Ser or Thr and the L2A5 Fab. The sugar moieties are similarly oriented in the paratope of mAb, with the Neu5Ac moiety establishing key interactions with the receptor and the GalNAc moiety providing additional contacts. Furthermore, L2A5 exhibits fine specificity toward cancer-related MUC1 and MUC4 mucin-derived sTn glycopeptides, which might contribute to its selective targeting against tumor cells. This newfound knowledge holds promise for the rational improvement and potential application of this anti-sTn antibody in diagnosis and targeted therapy against sTn expressing cancers such as breast, colorectal, and bladder cancer, improving patient care.